Re: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list

[Fischl, Bruce]

I think you just did 😊

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Paolo Zanotti Fregonara
Sent: Monday, June 8, 2020 10:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list


External Email - Use Caution

Hi

Would it be possible to post this job offer to the mailing list?

Thanks
Paolo
-- Forwarded message -
From: 
mailto:freesurfer-requ...@nmr.mgh.harvard.edu>>
Date: Mon, Jun 8, 2020 at 10:30 AM
Subject: Welcome to the "Freesurfer" mailing list
To: mailto:pzfregon...@gmail.com>>


Welcome to the 
Freesurfer@nmr.mgh.harvard.edu mailing 
list!

To post to this list, send your email to:

  freesurfer@nmr.mgh.harvard.edu

General information about the mailing list is at:

  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

If you ever want to unsubscribe or change your options (eg, switch to
or from digest mode, change your password, etc.), visit your
subscription page at:

  
https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer/pzfregonara%40gmail.com


You can also make such adjustments via email by sending a message to:

  
freesurfer-requ...@nmr.mgh.harvard.edu

with the word `help' in the subject or body (don't include the
quotes), and you will get back a message with instructions.

You must know your password to change your options (including changing
the password, itself) or to unsubscribe.  It is:

  Paolofreesurfer73

Normally, Mailman will remind you of your 
nmr.mgh.harvard.edu mailing
list passwords once every month, although you can disable this if you
prefer.  This reminder will also include instructions on how to
unsubscribe or change your account options.  There is also a button on
your options page that will email your current password to you.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Splitting surface overlay into separate files

[Fischl, Bruce]

You could also do it pretty easily in matlab or python

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, June 12, 2020 10:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Splitting surface overlay into separate files

When you say "surface" do you mean a surface overlay or a surface with xyz and 
neighbor relations? Assuming you mean an overlay (eg, something in an mgh or 
mgz file), you can try fscalc. Or do you have 25 frames  in a single file and 
you want to split them into separate files? You might be able to convert the 
mgh/mgz file to nii and use FSL tools and then convert them back (sometimes 
works, sometimes not)
On 6/12/2020 10:24 AM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

Apologies if this is a rather simple question. Is there a FreeSurfer equivalent 
of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz 
file. I want to separate each atlas region into a different file, so that I end 
up with 25 surface atlas regions. Is there a command that could achieve this?

My next question is whether or not there is a Freesurface command that can be 
used to complete surface based correlations. For example, if I want to check 
for the overlap between two ROIs. I have been using fslcc to do this in the 
volume, but perhaps freesurfer has something similar to do this on the surface?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

[Fischl, Bruce]

Hi Mason

You should be able to load the overlay and the ROIs into matlab, then pick out 
the vertices in each ROI from the overlay and save them separately. Just be 
careful about the one-based indexing in matlab. That is, if your ROI is in a 
label file and you read the vertex indices from it, you need to add 1 to the 
index that point into the overlay.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Friday, June 12, 2020 7:35 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}


External Email - Use Caution
Hi Doug,

Yes, I mean a surface overlay, it is the mgz format. It essentially has 25 
visual areas, shown in the attached. I wanted to split them up, so that each 
ROI is its own label. I saw I could use mri_cor2label, but is there a better 
way?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Douglas N. Greve" 
mailto:dgr...@mgh.harvard.edu>>
Reply to: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 12 June 2020 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files

When you say "surface" do you mean a surface overlay or a surface with xyz and 
neighbor relations? Assuming you mean an overlay (eg, something in an mgh or 
mgz file), you can try fscalc. Or do you have 25 frames  in a single file and 
you want to split them into separate files? You might be able to convert the 
mgh/mgz file to nii and use FSL tools and then convert them back (sometimes 
works, sometimes not)
On 6/12/2020 10:24 AM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

Apologies if this is a rather simple question. Is there a FreeSurfer equivalent 
of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz 
file. I want to separate each atlas region into a different file, so that I end 
up with 25 surface atlas regions. Is there a command that could achieve this?

My next question is whether or not there is a Freesurface command that can be 
used to complete surface based correlations. For example, if I want to check 
for the overlap between two ROIs. I have been using fslcc to do this in the 
volume, but perhaps freesurfer has something similar to do this on the surface?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk
Tel: 02920 879628
Web: Cardiff University 
webpage
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk
Ffôn: 02920 879628



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from 
"eur03.safelinks.protection.outlook.com" claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all hanging, how to examine defect

[Fischl, Bruce]

Hi Ken

If it is hanging trying to correct a defect it usually means the defect is 
large. This is typically the case when something else has gone wrong (skull 
stripping left stuff around, aseg failure, or pathology in the brain). There is 
a tutorial on checking for defects on our wiki

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_tktools

but you should also load the ?h.defect_labels overlay on the ?h.inflated.nofix 
surface to localize the big defect

cheers
Bruce


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of KennethSPrice
Sent: Monday, June 15, 2020 4:32 AM
To: Freesurfer support list 
Subject: [Freesurfer] recon-all hanging, how to examine defect


External Email - Use Caution
Hello freesurfers,

I am running recon-all on one of my subjects and it is hanging on a defect. How 
do I examine the reason it is hanging? Freeview the defect? Any help would be 
appreciated.

Thanks,
Ken


Sent with ProtonMail Secure Email.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

[Fischl, Bruce]

Hi Mason

What do you mean you “just get a series of letters/symbols”? Can you send us 
the commands you ran and the screen output?

Cheers
Bruce


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Monday, June 15, 2020 6:15 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}


External Email - Use Caution
Hi Bruce and Doug,

I tried to load the overlay into Matlab, but that doesn’t work, I just get a 
series of letters/symbols. The surface overlay is in .mgz format. Using  
mri_cor2label works great for getting each roi into a label format, but I would 
also like them each in a .nii.gz format. Do you have any suggestions for this?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Fischl, Bruce" 
mailto:bfis...@mgh.harvard.edu>>
Reply to: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Saturday, 13 June 2020 at 03:02
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}

Hi Mason

You should be able to load the overlay and the ROIs into matlab, then pick out 
the vertices in each ROI from the overlay and save them separately. Just be 
careful about the one-based indexing in matlab. That is, if your ROI is in a 
label file and you read the vertex indices from it, you need to add 1 to the 
index that point into the overlay.

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Friday, June 12, 2020 7:35 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}


External Email - Use Caution
Hi Doug,

Yes, I mean a surface overlay, it is the mgz format. It essentially has 25 
visual areas, shown in the attached. I wanted to split them up, so that each 
ROI is its own label. I saw I could use mri_cor2label, but is there a better 
way?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Douglas N. Greve" 
mailto:dgr...@mgh.harvard.edu>>
Reply to: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 12 June 2020 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files

When you say "surface" do you mean a surface overlay or a surface with xyz and 
neighbor relations? Assuming you mean an overlay (eg, something in an mgh or 
mgz file), you can try fscalc. Or do you have 25 frames  in a single file and 
you want to split them into separate files? You might be able to convert the 
mgh/mgz file to nii and use FSL tools and then convert them back (sometimes 
works, sometimes not)
On 6/12/2020 10:24 AM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

Apologies if this is a rather simple question. Is there a FreeSurfer equivalent 
of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz 
file. I want to separate each atlas region into a different file, so that I end 
up with 25 surface atlas regions. Is there a command that could achieve this?

My next question is whether or not there is a Freesurface command th

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

[Fischl, Bruce]

You need to use load_mgh or MRIread (which we distribute)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Tuesday, June 16, 2020 10:26 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}


External Email - Use Caution
Hi Bruce,

I just used the load command. See below.

>> load('rh.wang15_mplbl.mgz')
Error using load
Unknown text on line number 1 of ASCII file rh.wang15_mplbl.mgz
+u�^[1]�".


Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Fischl, Bruce" 
mailto:bfis...@mgh.harvard.edu>>
Reply to: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, 15 June 2020 at 15:44
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}

Hi Mason

What do you mean you “just get a series of letters/symbols”? Can you send us 
the commands you ran and the screen output?

Cheers
Bruce


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Monday, June 15, 2020 6:15 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}


External Email - Use Caution
Hi Bruce and Doug,

I tried to load the overlay into Matlab, but that doesn’t work, I just get a 
series of letters/symbols. The surface overlay is in .mgz format. Using  
mri_cor2label works great for getting each roi into a label format, but I would 
also like them each in a .nii.gz format. Do you have any suggestions for this?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>
Tel: 02920 879628
Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->
Mason T Wells, MSc
Myfyriwr PhD
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU

E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>
Ffôn: 02920 879628


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Fischl, Bruce" 
mailto:bfis...@mgh.harvard.edu>>
Reply to: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Saturday, 13 June 2020 at 03:02
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}

Hi Mason

You should be able to load the overlay and the ROIs into matlab, then pick out 
the vertices in each ROI from the overlay and save them separately. Just be 
careful about the one-based indexing in matlab. That is, if your ROI is in a 
label file and you read the vertex indices from it, you need to add 1 to the 
index that point into the overlay.

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Friday, June 12, 2020 7:35 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Splitting surface overlay into separate files 
{Disarmed}


External Email - Use Caution
Hi Doug,

Yes, I mean a surface overlay, it is the mgz format. It essentially has 25 
visual areas, shown in the attached. I wanted to split them up, so that each 
ROI is its own label. I saw I could use mri_cor2label, but is there a better 
way?

Cheers,
Mason

Mason T Wells, MSc
PhD student
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK

Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.u

Re: [Freesurfer] Correcting recon-all output (missing parts in pial surface)

[Fischl, Bruce]

Phew!

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michael
Sent: Wednesday, June 17, 2020 5:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Correcting recon-all output (missing parts in pial 
surface)


External Email - Use Caution
Thank you for your quick response. The yellow line is the pial surface.

Best,
Michael

Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> schrieb 
am Mi., 17. Juni 2020, 21:12:
Hi Michael

Yes, that should work. Is the surface you are showing below the white or pial? 
Hopefully the pial (using the color we typically use for the ?h.white). If it 
is the white then our segmentation needs to be adjusted as well

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Michael
Sent: Wednesday, June 17, 2020 8:24 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Correcting recon-all output (missing parts in pial 
surface)


External Email - Use Caution
Hello,
I ran recon-all on a post-surgery MRI scan. Because of the resection area
FreeSurfer did not include certain parts which should be included. What is the
correct way of correcting this?

I thought about editing the wm.mgz file by adding missing white matter using a 
brush value of 255 and erase white matter with a value of 1. Followed by 
re-creating the surfaces using:

recon-all -autorecon2-wm -autorecon3 -subjid ...
Thank you very much.
Best Regards,
Michael
[fs.png]

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Fischl, Bruce]

mri_surf2surf will do it, but you are probably better off going directly to 
fsaverage rather than downsampling and upsampling

cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tim Schäfer
Sent: Friday, June 19, 2020 9:00 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 162k 
fsaverage mesh, but once you have the full fsaverage version, to convert to 
gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  wrote:
> 
> 
> External Email - Use Caution
> 
> The appropriate GIFTI extension for that would be .func.gii.  What fsaverage# 
> space is that?  Hopefully FreeSurfer provides a tool to convert that to GIFTI 
> in full resolution fsaverage space and from there we can help you get it to 
> CIFTI in fs_LR.
> 
> Matt.
> 
> From:  on behalf of "Katsumi, 
> Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
> HCP format
> 
> 
> Hi Matt,
> 
> For instance, I have a statistical map (e.g., showing magnitude of functional 
> connectivity at each vertex) that has been computed in 16k fsaverage space 
> that I want to display on a fs_LR surface. I was wondering if there’s a way 
> to convert this file (which is in .mgh extension now) to .dscalar so it’d be 
> CIFTI/wb compatible.
> 
> Thanks,
> Yuta
> 
> From:  on behalf of "Glasser, 
> Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
> HCP format
> 
> 
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
> 
> Matt.
> 
> From:  on behalf of "Katsumi, 
> Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
> format
> 
> 
> Dear FreeSurfer community,
> 
> I would like to be able to display OVERLAY files generated in FreeSurfer on a 
> surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The HCP team states 
> in their documentation 
> (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
>  that any surfaces to be converted to fs_LR need to be in .gii first, but I 
> know mris_convert doesn’t take overlay files as input. It would be great if 
> you could please let me know how I might be able to achieve this task.
> 
> Thanks,
> Yuta
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> 
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy 
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

[Fischl, Bruce]

In general almost all of our binaries will read or write almost all formats we 
support. There are some exceptions to this, but it is generally true

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Katsumi, Yuta
Sent: Friday, June 19, 2020 9:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

Thanks, Tim and Matt. I made a typo earlier - I meant to say that my overlay 
files are already in full fsaverage space with ~164k vertices.

I also thought that mri_convert doesn’t take .gii as output, but the command 
that Tim suggested below does indeed seem to work. 

Thanks,
Yuta


On 6/19/20, 9:05 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Glasser, Matthew"  wrote:

External Email - Use Caution

Is GIFTI a legal output type for mri_convert? I though it only could be 
outputted by mris_convert (which does appear to allow .mgh and .gii).

Matt.

On 6/19/20, 8:00 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tim Schäfer"  wrote:

* External Email - Caution *

External Email - Use Caution

I can't telt you how to get your data from 16k fsaverage to the full 
162k fsaverage mesh, but once you have the full fsaverage version, to convert 
to gifti, just do:

  mri_convert yourfile.mgh yourfile.func.gii

Best,

Tim

> On June 19, 2020 at 1:10 PM "Glasser, Matthew"  
wrote:
>
>
> External Email - Use Caution
>
> The appropriate GIFTI extension for that would be .func.gii.  What 
fsaverage# space is that?  Hopefully FreeSurfer provides a tool to convert that 
to GIFTI in full resolution fsaverage space and from there we can help you get 
it to CIFTI in fs_LR.
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:43 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> Hi Matt,
>
> For instance, I have a statistical map (e.g., showing magnitude of 
functional connectivity at each vertex) that has been computed in 16k fsaverage 
space that I want to display on a fs_LR surface. I was wondering if there’s a 
way to convert this file (which is in .mgh extension now) to .dscalar so it’d 
be CIFTI/wb compatible.
>
> Thanks,
> Yuta
>
> From:  on behalf of "Glasser, 
Matthew" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 10:37 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] Visualization of FreeSurfer overlays in the 
HCP format
>
>
> External Email - Use Caution
> What kind of data does one display in an “OVERLAY” file?
>
> Matt.
>
> From:  on behalf of "Katsumi, 
Yuta" 
> Reply-To: Freesurfer support list 
> Date: Thursday, June 18, 2020 at 5:43 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Visualization of FreeSurfer overlays in the HCP 
format
>
>
> Dear FreeSurfer community,
>
> I would like to be able to display OVERLAY files generated in 
FreeSurfer on a surface in the HCP’s Workbench (e.g., on fs_LR surf.gii). The 
HCP team states in their documentation 
(https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?)
 that any surfaces to be converted to fs_LR need to be in .gii first, but I 
know mris_convert doesn’t take overlay files as input. It would be great if you 
could please let me know how I might be able to achieve this task.
>
> Thanks,
> Yuta
>
> 
> The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If you are 
not the intended recipient, be advised that any unauthorized use, disclosure, 
copying or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this email in error, 
please immediately notify the sender via telephone or return mail.
>
> 
> The materials in this message are private and may contain Protected 
Healthcare Information or other information of a sensitive nature. If you are 
not the intended recipient, be advised that any unauthorized use, disclosure, 
copying or the taking of any action in reliance on the contents of this 
information is strictly prohibited. If you have received this email in error, 
please immediately notify the sender via telephone or return mail.

Re: [Freesurfer] Brodmann area labels

[Fischl, Bruce]

Hi Peng

I think 'lh.BA3b_exvivo.label' is the label you want. The _exvivo just means 
that the data that went into the prediction was acquired on ex vivo brains.
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peng Liu
Sent: Wednesday, June 24, 2020 7:38 AM
To: Freesurfer support list 
Subject: [Freesurfer] Brodmann area labels


External Email - Use Caution
Dear Freesurfer experts,

I was trying to perform some ROI analysis with results obtained from recon-all. 
However I noticed that after recon-all, the labels created were like 
'lh.BA3b_exvivo.label', whereas the labels I would want to create are like 
'lh.BA3b.label'.

I have tried mri_annotation2label command, but the results I got were not as 
wanted either.

Does anyone know how to create labels like 'lh.BA3b.label'?

Any help would be appreciated a lot!

Many Thanks

PL

[Otto-von-Guericke University 
Magdeburg][https://www.dzne.de/typo3temp/assets/_processed_/c/f/csm_logo_de_9eb671b7ff.png]

Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: 
peng@med.ovgu.de/peng@dzne.de
Phone: +49 391 67 25074
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Brodmann area labels

[Fischl, Bruce]

Can you elaborate? What do you mean it is not working as it should be?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peng Liu
Sent: Thursday, June 25, 2020 7:23 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brodmann area labels


External Email - Use Caution
Hi Bruce,

I have tried this label, but it seems not working as it should be. That is why 
I wanted to create labels like before.

Thank you so much!

PL

On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Peng

I think 'lh.BA3b_exvivo.label' is the label you want. The _exvivo just means 
that the data that went into the prediction was acquired on ex vivo brains.
Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peng Liu
Sent: Wednesday, June 24, 2020 7:38 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Brodmann area labels


External Email - Use Caution
Dear Freesurfer experts,

I was trying to perform some ROI analysis with results obtained from recon-all. 
However I noticed that after recon-all, the labels created were like 
'lh.BA3b_exvivo.label', whereas the labels I would want to create are like 
'lh.BA3b.label'.

I have tried mri_annotation2label command, but the results I got were not as 
wanted either.

Does anyone know how to create labels like 'lh.BA3b.label'?

Any help would be appreciated a lot!

Many Thanks

PL

[Otto-von-Guericke University 
Magdeburg][https://www.dzne.de/typo3temp/assets/_processed_/c/f/csm_logo_de_9eb671b7ff.png]

Peng Liu, PhD Candidate

Institut für Kognitive Neurologie und Demenzforschung (IKND)
Otto-von-Guericke Universität Magdeburg
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)

Leipziger Str. 44| Haus 64| Raum 217
39120 Magdeburg, Deutschland

Email: 
peng@med.ovgu.de/peng@dzne.de<http://peng@med.ovgu.de/peng@dzne.de>
Phone: +49 391 67 25074
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Brodmann area labels

[Fischl, Bruce]

Hi Peng

In general you need to give us a lot more information. What ROI analysis are 
you doing? What command  did you type? What was the screen output of it? That 
kind of thing

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peng Liu
Sent: Friday, June 26, 2020 4:51 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Brodmann area labels


External Email - Use Caution
Not exactly. I can successfully create a nifti mask with this exvivo label, and 
the brain area it highlighted is correct from observation. But when I try to 
employ this mask to ROI analysis. The results I got are exactly the same, with 
and without this mask.

That is why I said it seems not working.

If exvivo label is the same label as I used before, I will further look into 
the script and parameter setups.

Thank you for all your help

PL

On Thu, 25 Jun 2020 at 19:20, Tim Schäfer 
mailto:ts%2...@rcmd.org>> wrote:
External Email - Use Caution

What do you mean with 'not working'? Is an incorrect area highlighted on the 
brain? Does some command you are using respond with an error message?

Tim

> On June 25, 2020 at 5:33 PM Peng Liu 
> mailto:claudialiu1...@gmail.com>> wrote:
>
>
> External Email - Use Caution
>
> I usually convert BA3b.label to a nifti mask with SPM to perform ROI
> analysis. But with exvivo label, the mask seems not working.
>
> Many Thanks
>
> PL
>
> On Thu, 25 Jun 2020 at 16:24, Fischl, Bruce 
> mailto:bfis...@mgh.harvard.edu>> wrote:
>
> > Can you elaborate? What do you mean it is not working as it should be?
> >
> >
> >
> > *From:* 
> > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >  <
> > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
> >  *On Behalf Of *Peng Liu
> > *Sent:* Thursday, June 25, 2020 7:23 AM
> > *To:* Freesurfer support list 
> > mailto:freesurfer@nmr.mgh.harvard.edu>>
> > *Subject:* Re: [Freesurfer] Brodmann area labels
> >
> >
> >
> > *External Email - Use Caution*
> >
> > Hi Bruce,
> >
> >
> >
> > I have tried this label, but it seems not working as it should be. That is
> > why I wanted to create labels like before.
> >
> >
> >
> > Thank you so much!
> >
> >
> >
> > PL
> >
> >
> >
> > On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce 
> > mailto:bfis...@mgh.harvard.edu>>
> > wrote:
> >
> > Hi Peng
> >
> >
> >
> > I think 'lh.BA3b*_exvivo*.label' is the label you want. The _exvivo just
> > means that the data that went into the prediction was acquired on ex vivo
> > brains.
> >
> > Cheers
> >
> > Bruce
> >
> >
> >
> > *From:* 
> > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> >  <
> > freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
> >  *On Behalf Of *Peng Liu
> > *Sent:* Wednesday, June 24, 2020 7:38 AM
> > *To:* Freesurfer support list 
> > mailto:freesurfer@nmr.mgh.harvard.edu>>
> > *Subject:* [Freesurfer] Brodmann area labels
> >
> >
> >
> > *External Email - Use Caution*
> >
> > Dear Freesurfer experts,
> >
> >
> >
> > I was trying to perform some ROI analysis with results obtained from
> > recon-all. However I noticed that after recon-all, the labels created were
> > like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create
> > are like 'lh.BA3b.label'.
> >
> >
> >
> > I have tried mri_annotation2label command, but the results I got were not
> > as wanted either.
> >
> >
> >
> > Does anyone know how to create labels like 'lh.BA3b.label'?
> >
> >
> >
> > Any help would be appreciated a lot!
> >
> >
> >
> > Many Thanks
> >
> >
> >
> > PL
> >
> > 
> >
> > [image: Otto-von-Guericke University Magdeburg]
> >
> >
> >
> > Peng Liu, PhD Candidate
> >
> >
> >
> > Institut für Kognitive Neurologie und Demenzforschung (IKND)
> >
> > Otto-von-Guericke Universität Magdeburg
> >
> > Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE)
> >
> >
> >
> > Leipziger Str. 44| Haus 64| Raum 217
> >
> > 39120 Magdeburg, Deutsch

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Fischl, Bruce]

HI Angela

Can you send us the complete command line and screen output of the commands you 
ran that worked and the ones that failed?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 8:03 AM
To: Freesurfer support list 
Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution
Dear Freesurfer experts,
I have a problem with a T1 volume of my dataset and I am not able to understand 
it.
This volume was correctly analyzed by Freesurfer 6.
Whan I run recon-all with Freesurfer 7.1 the following error appear:

Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 13:46:17 CEST 2020






Using Freeview I was not able to see the volume and when I tried, as suggested 
in the support list, to run mri_info:




mri_info(21013,0x11e0d7dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(21013,0x11e0d7dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!








When I tried to run mri_info with the file rawavg.mgz (from previous analysis 
with Freesurfer 6) the same error message appeared (and Freeview was not able 
to open it). But when I used the file orig.mgz, I obtained the below output and 
Freeview was able to open the volume. But when I tried to use the orig.mgz file 
as the input file (renamed 001.mgz) in the subj/mri/orig folder, again the 
error output appear (ERROR: input(s) cannot have multiple frames!). What is the 
problem according to you?
Thank you for any help
Angela




Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Fischl, Bruce]

Are you sure 102.mgz is from our analysis previously? We typically name the 
volumes 001.mgz, 002.mgz, etc

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 1:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution
Sure!
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

angelafavaro% mri_info 1023.mgz
mri_info(77711,0x1125ffdc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77711,0x1125ffdc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!

mri_info rawavg.mgz
mri_info(77716,0x11438bdc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77716,0x11438bdc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043, failed to calloc 975188992 bytes!


mri_info orig.mgz
Volume information for orig.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.






Il giorno 28 giu 2020, alle ore 17:51, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> ha scritto:

HI Angela

Can you send us the complete command line and screen output of the commands you 
ran that worked and the ones that failed?

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 8:03 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Dear Freesurfer experts,
I have a problem with a T1 volume of my dataset an

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Fischl, Bruce]

Hmmm, can you send us the volume offlist?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 4:53 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution
Yes, I am sure
Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and 
mri_info  worked:

recon-all -all -s subj102
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova
Actual FREESURFER_HOME /Applications/freesurfer
Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 20:26:31 
PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 22:44:04 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
….
…..


mri_info subj102/mri/orig/102.mgz
Volume information for subj102/mri/orig/102.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.



Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> ha scritto:

Are you sure 102.mgz is from our analysis previously? We typically name the 
volumes 001.mgz, 002.mgz, etc….

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 1:49 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Sure!
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error code=3)
mri_info(77526,0x11d011dc0) malloc: *** set a breakpoint in malloc_error_break 
to debug
error: Cannot allocate memory
error: znzTAGskip: tag=1768777043

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

[Fischl, Bruce]

And how did you generate the volumes? I wouldn’t name them 001.mgz, that will 
end up being confusing. Maybe something like sub.001.mgz might be better, since 
otherwise we might overwrite some of them

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 4:53 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!


External Email - Use Caution
Yes, I am sure
Now I tried to use Freesurfer 6.0 again for that volume and both recon-all and 
mri_info  worked:

recon-all -all -s subj102
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/prova
Actual FREESURFER_HOME /Applications/freesurfer
Darwin MacBookiAngela2 16.7.0 Darwin Kernel Version 16.7.0: Sun Jun  2 20:26:31 
PDT 2019; root:xnu-3789.73.50~1/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 22:44:04 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/prova/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
….
…..


mri_info subj102/mri/orig/102.mgz
Volume information for subj102/mri/orig/102.mgz
  type: MGH
dimensions: 256 x 256 x 256
   voxel sizes: 1.00, 1.00, 1.00
  type: UCHAR (0)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 2250.00 msec, TE: 3.03 msec, TI: 900.00 msec, flip angle: 9.00 
degrees
   nframes: 1
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =  -0., c_r =-2.5219
  : x_a =   0., y_a =  -0., z_a =   1., c_a =10.8637
  : x_s =  -0., y_s =  -1., z_s =  -0., c_s =   -32.3759

talairach xfm : 
/Users/angelafavaro/Desktop/aachen_free/subj102/mri/transforms/talairach.xfm
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.  -0.   125.4781
0.  -0.   1.  -117.1363
   -0.  -1.  -0.95.6241
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   125.4781
0.  -0.  -1.95.6241
0.   1.  -0.   117.1363
   -0.  -0.  -0. 1.



Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> ha scritto:

Are you sure 102.mgz is from our analysis previously? We typically name the 
volumes 001.mgz, 002.mgz, etc….

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Angela Favaro
Sent: Sunday, June 28, 2020 1:49 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution
Sure!
thank you for any help!
Angela

angelafavaro% recon-all -all -s subj102
Subject Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
Current Stamp: freesurfer-darwin-macOS-7.1.0-20200511-813297b
INFO: SUBJECTS_DIR is /Users/angelafavaro/Desktop/Aachen
Actual FREESURFER_HOME /Applications/freesurfer/7.1.0
-rw-rw-r--  1 angelafavaro  staff  143379 Jun 28 13:46 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
#
#@# MotionCor Sun Jun 28 19:40:10 CEST 2020
Found 1 runs
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/Users/angelafavaro/Desktop/Aachen/subj102/mri/orig/102.mgz has  frames
Darwin iMac-di-Angela 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 
PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64

recon-all -s subj102 exited with ERRORS at Sun Jun 28 19:40:11 CEST 2020

For more details, see the log file 
/Users/angelafavaro/Desktop/Aachen/subj102/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Then I copied 102.mgz in a different folder. I also copied in this folder the 
files 102.mgz (renamed 1023.mgz), orig.mgz and rawavg.mgz from a previous 
(successful) analysis with Freesurfer 6.0

angelafavaro% mri_info 102.mgz
mri_info(77526,0x11d011dc0) malloc: can't allocate region
*** mach_vm_map(size=8386104309919531008) failed (error 

Re: [Freesurfer] Lesioned hemisphere

[Fischl, Bruce]

What is the error? You should be able to run through to the surface generation, 
then only run the hemi you want

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Alina Rojas
Sent: Monday, July 6, 2020 10:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Lesioned hemisphere

External Email - Use Caution

Hello Freesurfer experts,

I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all 
breaks and gives an error at the white matter segmentation, what I understand. 
I don’t need the data from the lesioned hemisphere, I need the cortical 
thickness from the healthy one. Is there a possibility to only run one 
hemisphere through freesurfer? Or to project the healthy one on to the lesioned 
to have an intact brain and run recon-all succesfully?

Thanks,

Alina

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Lesioned hemisphere

[Fischl, Bruce]

From the log file it got to the surface stuff and died there. You should be 
able to run recon-all with the -hemi [lr]h switch to just run one hemi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Alina Rojas
Sent: Monday, July 6, 2020 11:23 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Lesioned hemisphere


External Email - Use Caution
Hello Bruce,

Thanks for the quick answer! I attached the recon-all.log file and a 
visualization of the subjects problem.
How can I run only one hemisphere?

Thanks,

Alina






Am 06.07.2020 um 16:32 schrieb Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>:

What is the error? You should be able to run through to the surface generation, 
then only run the hemi you want

Cheers
Bruce

-Original Message-
From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Alina Rojas
Sent: Monday, July 6, 2020 10:22 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Lesioned hemisphere

   External Email - Use Caution

Hello Freesurfer experts,

I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all 
breaks and gives an error at the white matter segmentation, what I understand. 
I don’t need the data from the lesioned hemisphere, I need the cortical 
thickness from the healthy one. Is there a possibility to only run one 
hemisphere through freesurfer? Or to project the healthy one on to the lesioned 
to have an intact brain and run recon-all succesfully?

Thanks,

Alina

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cortical thickness

[Fischl, Bruce]

yes

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nasiriavanaki, Zahra
Sent: Monday, July 6, 2020 12:31 PM
To: Freesurfer support list 
Subject: [Freesurfer] cortical thickness

Hi Freesurfer experts

I have a question about the way FS calculates cortical thickness and I 
appreciate if you could please respond.
I calculated the cortical thickness using read_curv script in a specific ROI in 
parietal lobe. 
The mean thickness at that area was 2.4. Does this number show the cortical 
thickness in millimeter? 

Thanks
MOna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] cortical thickness

[Fischl, Bruce]

I'm not sure I understand your question. We compute the distance between 
minimum distances between the white and pial in mm, then compute the minimum 
between the pial and the white, then average them (all in mm)

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nasiriavanaki, Zahra
Sent: Monday, July 6, 2020 1:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] cortical thickness

Thanks for your response Bruce.
Does FS calculate the distance between the surface and CSF border in Euclidean 
and then converts it into mm?

Thanks
Mona


> On Jul 6, 2020, at 12:40 PM, Fischl, Bruce  wrote:
> 
> yes
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Nasiriavanaki, Zahra
> Sent: Monday, July 6, 2020 12:31 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] cortical thickness
> 
> Hi Freesurfer experts
> 
> I have a question about the way FS calculates cortical thickness and I 
> appreciate if you could please respond.
> I calculated the cortical thickness using read_curv script in a specific ROI 
> in parietal lobe. 
> The mean thickness at that area was 2.4. Does this number show the cortical 
> thickness in millimeter? 
> 
> Thanks
> MOna
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] discontiguous regions assigned to same label by mris_divide_parcellation

[Fischl, Bruce]

Hi Chris

If you can upload this subject and let us know exactly which parcels are 
duplicated we will take a look

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mcnorgan, Christopher
Sent: Saturday, July 11, 2020 1:55 PM
To: Freesurfer Mailing List 
Subject: [Freesurfer] discontiguous regions assigned to same label by 
mris_divide_parcellation


External Email - Use Caution
I’ve been using the .annot files generated by group-level GLM results for 
functional masks for task-related functional connectivity studies.
Depending on threshold and contrast, the clusters can be quite large, and I 
would prefer to use the mris_divide_parcellation utility to break the clusters 
up into smaller subregions, and generally use the size threshold to make the 
regions roughly equal size.

One quirk of mris_divide_parcellation is that, because it divides along the 
longest axis, if I want my final region sizes to be small (relative to the size 
of the whole cluster), I often find that the subdivisions take on the form of 
many narrow bands perpendicular to the axis of division. I have attempted to 
combat this by applying the utility in two passes: in the first pass, I might 
call:
   mris_divide_parcellation fsaverage lh mycontrast.annot 1600 mycontrast_1600
This first breaks up large clusters into 1600mm2 subclusters along their 
longest axes
If my goal is to have 400mm regions, I then call mris_divide_parcellation on 
the new annotation:
   mris_divide_parcellation fsaverage lh mycontrast_1600.annot 400 
mycontrast_400
This has the desired effect of generating roughly 400mm regions that are 
roughly square, at least, compared to the very narrow regions I would have 
gotten had I just done a single pass using 400mm subdivisions from the original 
annotation.

The problem I am having is that the subdivisions in the second pass appear to 
be assigning discontiguous subdivisions of the same source cluster to the same 
label. An example is attached. The subdivisions have the proportions I’m 
looking for, but two regions at opposite ends of the same cluster have the same 
label (there are actually three pairs of noncontiguous regions with the same 
label in this large cluster). I am wondering if there is any way that this can 
be avoided?
[cid:image001.jpg@01D65793.8E8331E0]
/**
* Chris McNorgan
* Assistant Professor
* Department of Psychology
* University at Buffalo,
* The State University of New York
* http://ccnlab.buffalo.edu/
* Office: 716.645.0236
* Lab: 716.645.0222
**/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] The input for FreeSurfer

[Fischl, Bruce]

Hi Hengameh

You can try, but 3mm may be too thick for accurate surface models. Once you 
have too many voxels that contain both sides of a sulcus it is difficult to 
recover accurate surfaces. Note that our inputs don’t have to be mprage, but 3D 
acquisitions are highly recommended

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Hengameh Marzbani
Sent: Friday, July 17, 2020 8:23 AM
To: Freesurfer support list 
Subject: [Freesurfer] The input for FreeSurfer


External Email - Use Caution

Hello Freesurfer developers,



I have T1 weighted MRI images which are not MPRAGE. They are 2 dimensional 
sagittal or axial images with 3mm thickness (1.5 Tesla).

Can I analyze these images by FreeSurfer?

If yes, what tips should I consider?



Thank you in advance,

Best regards,

Hengameh

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: Fwd: question regarding mri_vol2label

[Fischl, Bruce]

Hi Julie

I don’t think we have anything that will do this out-of-the-box, but it should 
be easy enough to do in matlab or python. The label files are a text format and 
we provide .m and .py files to read them. Alternatively you could combine all 
the labels into a single parcellation file /subject/hemi and read that in (but 
it is not a text format)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julie Ottoy
Sent: Friday, July 17, 2020 10:59 AM
To: Freesurfer support list 
Subject: [Freesurfer] Fwd: Fwd: question regarding mri_vol2label


External Email - Use Caution
Hi FS team,

I was wondering if you could take a look at the question below. Thanks!

-- Forwarded message -
From: Julie Ottoy mailto:julie.jj.ot...@gmail.com>>
Date: Fri, 10 Jul 2020 at 20:49
Subject: Re: [Freesurfer] Fwd: question regarding mri_vol2label
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>

Thank you for your reply. It worked to convert to surface label :)
When i overlay the surface labels on the pial surface, I can view a histogram 
showing the number of vertices versus the numbers of labels i have. As a 
follow-up question, do you know how I could extract a txt file that gives me 
the vertices with their corresponding label number. For example, for 10,000 
vertices and 100 labels, I'd like to get a txt file with 10,000 rows and each 
row has a label value between 1 and 100.

Thank you for your help!

On Fri, 10 Jul 2020 at 16:28, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
That will create a volume label, not a surface label (but it should not have 
been empty -- look in the label (it is just a text file)). To get a surface 
label, first map the volume to the surface with something like
mri_vol2surf --mov parcellationvolumes.nii.gz --projfrac-max -.5 1 .1 --hemi lh 
--o lh.parcellationvolumes.mgz --regheader subject
 mri_cor2label --i lh.parcellationvolumes.mgz --id 20 --surf subject lh --l 
lh.20.label

On 7/10/2020 3:46 PM, Julie Ottoy wrote:

External Email - Use Caution
Hi Freesurfer team

I am trying to convert parcellation (cortical) volumes that I acquired through 
another platform into surface labels using freesurfer. I tried following code 
to convert the volume with ID 20 from the parcellationvolumes.nii.gz file into 
a label

mri_cor2label  --i dir/parcellationvolumes.nii.gz --id 20 --l dir/20.label

Although the code runs fine and finishes successfully, whenever I try to open 
the created label in freeview, it says that the label is empty.

Any idea what I am doing wrong? Do you have an easier way to project all ROI 
volumes onto the surface?

A second related question: I have run the recon-all for T1 of the subject and 
it creates rh.pial and lh.pial. I was wondering whether the transformation to 
go from T1 volume to the surface is saved somewhere and whether I can apply 
this transformation to convert my cortical volume parcellations into surface 
parcellations?

Thank you for your help!
Best regards
Julie


___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Converting volume to icosahedron surface

[Fischl, Bruce]

Hi Teresa

You should be able to load it as an overlay on the fsaverage4 subject. Note 
that you aren't converting the volume to a surface. Rather you are sampling it 
onto the surface. Have you run recon-all?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Tse, Teresa
Sent: Saturday, July 18, 2020 6:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Converting volume to icosahedron surface


External Email - Use Caution
Hi all,

I am trying to convert a volume file (fMRI data in nifti format) into an 
icosahedron (4th order) surface using Freesurfer's mri_vol2surf command. I have 
been using nipype as a wrapper for Freesurfer and the other packages that I 
need for my processing. The command that nipype ran is:

mri_vol2surf
--hemi lh
--icoorder 4
--o 
/dev/shm/RT_processing/_hemi_lh/to_surface/lh.003-FunctionalCMRR-2mm69sl1p5s_mcf.mgz
--reg /dev/shm/RT_processing/convert_xfm/InplanetoAnatomy.xfm
--projfrac-avg 0.000 1.000 0.100
--mov 
/dev/shm/RT_processing/motion_correction/003-FunctionalCMRR-2mm69sl1p5s_mcf.nii.gz
--trgsubject ico

The output of this command is a mgz file (attached to this email). I was unable 
to view this mgz file using Freeview's "Load surface" (I get the error 
"freadFloat: fread failed"). I was able to load the mgz file into Matlab using 
the load_mgh function. It loaded as a 2562 length vector (consistent with the 
number of vertices of a ico-4 surface). I have several questions regarding the 
output of the mri_vol2surf command that was run.

1) I am unsure as to whether the command that was used is correct, and whether 
the output mgz file that I got is the correct or expected output. What do the 
values of the vector represent?
2) Do you know how to load and view the output mgz file in Freeview? Is it 
supposed to be an overlay or annotation to an ico-4 surface file? If so, where 
would I find this ico-4 surface?
3) How do I find documentation and information about the icosahedron surface in 
Freesurfer?

Many thanks,
Teresa

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM

[Fischl, Bruce]

Hi Nils

There are expert options for this. You can specify things like -min_white 90 to 
some of the programs like mri_segment and the surface placement stuff

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nils Böer
Sent: Wednesday, July 29, 2020 3:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FS 7.1.0 - Editing intensity values for WM


External Email - Use Caution
Hello everyone,

I just have a short question, because I can't find anything helpful in the 
tutorials.

In my MRI scans freesurfer includes areas to the white matter, even though 
visual inspection concludes that the area should be grey matter. Is there a 
possibility to change the value at which freesurfer includes areas to the WM, 
which i can just change? For example freesurfer includes areas to the WM with 
intensity values below 85 and i want to change that.

I'd be thankful for any feedback/links to guides.

Best regards,

Nils
--

Nils Böer
Research Assistant with Bachelor Degree (WHB)
Psychology and Movement
University of Paderborn
Department of Sports and Health
Warburger Str. 100
33098 Paderborn
Room: Sp 1.401
Email: nils.tobia...@gmail.com / 
nbo...@mail.uni-paderborn.de
Web: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/
 
https://sug.uni-paderborn.de/department/it/

[https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]
Virenfrei. 
www.avast.com

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Converting sulc files

[Fischl, Bruce]

Hi Dimitrios

Check out the help for mris_convert and replace lh.thickness with lh.sulc (they 
are in the same 'curv' format)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Alexopoulos, Dimitrios
Sent: Monday, August 3, 2020 6:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Converting sulc files


External Email - Use Caution
Is there a command that will convert the
?h.sulc to ascii, i.e. depth at each vertex?

Get Outlook for Android


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Needing advises for results in my study.

[Fischl, Bruce]

Hi Haewon

The problem is that you will never be able to distinguish a scanner effect from 
a real biological effect since they are in the same subspace. At the very least 
you should find some control data on both scanners to show that there is no 
bias in the direction of the effect you are finding.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Haewon Roh
Sent: Thursday, August 6, 2020 12:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Needing advises for results in my study.


External Email - Use Caution
Hi.

Recently, I analyzed patients who have taken 1.5T MRI ; (Because they had to go 
in MRI room with some metal materials) and normal controls who took 3.0T MRI. 
And, after recon and preprocessing of each group of patients and controls in 
freesurfer v6, I've found that many cortices of patients (1.5T MRI) were 
significantly reduced, compared with normal age-sex matched controls (3.0T 
MRI). When I searched in order to know if there is difference between 1.5T vs 
3.0T MRI and magnetic field can make a huge difference in calculating volumes 
or thickness of cortices in Freesurfer, I can find only one article by Heinen 
and his colleague, reporting there is no big difference and different(1.5 vs 
3.0T) magnetic field strength cannot make a significant difference. (Plos ONE, 
2016)

Furthermore, given that data which is taken in 1.5T MRI is more likely to have 
more increased volumes or thickness of cerebral cortices than those of 3.0T 
MRI, I think that reduced cortical volumes which are calculated using 1.5T MRI 
have more significance than controls of 3.0T MRI...

Is it true that different magnetic strengths of MRI cannot change the result 
significantly in Freesurfer?

Thank you always!


--
Hae Won ROH, M.D.

H.P: +82-10-4341-8142
E-mail: rofree...@gmail.com
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Recon-all Soft Errors

[Fischl, Bruce]

Can you upload an example dataset? It looked like an intensity normalization 
failure that probably caused a topological defect

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Elana Sarabin
Sent: Friday, August 7, 2020 11:08 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all Soft Errors


External Email - Use Caution
More so that the brainmask.mgz is missing a lot of both grey and white matter. 
For some the area cut out in brainmask is much smaller and for others it is 
large just like the photo I sent. I am wondering if there is a way to fix this 
since 50% of my participants scans look like this.

Thanks,
Elana

Get Outlook for iOS<https://aka.ms/o0ukef>

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Friday, August 7, 2020 8:17:42 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all Soft Errors

[△EXTERNAL]

This error shows a massive failure. Is this what you are describing as:

includes areas to the white matter, even though visual inspection concludes 
that the area should be grey matter.




On 8/6/2020 9:00 PM, Elana Sarabin wrote:

External Email - Use Caution

Here is one photo. Seems this is the most I can send at once. Most errors look 
just like this however sometimes larger and sometimes smaller.



Best,

Elana



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, August 4, 2020 at 8:01 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors



[△EXTERNAL]



Can you send a picture of the type of errors you are seeing?

On 7/31/2020 9:03 AM, Elana Sarabin wrote:

External Email - Use Caution



Here is the recon-all.log file.



Thanks,

Elana



-Original Message-

From: Elana Sarabin

Sent: July 30, 2020 10:21 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: Recon-all Soft Errors



Here is the recon-all.log file.



Thanks,

Elana



-Original Message-

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>

Sent: July 30, 2020 10:00 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Freesurfer Digest, Vol 197, Issue 59



[△EXTERNAL]







Send Freesurfer mailing list submissions to

freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>



To subscribe or unsubscribe via the World Wide Web, visit

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

or, via email, send a message with subject or body 'help' to


freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>



You can reach the person managing the list at


freesurfer-ow...@nmr.mgh.harvard.edu<mailto:freesurfer-ow...@nmr.mgh.harvard.edu>



When replying, please edit your Subject line so it is more specific than "Re: 
Contents of Freesurfer digest..."





Today's Topics:



   1. FS 7.1.0 - Editing intensity values for WM (Nils B?er)

   2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Bruce)

   3. Creating .annot file for a mri_decimate downsampeld   version

  of pial surface (Donelson Berger)

   4. GONE: -make to recon-all (Johnson, Hans J)

   5. Re: fsgd file - glmfit error

  (Lab of Autism and Developmental Neuroscience,Lab of Autism and 
Developmental Neuroscience)

   6. Re: Recon-all Soft Errors (Zollei, Lilla,Ph.D.)

   7. bad interpreter: No such file or directory error

  (Hengameh Marzbani)

   8. Re: overlapping/ superimposing regions of one analysis over

  another (Douglas N. Greve)

   9. Re: Creating .annot file for a mri_decimate downsampeld

  version of pial surface (Douglas N. Greve)

  10. Re: Recon-all Soft Errors (Douglas N. Greve)

  11. Re: Coregistration to MNI (Douglas N. Greve)

  12. mri_aparc2aseg: how to remove redundant output labels? (Ellen Ji)

  13. Re: bad interpreter: No such file or directory error (fsbuild)





--



Message: 1

Date: Wed, 29 Jul 2020 21:27:03 +0200

From: Nils B?er <mailto:nils.tobia...@g

Re: [Freesurfer] Directories not populating after recon-all

[Fischl, Bruce]

Hi Rohin

Can you send us your command line and full screen output? Probably you need to 
include th e-all directive to recon-all

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rohin Singh
Sent: Friday, August 7, 2020 10:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Directories not populating after recon-all

External Email - Use Caution

Hello,

I am a student at the Mayo Clinic trying to do a project with fresurfer. When I 
run recon-all, it only creates one file “001.mgz” in the MRI directory and the 
rest of the folders are blank. I am not sure why this is as it completes the 
process without any errors and I followed the set up instructions exactly.

Any help would be greatly appreciated.

Thanks,
Rohin Singh 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Recon-all Soft Errors

[Fischl, Bruce]

Hi Elana

You say it happens on 50% of your participants. Can you pick one and upload the 
entire gzipped and tarred directory for that subject?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Elana Sarabin
Sent: Saturday, August 8, 2020 10:07 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Recon-all Soft Errors


External Email - Use Caution
Sorry I’m not sure I know what you mean when you say an example dataset.

Regards,
Elana

Get Outlook for iOS<https://aka.ms/o0ukef>

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, August 7, 2020 9:17:24 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all Soft Errors

[△EXTERNAL]


Can you upload an example dataset? It looked like an intensity normalization 
failure that probably caused a topological defect



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Elana Sarabin
Sent: Friday, August 7, 2020 11:08 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all Soft Errors



External Email - Use Caution

More so that the brainmask.mgz is missing a lot of both grey and white matter. 
For some the area cut out in brainmask is much smaller and for others it is 
large just like the photo I sent. I am wondering if there is a way to fix this 
since 50% of my participants scans look like this.



Thanks,

Elana



Get Outlook for iOS<https://aka.ms/o0ukef>



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Friday, August 7, 2020 8:17:42 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Recon-all Soft Errors



[△EXTERNAL]



This error shows a massive failure. Is this what you are describing as:

includes areas to the white matter, even though visual inspection concludes 
that the area should be grey matter.





On 8/6/2020 9:00 PM, Elana Sarabin wrote:

External Email - Use Caution

Here is one photo. Seems this is the most I can send at once. Most errors look 
just like this however sometimes larger and sometimes smaller.



Best,

Elana



From: 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of "Douglas N. Greve" 
<mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, August 4, 2020 at 8:01 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all Soft Errors



[△EXTERNAL]



Can you send a picture of the type of errors you are seeing?

On 7/31/2020 9:03 AM, Elana Sarabin wrote:

External Email - Use Caution



Here is the recon-all.log file.



Thanks,

Elana



-Original Message-

From: Elana Sarabin

Sent: July 30, 2020 10:21 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: Recon-all Soft Errors



Here is the recon-all.log file.



Thanks,

Elana



-Original Message-

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>

Sent: July 30, 2020 10:00 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Freesurfer Digest, Vol 197, Issue 59



[△EXTERNAL]







Send Freesurfer mailing list submissions to

freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>



To subscribe or unsubscribe via the World Wide Web, visit

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

or, via email, send a message with subject or body 'help' to


freesurfer-requ...@nmr.mgh.harvard.edu<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>



You can reach the person managing the list at


freesurfer-ow...@nmr.mgh.harvard.edu<mailto:freesurfer-ow...@nmr.mgh.harvard.edu>



When replying, please edit your Subject line so it is more specific than "Re: 
Contents of Freesurfer digest..."





Today's Topics:



   1. FS 7.1.0 - Editing intensity values for WM (Nils B?er)

   2. Re: FS 7.1.0 - Edi

Re: [Freesurfer] Available brain atlases in freesurfer in surface format!!

[Fischl, Bruce]

Hi Shreyas

Which surface atlas do you mean? We have several and they are stored in 
different formats. The folding ones are stored as multi-frame spherical tif 
files, while the parcellations are in an internal format (.gcs). The are all 
freely available and included with every FreeSurfer installation

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Shreyas Indurkar
Sent: Thursday, August 13, 2020 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Available brain atlases in freesurfer in surface format!!


External Email - Use Caution
Dear Freesurfer Experts,

I came to know that freesurfer software contains atlas/atlases in surface 
format (.gii or similar). If yes, how is it possible to get access to these 
atlases?

Thank you


Sincerely,
Shreyas Indurkar
Max Planck Institute for Biological Cybernetics,
Tuebingen, Germany.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

[Fischl, Bruce]

Hi Barbara

We run a *ton* of tests on thousands of subjects from different scanners and 
different kinds of pathology before we do a major release. This hasn't been 
done yet with fastsurfer as it is a huge amount of work

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Barbara Kreilkamp
Sent: Thursday, August 20, 2020 10:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

External Email - Use Caution

Dear all,

I noticed FastSurfer also seems to run with a 7.1.0 FS version.

Or is there any reason not to do this?

Thank you,

Kind wishes,
Barbara


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all output resolution

[Fischl, Bruce]

Yes, that is correct. The "conform" step resamples to 1mm isotropic (among 
other things)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Billah, Tashrif
Sent: Tuesday, August 25, 2020 10:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all output resolution

Hi all,

Is the resolution of mri/*mgz files produced by `recon-all -all` always 1mm^3 
regardless of the resolution of my input unless -hires is used?

This is what I found in recon-all.log:

without --hires:
mri_convert 001/mri/rawavg.mgz 001/mri/orig.mgz --conform

I believe the `--conform` flag does the resampling for all resolution.

with -hires:
mri_convert 434/mri/rawavg.mgz 434/mri/orig.mgz --conform_min

Best,
Tashrif
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FS educ links

[Fischl, Bruce]

Sure, that is fine

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of John Absher
Sent: Tuesday, August 25, 2020 1:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] FS educ links


External Email - Use Caution
Hi,
We're implementing freesurfer and other neuroimaging applications on the High 
Performance Computing center. To help more users get up to speed quickly, I'm 
trying to pull together up-to-date freesurfer/freeview educational materials 
into a single online resource. Is it OK to link directly to available online 
resources/tutorials/videos/datasets as long as I include appropriate 
attributions? If not, how do I go about getting permissions?

Warm Regards,

John R. Absher, MD, FAAN
Clinical Associate Professor, University of South Carolina School of Medicine 
Greenville
Department of Internal Medicine, Division of Neurology
Clinical Assistant Professor, Clemson University School of Health Research 
(CUSHR)
Graduate Faculty, Clemson University School of Public Health Sciences
Prisma Health-Upstate
200 Patewood Drive, Suite 350B
Greenville, SC 29615
john.abs...@prismahealth.org or 
jabs...@greenvillemed.sc.edu or 
jabs...@clemson.edu
864-454-4500 (office)
864-350-6655 (mobile)
864-454-4505 (fax)

[cid:image001.jpg@01D67AE0.CC892010]

Inspire health. Serve with compassion. Be the difference.


CONFIDENTIALITY NOTICE
This message is intended only for the use of the individual or entity to which 
it is addressed and may contain information that is privileged, confidential 
and exempt from disclosure under applicable law. If the reader of this message 
is not the intended recipient, you are hereby notified that any dissemination, 
distribution, or copying of this communication is strictly prohibited by law. 
If you have received this communication in error, please notify me immediately.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Hi Jie

I would start by looking at your input volume in freeview:

freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii

and make sure that the orientation it displays in is correct (that is, that 
what freeview thinks is anterior/superior/left are indeed those directions). 
Usually when we see this type of failure it is because the direction cosines in 
the input volume are incorrect (typically because the volume was at some point 
converted to analyze format). Not always, but usually.

Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Thursday, August 27, 2020 11:21 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Hi, Andrew

   Attached is the right recon-all.log file, please check it.
   I am new to the freesurfer, so really need you advice, Thanks

Kind Regards,
Jie


> -Original Messages-
> From: "Hoopes, Andrew"  Sent Time: 2020-08-26 
> 10:17:00 (Wednesday)
> To: "Freesurfer support list" 
> Cc: 
> Subject: Re: [Freesurfer] recon-all error
> 
> Hi Jie, this appears to be the log for your original issue, and not the 
> talairach registration failure.
> Andrew
> 
> On 8/25/20, 9:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> 
> External Email - Use Caution
> 
> Hi Andrew
> 
> Thanks fro your response.
> I have soruced the Freesurfer. 
> Attached is the recon-all log.  
> 
> Best,
> Jie
> 
> 
> > -Original Messages-
> > From: "Hoopes, Andrew" 
> > Sent Time: 2020-08-24 22:22:28 (Monday)
> > To: "Freesurfer support list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Hi Jie,
> > 
> > Can you send the subject's full recon-all.log file to provide some more 
> context for this failure? Usually this error is due to a poor registration, 
> but there might be something else going wrong here based on those p values. 
> Have you sourced freesurfer in your environment? Adding the freesurfer bin 
> dir to your PATH will provide access to binaries, but there are a few other 
> PATH variables and settings that get configured by running `source 
> $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> > 
> > best
> > Andrew
> > 
> > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
> of Jie Zhao"  zjuzhao...@zju.edu.cn> wrote:
> > 
> > External Email - Use Caution
> > 
> > Hi, Tim
> > 
> > Thanks for your quick response.
> > I set the PATH environment varible to include Freesurfer binary 
> directory.
> > 
> > I have the new problem when using recon-all , the error is like 
> this:
> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm 
> ***FAILED*** (p=0., pval=0. < threshold=0.0050
> > 
> > How can solve this error? 
> > 
> > Regards,
> > Jie
> > 
> > > -原始邮件-
> > > 发件人: "Tim Schäfer" 
> > > 发送时间: 2020-08-23 16:24:28 (星期日)
> > > 收件人: "Freesurfer support list" 
> > > 抄送: 
> > > 主题: Re: [Freesurfer] recon-all error
> > > 
> > > External Email - Use Caution
> > > 
> > > What happems if you type 'mri_ca_label' in your shell?
> > > 
> > > Did you setup your PATH environment variable to include the 
> Freesurfer binary directory?
> > > 
> > > Tim
> > > 
> > > > On August 23, 2020 at 9:34 AM Jie Zhao  
> wrote:
> > > > 
> > > > 
> > > > External Email - Use Caution
> > > > 
> > > > Dear freesurfer developer: 
> > > > 
> > > > I am using Freesurfer 7.1.1 and encounter an error like this 
> when using recon-all :
> > > > 
> > > > zhao@zhao-VirtualBox:~$ export 
> SUBJECTS_DIR=/usr/local/freesurfer/subjects
> > > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i sample-002.nii.gz 
> -autorecon1
> > > > Subject Stamp: 
> freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > > Current Stamp: 
> freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
> > > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > > > Actual FREESURFER_HOME /usr/local/freesurfer
> > > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP Tue Apr 
> 24 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> > > > Segmentation fault
> > > > ERROR: Executable 'mri_ca_label -all-info failed! Is it missing 
> from the distribution?'
> > > > 
> > > > What can I do to fix this?  Thanks
> > > > 
> > > > 
> > > > 
> > > > 
> > > > Best regards
> > > > 
>  

Re: [Freesurfer] How to re-run recon-all

[Fischl, Bruce]

Hi Aldo

You should be able to use recon-all -make all ... to run anything that did not 
complete. You might have to specify the -no-isrunning (or something like that) 
flag if it didn't terminate cleanly

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Camargo, Aldo
Sent: Friday, August 28, 2020 3:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to re-run recon-all


External Email - Use Caution
Hi Freeserufer experts:

By mistake I cancel the recon-all when it was about 3 hours of processing. 
There is a way to re-run the recon-all and that continues where it was stopped ?

Thanks a lot,

Aldo

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How can I get only aparc+aseg.mgz

[Fischl, Bruce]

Sorry, there is no real shortcut for that - you have to run pretty much 
everything

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Camargo, Aldo
Sent: Friday, August 28, 2020 9:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How can I get only aparc+aseg.mgz


External Email - Use Caution
Hi Freesurfer experts:

I would like to get the aparc+aseg.mgz file, which options of recon-all should 
I use to get only that file. Because recon-all takes several hours.

Have a nice day,

Aldo

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Piriform gyrus and other regions of the olfactory pathway

[Fischl, Bruce]

Hi Diógenes

If there are regions that are not in any of our parcellations that you want to 
obtain measures for, you can manually label them on the fsaverage surface, then 
use mri_label2label to map them to each individual subject and use 
mris_anatomical_stats -l  to get the measures you want.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Diógenes Bispo
Sent: Saturday, August 29, 2020 6:10 AM
To: Freesurfer support list 
Subject: [Freesurfer] Piriform gyrus and other regions of the olfactory pathway


External Email - Use Caution
Dear,

I would like to know how do I get thickness and cortical volume measurements of 
the piriform gyrus in Freesurfer version 7, as well as other regions of the 
olfactory pathway.

Thanks.

Diógenes Bispo
Neuroradiologist
diogenesdi...@gmail.com

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] How to re-run recon-all

[Fischl, Bruce]

Oh, sorry, I didn't realize that

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Saturday, August 29, 2020 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] How to re-run recon-all

For version 7, -make all does not work anymore :(
On 8/28/2020 4:26 PM, Camargo, Aldo wrote:

External Email - Use Caution
Thanks a lot Bruce,

Aldo

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Fischl, Bruce 
<mailto:bfis...@mgh.harvard.edu>
Sent: Friday, August 28, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] How to re-run recon-all


Hi Aldo



You should be able to use recon-all -make all ... to run anything that did not 
complete. You might have to specify the -no-isrunning (or something like that) 
flag if it didn't terminate cleanly



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Camargo, Aldo
Sent: Friday, August 28, 2020 3:11 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] How to re-run recon-all



External Email - Use Caution

Hi Freeserufer experts:



By mistake I cancel the recon-all when it was about 3 hours of processing. 
There is a way to re-run the recon-all and that continues where it was stopped ?



Thanks a lot,



Aldo





___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Why do you want to change it? Can you post a snapshot from freeview so we can 
make sure we are on the same page?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 12:25 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Hi Bruce

Thank you for quick answer。

I tryrd the freeview -v /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my 
freeview orienatation is RAS. could you tell me how to change it from RAS to 
(ASL)anterior/superior/left. Thanks

Best,
Jie



> -原始邮件-
> 发件人: "Fischl, Bruce" 
> 发送时间: 2020-08-27 23:39:20 (星期四)
> 收件人: "Freesurfer support list" 
> 抄送: 
> 主题: Re: [Freesurfer] recon-all error
> 
> Hi Jie
> 
> I would start by looking at your input volume in freeview, my orientation on 
> freeview is RAS. Could you tell me 
> 
> freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> 
> and make sure that the orientation it displays in is correct (that is, that 
> what freeview thinks is anterior/superior/left are indeed those directions). 
> Usually when we see this type of failure it is because the direction cosines 
> in the input volume are incorrect (typically because the volume was at some 
> point converted to analyze format). Not always, but usually.
> 
> Cheers
> Bruce
> 
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Jie Zhao
> Sent: Thursday, August 27, 2020 11:21 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] recon-all error
> 
> External Email - Use Caution
> 
> Hi, Andrew
> 
>Attached is the right recon-all.log file, please check it.
>I am new to the freesurfer, so really need you advice, Thanks
> 
> Kind Regards,
> Jie
> 
> 
> > -Original Messages-
> > From: "Hoopes, Andrew"  Sent Time: 2020-08-26 
> > 10:17:00 (Wednesday)
> > To: "Freesurfer support list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Hi Jie, this appears to be the log for your original issue, and not the 
> > talairach registration failure.
> > Andrew
> > 
> > On 8/25/20, 9:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> > Jie Zhao"  > zjuzhao...@zju.edu.cn> wrote:
> > 
> > External Email - Use Caution
> > 
> > Hi Andrew
> > 
> > Thanks fro your response.
> > I have soruced the Freesurfer. 
> > Attached is the recon-all log.  
> > 
> > Best,
> > Jie
> > 
> > 
> > > -Original Messages-
> > > From: "Hoopes, Andrew" 
> > > Sent Time: 2020-08-24 22:22:28 (Monday)
> > > To: "Freesurfer support list" 
> > > Cc: 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > Hi Jie,
> > > 
> > > Can you send the subject's full recon-all.log file to provide some 
> > more context for this failure? Usually this error is due to a poor 
> > registration, but there might be something else going wrong here based on 
> > those p values. Have you sourced freesurfer in your environment? Adding the 
> > freesurfer bin dir to your PATH will provide access to binaries, but there 
> > are a few other PATH variables and settings that get configured by running 
> > `source $FREESURFER_HOME/SetUpFreeSurfer.sh`.
> > > 
> > > best
> > > Andrew
> > > 
> > > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> > behalf of Jie Zhao"  > zjuzhao...@zju.edu.cn> wrote:
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi, Tim
> > > 
> > > Thanks for your quick response.
> > > I set the PATH environment varible to include Freesurfer binary 
> > directory.
> > > 
> > > I have the new problem when using recon-all , the error is like 
> > this:
> > > ERROR: talairach_afd: Talairach Transform: 
> > transforms/talairach.xfm ***FAILED*** (p=0., pval=0. < 
> > threshold=0.0050
> > > 
> > > How can solve this error? 
> > > 
> > > Regards,
> > > Jie
> > > 
> > > > -原始邮件-
> > > > 发件人: "Tim Schä

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Hi Jie

The orientations are incorrect. What freeview thinks is anterior/posterior 
(labeled with "A" and "P") is actually inferior/superior. Do you have the 
dicoms from this dataset? If not, how was it converted? You need to orient it 
properly so it shows correctly in freeview before we will be able to process it.

Cheers
Bruce

-

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Saturday, August 29, 2020 10:08 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Here is the snapshot of my freeview window attached.


> -Original Messages-
> From: "Fischl, Bruce"  Sent Time: 2020-08-30 
> 02:07:50 (Sunday)
> To: "Freesurfer support list" 
> Cc: 
> Subject: Re: [Freesurfer] recon-all error
> 
> Why do you want to change it? Can you post a snapshot from freeview so we can 
> make sure we are on the same page?
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Jie Zhao
> Sent: Saturday, August 29, 2020 12:25 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] recon-all error
> 
> External Email - Use Caution
> 
> Hi Bruce
> 
> Thank you for quick answer。
> 
> I tryrd the freeview -v 
> /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my freeview 
> orienatation is RAS. could you tell me how to change it from RAS to 
> (ASL)anterior/superior/left. Thanks
> 
> Best,
> Jie
> 
> 
> 
> > -原始邮件-
> > 发件人: "Fischl, Bruce" 
> > 发送时间: 2020-08-27 23:39:20 (星期四)
> > 收件人: "Freesurfer support list" 
> > 抄送: 
> > 主题: Re: [Freesurfer] recon-all error
> > 
> > Hi Jie
> > 
> > I would start by looking at your input volume in freeview, my 
> > orientation on freeview is RAS. Could you tell me
> > 
> > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > 
> > and make sure that the orientation it displays in is correct (that is, that 
> > what freeview thinks is anterior/superior/left are indeed those 
> > directions). Usually when we see this type of failure it is because the 
> > direction cosines in the input volume are incorrect (typically because the 
> > volume was at some point converted to analyze format). Not always, but 
> > usually.
> > 
> > Cheers
> > Bruce
> > 
> > 
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
> >  On Behalf Of Jie Zhao
> > Sent: Thursday, August 27, 2020 11:21 AM
> > To: Freesurfer support list 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > External Email - Use Caution
> > 
> > Hi, Andrew
> > 
> >Attached is the right recon-all.log file, please check it.
> >I am new to the freesurfer, so really need you advice, Thanks
> > 
> > Kind Regards,
> > Jie
> > 
> > 
> > > -Original Messages-
> > > From: "Hoopes, Andrew"  Sent Time: 
> > > 2020-08-26
> > > 10:17:00 (Wednesday)
> > > To: "Freesurfer support list" 
> > > Cc: 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > Hi Jie, this appears to be the log for your original issue, and not the 
> > > talairach registration failure.
> > > Andrew
> > > 
> > > On 8/25/20, 9:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf 
> > > of Jie Zhao"  > > zjuzhao...@zju.edu.cn> wrote:
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi Andrew
> > > 
> > > Thanks fro your response.
> > > I have soruced the Freesurfer. 
> > > Attached is the recon-all log.  
> > > 
> > > Best,
> > > Jie
> > > 
> > > 
> > > > -Original Messages-
> > > > From: "Hoopes, Andrew" 
> > > > Sent Time: 2020-08-24 22:22:28 (Monday)
> > > > To: "Freesurfer support list" 
> > > > Cc: 
> > > > Subject: Re: [Freesurfer] recon-all error
> > > > 
> > > > Hi Jie,
> > > > 
> > > > Can you send the subject's full recon-all.log file to provide some 
> > > more context for this failure? Usually this error is due to a poor 
> > > registration, but there might be something else going wrong here based on 
> > &g

Re: [Freesurfer] midline to cut the brain stem into Left and Right

[Fischl, Bruce]

That is reasonable

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of ???
Sent: Tuesday, September 1, 2020 12:11 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] midline to cut the brain stem into Left and Right


External Email - Use Caution
Thanks!
I have a work-around solution but want to hear your comment on it.

I use the TLRC transform matrix in mri/transform to translate the coordinates 
in native to TLRC, so that the origin set to anterior commisure. Then I cut the 
brain stem to left and right, by x>0 and x<0, then I use the inverse matrix to 
translate the left and right brain stem back.

How do you feel about this?

Many thanks!
Mengxing


On Tue, Sep 1, 2020 at 4:42 PM Douglas Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:
Not that I know of, sorry
On 9/1/20 10:20 AM, 刘梦醒 wrote:

External Email - Use Caution
Hi Freesurfer group,

For some reason, I have to use the left and right brain stem separately.
I wonder if there is one way to have a midline, to cut the brain stem into Left 
and Right?

Many thanks,
Mengxing



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Hi Jie,

Is this a scan of a non-human primate?

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Thursday, September 3, 2020 9:34 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Hi, Bruce

I reorineted the views in freesurfer , But the result was wrong again . Please 
check the figure attached, Is there any problem.

BTW, I got the Dicom file, it is .IMA format. How can I use it?

Thanks!
Jie


> -Original Messages-
> From: "Fischl, Bruce"  Sent Time: 2020-08-30 
> 10:14:46 (Sunday)
> To: "Freesurfer support list" 
> Cc: 
> Subject: Re: [Freesurfer] recon-all error
> 
> Hi Jie
> 
> The orientations are incorrect. What freeview thinks is anterior/posterior 
> (labeled with "A" and "P") is actually inferior/superior. Do you have the 
> dicoms from this dataset? If not, how was it converted? You need to orient it 
> properly so it shows correctly in freeview before we will be able to process 
> it.
> 
> Cheers
> Bruce
> 
> -
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Jie Zhao
> Sent: Saturday, August 29, 2020 10:08 PM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] recon-all error
> 
> External Email - Use Caution    
> 
> Here is the snapshot of my freeview window attached.
> 
> 
> > -Original Messages-
> > From: "Fischl, Bruce"  Sent Time: 
> > 2020-08-30
> > 02:07:50 (Sunday)
> > To: "Freesurfer support list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Why do you want to change it? Can you post a snapshot from freeview so we 
> > can make sure we are on the same page?
> > 
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  On Behalf Of Jie Zhao
> > Sent: Saturday, August 29, 2020 12:25 PM
> > To: Freesurfer support list 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > External Email - Use Caution
> > 
> > Hi Bruce
> > 
> > Thank you for quick answer。
> > 
> > I tryrd the freeview -v
> > /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my freeview 
> > orienatation is RAS. could you tell me how to change it from RAS to 
> > (ASL)anterior/superior/left. Thanks
> > 
> > Best,
> > Jie
> > 
> > 
> > 
> > > -原始邮件-
> > > 发件人: "Fischl, Bruce" 
> > > 发送时间: 2020-08-27 23:39:20 (星期四)
> > > 收件人: "Freesurfer support list" 
> > > 抄送: 
> > > 主题: Re: [Freesurfer] recon-all error
> > > 
> > > Hi Jie
> > > 
> > > I would start by looking at your input volume in freeview, my 
> > > orientation on freeview is RAS. Could you tell me
> > > 
> > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > > 
> > > and make sure that the orientation it displays in is correct (that is, 
> > > that what freeview thinks is anterior/superior/left are indeed those 
> > > directions). Usually when we see this type of failure it is because the 
> > > direction cosines in the input volume are incorrect (typically because 
> > > the volume was at some point converted to analyze format). Not always, 
> > > but usually.
> > > 
> > > Cheers
> > > Bruce
> > > 
> > > 
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  On Behalf Of Jie Zhao
> > > Sent: Thursday, August 27, 2020 11:21 AM
> > > To: Freesurfer support list 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi, Andrew
> > > 
> > >Attached is the right recon-all.log file, please check it.
> > >I am new to the freesurfer, so really need you advice, Thanks
> > > 
> > > Kind Regards,
> > > Jie
> > > 
> > > 
> > > > -Original Messages-
> > > > From: "Hoopes, Andrew"  Sent Time: 
> > > > 2020-08-26
> > > > 10:17:00 (Wednesday)
> > > > To: "Freesurfer support list" 
> > > > Cc: 
> > > > Subject: Re: [Freesurfer] recon-all error
> > > > 
> > > > Hi Jie, this appears to be the log for your original issue, and not the 
> > > > talairach registrat

Re: [Freesurfer] how to calculate Euler number

[Fischl, Bruce]

Hi Colleen

After correction the Euler number should be exactly 2. If it is not, it means 
the surface is not topologically equivalent to a sphere. Every defect (hole or 
handle) will decrease it by 2, so an Euler number of -18 (like your lh below) 
is:

# of holes = (2-euler_number)/2 = (2--18)/2 = 10

Make sense?

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of C.P.E. Rollins
Sent: Thursday, September 3, 2020 12:17 PM
To: Freesurfer 
Subject: [Freesurfer] how to calculate Euler number

External Email - Use Caution

Dear Freesurfer Developers,

It is not clear to me how to calculate the Euler number. Using mri_segstats 
reports something like:
Computing euler number
orig.nofix lheno =  -18, rheno = -20
orig.nofix lhholes =   10, rhholes = 11
However, I had understood from previous comments that the Euler number should 
be around 2. I'm wondering which of the above numbers I could report.

Thanks,
Colleen

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] how to calculate Euler number

[Fischl, Bruce]

I guess that makes sense

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of C.P.E. Rollins
Sent: Thursday, September 3, 2020 12:48 PM
To: Freesurfer 
Subject: Re: [Freesurfer] how to calculate Euler number

External Email - Use Caution

Thanks for the clarification Bruce. Would it make sense then to report
-18 ? As suggested by the Rosen 2018 paper in Neuroimage.

Thanks again,
Colleen

On 2020-09-03 17:16, C.P.E. Rollins wrote:
> Dear Freesurfer Developers,
> 
> It is not clear to me how to calculate the Euler number. Using 
> mri_segstats reports something like:
> Computing euler number
> orig.nofix lheno =  -18, rheno = -20
> orig.nofix lhholes =   10, rhholes = 11
> However, I had understood from previous comments that the Euler number 
> should be around 2. I'm wondering which of the above numbers I could 
> report.
> 
> Thanks,
> Colleen

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all error

[Fischl, Bruce]

Oh. Talairach is a human atlas - you won't be able to register a macaque to it

Sorry
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Friday, September 4, 2020 4:21 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all error

External Email - Use Caution

Yes , It is the macaque subject from Siemens 7T MRI


> -原始邮件-
> 发件人: "Fischl, Bruce" 
> 发送时间: 2020-09-04 00:18:53 (星期五)
> 收件人: "Freesurfer support list" 
> 抄送: 
> 主题: Re: [Freesurfer] recon-all error
> 
> Hi Jie,
> 
> Is this a scan of a non-human primate?
> 
> Cheers
> Bruce
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Jie Zhao
> Sent: Thursday, September 3, 2020 9:34 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] recon-all error
> 
> External Email - Use Caution
> 
> Hi, Bruce
> 
> I reorineted the views in freesurfer , But the result was wrong again . 
> Please check the figure attached, Is there any problem.
> 
> BTW, I got the Dicom file, it is .IMA format. How can I use it?
> 
> Thanks!
> Jie
> 
> 
> > -Original Messages-
> > From: "Fischl, Bruce"  Sent Time: 
> > 2020-08-30
> > 10:14:46 (Sunday)
> > To: "Freesurfer support list" 
> > Cc: 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > Hi Jie
> > 
> > The orientations are incorrect. What freeview thinks is anterior/posterior 
> > (labeled with "A" and "P") is actually inferior/superior. Do you have the 
> > dicoms from this dataset? If not, how was it converted? You need to orient 
> > it properly so it shows correctly in freeview before we will be able to 
> > process it.
> > 
> > Cheers
> > Bruce
> > 
> > -
> > 
> > -Original Message-
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  On Behalf Of Jie Zhao
> > Sent: Saturday, August 29, 2020 10:08 PM
> > To: Freesurfer support list 
> > Subject: Re: [Freesurfer] recon-all error
> > 
> > External Email - Use Caution
> > 
> > Here is the snapshot of my freeview window attached.
> > 
> > 
> > > -Original Messages-
> > > From: "Fischl, Bruce"  Sent Time: 
> > > 2020-08-30
> > > 02:07:50 (Sunday)
> > > To: "Freesurfer support list" 
> > > Cc: 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > Why do you want to change it? Can you post a snapshot from freeview so we 
> > > can make sure we are on the same page?
> > > 
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > >  On Behalf Of Jie Zhao
> > > Sent: Saturday, August 29, 2020 12:25 PM
> > > To: Freesurfer support list 
> > > Subject: Re: [Freesurfer] recon-all error
> > > 
> > > External Email - Use Caution
> > > 
> > > Hi Bruce
> > > 
> > > Thank you for quick answer。
> > > 
> > > I tryrd the freeview -v
> > > /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my freeview 
> > > orienatation is RAS. could you tell me how to change it from RAS 
> > > to (ASL)anterior/superior/left. Thanks
> > > 
> > > Best,
> > > Jie
> > > 
> > > 
> > > 
> > > > -原始邮件-
> > > > 发件人: "Fischl, Bruce" 
> > > > 发送时间: 2020-08-27 23:39:20 (星期四)
> > > > 收件人: "Freesurfer support list" 
> > > > 抄送: 
> > > > 主题: Re: [Freesurfer] recon-all error
> > > > 
> > > > Hi Jie
> > > > 
> > > > I would start by looking at your input volume in freeview, my 
> > > > orientation on freeview is RAS. Could you tell me
> > > > 
> > > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii
> > > > 
> > > > and make sure that the orientation it displays in is correct (that is, 
> > > > that what freeview thinks is anterior/superior/left are indeed those 
> > > > directions). Usually when we see this type of failure it is because the 
> > > > direction cosines in the input volume are incorrect (typically because 
> > > > the volume was at some point converted to analyze format). Not always, 
> > > > but usually.
> > > > 
> > > > Cheers
> > > > Bruce
> > &g

Re: [Freesurfer] errors in the parcellation

[Fischl, Bruce]

Hi Mariana

Can you send us some images with arrows or something so we can see what you 
mean?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mariana Vallejo Azar
Sent: Friday, September 4, 2020 6:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] errors in the parcellation


External Email - Use Caution
Dear
When I visualize the parcellation of some subjects, I see some errors using 
Destrieux 2009 atlas: S Front Middle parcel furrow floods most of the 
homonymous gyrus. Lat Fis Vert is not identified correctly, among others 
errors. Is there any way to edit the parcellation?
Best regards
Cheers

Mariana V.A (Argentina)
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

[Fischl, Bruce]

Hi Caspar

Can you elaborate? What are the issues?
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Caspar M. Schwiedrzik
Sent: Monday, September 7, 2020 2:27 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] MEMPRAGE vs. MP2RAGE


External Email - Use Caution
Hi!
I was wondering whether the issues with surface reconstruction from MP2RAGE 
data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still 
persist in more recent releases of Freesurfer, and whether there is information 
to what extent they apply to 3T data?
Thank you!
Caspar

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

[Fischl, Bruce]

Oh, sorry, yes I remember now. I guess mp2rage naturally sacrifices some 
SNR/unit time to get flatter images.  I think Doug (and Jon, now included) can 
comment on this

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Caspar M. Schwiedrzik
Sent: Monday, September 7, 2020 2:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] MEMPRAGE vs. MP2RAGE


External Email - Use Caution
Hi Bruce,
In that paper, you reported that MP2RAGE underestimates cortical thickness 
relative to MEMPRAGE and also has slightly lower reproducibility.
Since Recon-all does not seem to have built in functionality to deal with the 
background noise in MP2RAGE, I am wondering whether you still recommend 
MEMPRAGE over MP2RAGE. I only have regular MPRAGE for comparison at the moment. 
Thank you,
Caspar

On Mon, Sep 7, 2020 at 19:56 Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:













Hi Caspar



Can you elaborate? What are the issues?

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>

On Behalf Of Caspar M. Schwiedrzik


Sent: Monday, September 7, 2020 2:27 AM


To: Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>


Subject: [Freesurfer] MEMPRAGE vs. MP2RAGE




External Email - Use Caution



Hi!



I was wondering whether the issues with surface reconstruction from MP2RAGE 
data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still 
persist in more recent releases of Freesurfer, and whether there is information 
to what

extent they apply to 3T data?



Thank you!



Caspar












___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>

https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8&m=xQ8Cowc6OmPjU8ym3EVysBmtoEVDE6H47AkCObdzVy8&s=cUIYIUPYlPPYzq9yUoARG1sjLpuraBvjMrsd31fx1g8&e=
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Extending the pial surface

[Fischl, Bruce]

Hi Monica

We need a bit more detail to figure out why things are going wrong. Can you 
send screenshots or upload a subject? Is the white matter in that region 
already 110? Sometimes adding control points in the subjacent wm will bring 
intensities up enough to correct the pial. You can also change the intensity 
targets in mris_make_surfaces if the control points don’t help, using expert 
opts

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Monica Bondy
Sent: Wednesday, September 9, 2020 10:58 AM
To: Freesurfer support list 
Subject: [Freesurfer] Extending the pial surface


External Email - Use Caution
Hi Freesurfer Developers,

I was hoping to get some advice on fixing pial surface error so we can 
calculate cortical thickness. In several patients, although the aseg is fine, 
the red outline for the pial surface is missing parts of the cortex (not the 
subcortical areas, those are alright). Unfortunately, we cannot use control 
points to edit the pial surface because there is no white matter in those parts 
of the brain. Is it possible to manually extend the pial surface to include the 
excluded cortex?

Also, I looked through the archive and found a similar question and read that 
overriding the intensity statistics that mris_make_surfaces computes 
automatically may solve my issue. If this is possible could I have some advice 
on how to do this?

Otherwise, if you have any advice to fix this problem we would greatly 
appreciate it.

Thanks,
Monica
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] ERROR | License file for FS 7.1

[Fischl, Bruce]

Hi Otília
tkmedit has been deprecated for a long time. Can you try freeview instead?

Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Otília C. d'Almeida
Sent: Friday, September 11, 2020 8:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR | License file for FS 7.1


External Email - Use Caution

Hi,

I'm struggling to use tkmedit with FreeSurfer 7.1.

For example, trying: tkmedit SUBJECT brainmask.mgz -surfs

The error message I got is:

--

GNU libc version:2.19

ERROR: Systems running GNU glibc version greater than 2.15 require a newly 
formatted license file (it's free). Please download a new one from the 
following page: /registration.html

--

All the registration steps were performed, and a license.txt file was sent. 
This file was copied to $FREESURFER_HOME. The problem remains. Anyone had the 
same issue? How did you solve it?

Also, here https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall it is said 
that the license.txt file have 3 lines. The info sent have more since the 
e-mail is also included. What is the format of the license file?

Thank you!

with kind regards,

Otília




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] left-right flip?

[Fischl, Bruce]

And what is your input to recon-all? If it is dicom you should be pretty 
confident that we will get it correct

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, September 15, 2020 10:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?

How are you checking the LR orientation?

On 9/15/2020 4:10 AM, Ellen Ji wrote:
>  External Email - Use Caution
>
> Dear experts,
>
> I recently performed recon-all on a set of subjects and the output 
> (aparcstats2table and asegstats2table) will be part of a meta-analysis of 
> other labs' cohorts. When assessing the asymmetry index direction (relative 
> size of left vs right hemisphere across multiple rois), our dataset shows an 
> inversion of the mean asymmetry index in several structures compared to the 
> other cohorts.
>
> For example, in our dataset, the lateral ventricle volume is on 
> average larger in the right hemisphere compared to the left, while the 
> opposite is true for all other cohorts. The same inversion of asymmetry is 
> visible in other structures that in general are more asymmetrical.
>
> In order to check this, I went through each T1 to make sure the orientation 
> was correct and indeed they are.
>
> Is there any possible way that there was a left-right inversion somewhere 
> during the recon-all pipeline? I want to make sure I did everything correctly 
> on our end and that the results are due to the biology and not a technical 
> mistake!
>
> I found this website on Left-right reversal, and it seems relevant to 
> my issue, but I'm not fully understanding what this means (how would 
> bias occur during segmentation?) - 
> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>
> Many thanks for your input,
> Ellen
>
> ---
>
> Ellen Ji, PhD
> Postdoctoral Research Fellow
> Psychiatric University Hospital
> University of Zürich
> ellen...@bli.uzh.ch
> homanlab.github.io/ellen/
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] a question on Talairach transformation

[Fischl, Bruce]

Hi Yi LI

We compute the registration to MNI but don't apply it. So those images are in 
native coordinates.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Yi Li
Sent: Tuesday, September 15, 2020 1:08 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] a question on Talairach transformation


External Email - Use Caution
Hi,

I am a beginner of Freesurfer. I would be grateful if you could help me 
understand the excellent software.

I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of 
autorecon2. Are these the images registered to MNI305 template?

In other words, is my understanding correct that brainmask.mgz is the image 
after orig.mgz is linearly registered to MNI305 (plus normalization and 
skullstripping), while brain.mgz is the image after normalized image is 
nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and 
further normalization)?

Thank you so much for your help in advance.

Best regards
Yi Li

---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation

[Fischl, Bruce]

the em_reg command computes a linear transform to our internal atlas, which is 
loosely in MNI coords also, but not the official way we support reporting MNI

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Yi Li 
Sent: Tuesday, September 15, 2020 2:32 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation


External Email - Use Caution

Thanks for the suggested command.



I am curious whether the following command also generates the transformation 
matrix in a different format (.lta format)? What is the difference between 
mri_em_register and talairach_avi which generates talairach.xfm?



mri_em_register brainmask.mgz 
$FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta



-Yi

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Tuesday, September 15, 2020 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation



Try
mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz


On 9/15/2020 1:24 PM, Yi Li wrote:

External Email - Use Caution

Is there command in freesurfer that applies the linear transform (I suppose 
talairach.xfm) to brainmask.mgz to get the registered image?



Best,

Yi



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve
Sent: Tuesday, September 15, 2020 1:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation



No, it is in native individual space. We compute a linear transform but do not 
apply it

On 9/15/2020 1:07 PM, Yi Li wrote:

External Email - Use Caution

Hi,



I am a beginner of Freesurfer. I would be grateful if you could help me 
understand the excellent software.



I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of 
autorecon2. Are these the images registered to MNI305 template?



In other words, is my understanding correct that brainmask.mgz is the image 
after orig.mgz is linearly registered to MNI305 (plus normalization and 
skullstripping), while brain.mgz is the image after normalized image is 
nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and 
further normalization)?



Thank you so much for your help in advance.



Best regards

Yi Li



---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.


___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] left-right flip?

[Fischl, Bruce]

Hi Ellen

Sorry to say it, but you really should start over. Not everything in the brain 
is bilaterally symmetric so processing and flipping won't be the same as 
flipping then processing.

Cheers
Bruce


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ellen Ji
Sent: Wednesday, September 16, 2020 3:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?

External Email - Use Caution

Hi Douglas,

I found the dicoms and confirm that the fiducial is on the opposite side 
relative to the nifti. Additionally, the PI just informed me that the fiducial 
was placed on the right side of the head and the nifti indicates left. I will 
enquire as to what method was used to convert from dicom as that appears to be 
the issue.

I already performed recon-all and aparcstats2table on the flipped nifti. 
Could you please advise if there is there an efficient way to deal with this or 
if I should start from the beginning?

Many thanks,

Ellen


On 9/15/2020 7:19 PM, Douglas N. Greve wrote:
> First we have to determine whether it is really LR flipped or not. Do 
> you still have the dicoms? If so, can you convert to mgz using 
> mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see 
> if the fiducial has changed sides relative to the nifti.
> That is a fiducial. And do you know what side the fiducial was placed 
> on? mri_info does not help. How did you convert from dicom?
>
> ps. Please make sure to post to the list and not to us personally

>
>
> On 9/15/2020 12:58 PM, Ellen Ji wrote:
>>   External Email - Use Caution
>>
>> group cc'd - thanks for the reminder.
>>
>> My input data was the niftis. Example: recon-all -i 1kl5011.nii 
>> -subjid
>> 1kl5011 -all
>>
>> Is there an efficient way to handle the flipped L-R or should I 
>> mri_convert the nifti and then do recon-all?
>>
>> (Assuming that I can't just switch lh_ and rh_ in the 
>> aparcstats2table)
>>
>> Ellen
>>
>> On 9/15/2020 6:51 PM, Fischl, Bruce wrote:
>>> Hi Ellen
>>>
>>> Can you cc the list so that others can respond? What was your input data? 
>>> Did you not have dicoms?
>>>
>>> Cheers
>>> Bruce
>>>
>>> -Original Message-
>>> From: Ellen Ji 
>>> Sent: Tuesday, September 15, 2020 12:38 PM
>>> To: Fischl, Bruce 
>>> Subject: Re: [Freesurfer] left-right flip?
>>>
>>>External Email - Use Caution
>>>
>>> Hi Bruce,
>>>
>>> Unfortunately I just found the fiducial and realised that the L-R is 
>>> incorrect. Can I simply switch the lh_ and rh_ output from aparcstats2table 
>>> or do I need to run mri_convert on the nifti and run recon-all from the 
>>> beginning again?
>>>
>>> Thanks,
>>>
>>> Ellen
>>>
>>> On 9/15/2020 5:44 PM, Fischl, Bruce wrote:
>>>> And what is your input to recon-all? If it is dicom you should be 
>>>> pretty confident that we will get it correct
>>>>
>>>> -Original Message-
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>  On Behalf Of Douglas N. 
>>>> Greve
>>>> Sent: Tuesday, September 15, 2020 10:17 AM
>>>> To: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] left-right flip?
>>>>
>>>> How are you checking the LR orientation?
>>>>
>>>> On 9/15/2020 4:10 AM, Ellen Ji wrote:
>>>>>  External Email - Use Caution
>>>>>
>>>>> Dear experts,
>>>>>
>>>>> I recently performed recon-all on a set of subjects and the output 
>>>>> (aparcstats2table and asegstats2table) will be part of a meta-analysis of 
>>>>> other labs' cohorts. When assessing the asymmetry index direction 
>>>>> (relative size of left vs right hemisphere across multiple rois), our 
>>>>> dataset shows an inversion of the mean asymmetry index in several 
>>>>> structures compared to the other cohorts.
>>>>>
>>>>> For example, in our dataset, the lateral ventricle volume is on 
>>>>> average larger in the right hemisphere compared to the left, while the 
>>>>> opposite is true for all other cohorts. The same inversion of asymmetry 
>>>>> is visible in other structures that in general are more asymmetrical.
>>>>>
>>>>> In order to check this, I went through each T1 to make sure the 
>>

Re: [Freesurfer] left-right flip?

[Fischl, Bruce]

I think so, but I defer to Doug

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Ellen Ji
Sent: Wednesday, September 16, 2020 11:05 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] left-right flip?


External Email - Use Caution

Thanks for your reply Bruce. Could you confirm if I can run mri_convert on the 
incorrectly flipped niftis to appropriately correct them? 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal)

Something like:

mri_convert --in_orientation LIA subject1.nii subject1_corrected.nii

best,

Ellen


On 9/16/2020 4:47 PM, Fischl, Bruce wrote:

Hi Ellen



Sorry to say it, but you really should start over. Not everything in the brain 
is bilaterally symmetric so processing and flipping won't be the same as 
flipping then processing.



Cheers

Bruce





-Original Message-

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Ellen Ji

Sent: Wednesday, September 16, 2020 3:41 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] left-right flip?



External Email - Use Caution



Hi Douglas,



I found the dicoms and confirm that the fiducial is on the opposite side 
relative to the nifti. Additionally, the PI just informed me that the fiducial 
was placed on the right side of the head and the nifti indicates left. I will 
enquire as to what method was used to convert from dicom as that appears to be 
the issue.



I already performed recon-all and aparcstats2table on the flipped nifti.

Could you please advise if there is there an efficient way to deal with this or 
if I should start from the beginning?



Many thanks,



Ellen





On 9/15/2020 7:19 PM, Douglas N. Greve wrote:

First we have to determine whether it is really LR flipped or not. Do

you still have the dicoms? If so, can you convert to mgz using

mri_convert one-dicom-file.dcm test.mgz Then look at test.mgz and see

if the fiducial has changed sides relative to the nifti.

That is a fiducial. And do you know what side the fiducial was placed

on? mri_info does not help. How did you convert from dicom?



ps. Please make sure to post to the list and not to us personally







On 9/15/2020 12:58 PM, Ellen Ji wrote:

  External Email - Use Caution



group cc'd - thanks for the reminder.



My input data was the niftis. Example: recon-all -i 1kl5011.nii

-subjid

1kl5011 -all



Is there an efficient way to handle the flipped L-R or should I

mri_convert the nifti and then do recon-all?



(Assuming that I can't just switch lh_ and rh_ in the

aparcstats2table)



Ellen



On 9/15/2020 6:51 PM, Fischl, Bruce wrote:

Hi Ellen



Can you cc the list so that others can respond? What was your input data? Did 
you not have dicoms?



Cheers

Bruce



-Original Message-

From: Ellen Ji <mailto:ellen...@bli.uzh.ch>

Sent: Tuesday, September 15, 2020 12:38 PM

To: Fischl, Bruce <mailto:bfis...@mgh.harvard.edu>

Subject: Re: [Freesurfer] left-right flip?



   External Email - Use Caution



Hi Bruce,



Unfortunately I just found the fiducial and realised that the L-R is incorrect. 
Can I simply switch the lh_ and rh_ output from aparcstats2table or do I need 
to run mri_convert on the nifti and run recon-all from the beginning again?



Thanks,



Ellen



On 9/15/2020 5:44 PM, Fischl, Bruce wrote:

And what is your input to recon-all? If it is dicom you should be

pretty confident that we will get it correct



-Original Message-

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 On Behalf Of Douglas N.

Greve

Sent: Tuesday, September 15, 2020 10:17 AM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] left-right flip?



How are you checking the LR orientation?



On 9/15/2020 4:10 AM, Ellen Ji wrote:

 External Email - Use Caution



Dear experts,



I recently performed recon-all on a set of subjects and the output 
(aparcstats2table and asegstats2table) will be part of a meta-analysis of other 
labs' cohorts. When assessing the asymmetry index direction (relative size of 
left vs right hemisphere across multiple rois), our dataset shows an inversion 
of the mean asymmetry index in several structures compared to the other cohorts.



For example, in our dataset, the lateral ventricle volume is on

average larger in the right hemisphere compared to the left, while the opposite 
is true for all other cohorts. The same inversion of asymmetry is visible in 
other structures that in general are more asymmetrical.



In order to check this, I went through each T1 to make sure the orientation was 
correct and indeed they are.



Is there any possible way that there wa

Re: [Freesurfer] Prescan normalize and freesurfer

[Fischl, Bruce]

And more details about the study would also help. What field strength? Was the 
transmit coil a body coil? In the end though I’m not sure we are going to be 
able to give you an answer as it is an empirical question as to whether 
including them increases your variance more than it increases your power

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Glasser, Matthew
Sent: Thursday, September 17, 2020 8:14 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From:  on behalf of "Mikolas, Pavol" 

Reply-To: Freesurfer support list 
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’ dataset and account for the 12% without this 
option as a covariate
  2.  Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with 
this, so that we proceed in the best manner.

Thank you, best regards

Pavol




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Prescan normalize and freesurfer

[Fischl, Bruce]

I agree. The 8 channel coils can be trouble as they usually don’t have very 
good SNR at the vertex, so you are likely to see  a lot of variance in the 
results in those regions

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Glasser, Matthew
Sent: Thursday, September 17, 2020 9:44 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
That alone will be a huge factor in variable SNR (and receive field).  Head 
coils are not interchangeable like that.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Matt,

unfortunately we have no highres T2w or FLAIR.
In this multicentric study, we tended to use the 12 head coil. However, some 
centers used a 8 or a 32 head coil.

Thanks

Pavol


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 14:14
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’ dataset and account for the 12% without this 
option as a covariate
  2.  Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with 
this, so that we proceed in the best manner.

Thank you, best regards

Pavol




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Prescan normalize and freesurfer

[Fischl, Bruce]

I would guess it is pretty important for a 12 channel also, although it depends 
on field strength and also needs a body coil transmit to be maximally 
effective. In general we use it whenever we can

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Glasser, Matthew
Sent: Thursday, September 17, 2020 10:15 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
Maybe Bruce or Doug wants to comment but probably if you are using a 12CH coil 
it isn’t so important to have on.  It’s pretty much required for a 32CH coil, 
as the bias field is quite fast.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 9:02 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer



External Email - Use Caution
Dear Matthew,

thank you for this important point. I will check this. There might be just a 
few subjects with 8 and 32 head coil, so that it should be possible to discard 
them without affecting the sample size too much.

Do you think, you could give use some general hint to the ‘prescan normalize’ 
option? We cannot guess the benefit for our analysis well. Generally, if the 
benefit is rather low, we would tend to use the data without ‘prescan 
normalize’. What do you think?

Thank you, all best

Pavol


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 15:44
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
That alone will be a huge factor in variable SNR (and receive field).  Head 
coils are not interchangeable like that.

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:22 AM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Matt,

unfortunately we have no highres T2w or FLAIR.
In this multicentric study, we tended to use the 12 head coil. However, some 
centers used a 8 or a 32 head coil.

Thanks

Pavol


Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Glasser, Matthew
Gesendet: Donnerstag, 17. September 2020 14:14
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] Prescan normalize and freesurfer


External Email - Use Caution
What head coil did you use?  Do you have a highres T2w or FLAIR?

Matt.

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Mikolas, Pavol" 
mailto:pavol.miko...@uniklinikum-dresden.de>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 17, 2020 at 7:12 AM
To: "'freesurfer@nmr.mgh.harvard.edu'" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Prescan normalize and freesurfer

External Email - Use Caution
Dear Freesurfer Developers,

I am analyzing the T1 Data of a multicentric study (N=309, 6 Centers) using 
Freesurfer. I found out, that most of the scans were performed with the 
‘prescan normalize’ option. However, by approx..  12 % of participants, this 
option is missing. I also have complete data of all participants WITHOUT 
prescan normalize. In this analysis, we are interested in the correlation of GM 
volume in specific ROIs with clinical symptoms. Now we have two options:


  1.  Use the ‘prescan normalize’ dataset and account for the 12% without this 
option as a covariate
  2.  Use the complete dataset without ‘prescan normalize’

It would be very helpful, if you could share your arguments / experience with 
this, so that we proceed in the best manner.

Thank you, best regards

Pavol




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Prot

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

[Fischl, Bruce]

I don’t think adding 100 will work as once it scales everything down that far 
you only have a couple of bits of representation in the conformed ( 1 
byte/voxel) images. Maybe someone else can comment on fixing nu_correct?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Caspar M. Schwiedrzik
Sent: Friday, September 18, 2020 5:04 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output


External Email - Use Caution
Hi!
I am having some issue at the interface between mri_nu_correct.mni and 
mri_normalize, using v5.3.
Specifically, the output when applying mri_nu_correct to a T1 is quite dark, 
with white matter in the range of 15. Contrast is ok. When I apply 
mri_normalize to nu, it does not scale the data to white matter 110. This 
happens with and without a brain mask, and with various other parameter choices.
I am tempted to just add 100 to all voxels.
Any advice?
Thank you,
Caspar

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] papers that have reported results using FS5.2

[Fischl, Bruce]

The issue was that some code was inserted into the surface deformation 
algorithm that helped the Wash U HCP images, but made the surfaces quite 
inaccurate on many other acquisitions. Are there actually papers that used it? 
I think we found the issue within a couple of weeks and retracted the version. 
I would be pretty cautious about using it – make sure the surfaces were 
visually inspected.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas Greve
Sent: Friday, September 18, 2020 10:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] papers that have reported results using FS5.2

I can't remember what the issues where, but I don't think they were all that 
bad, something with surface placement. Bruce might remember better than me
On 9/15/20 7:22 PM, Paul wrote:

External Email - Use Caution
Dear Freesurfer Developers,

With Freesurfer 5.2 being listed as deprecated, are there any possible issues 
with papers that have reported results using FS5.2?

Thanks,
Paul




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: non-white matter hypointensity

[Fischl, Bruce]

Yes, they are typically in gray matter, although I’m not sure we see them very 
often (sometimes in the basal ganglia I think)


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of L
Sent: Friday, September 18, 2020 11:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: non-white matter hypointensity


External Email - Use Caution
Dear experts,

I am wondering what the non-white matter hypointensity refers to. Does it refer 
to hypointensity in subcortical regions or all brain regions except white 
matter? When we do data analysis using volume results from ROI tables, we found 
a greater volume of non-wm hypointensity in depressed subjects with- than 
without high vascular risk factors. However, I am not sure where the non-white 
matter hypointensity ROI covers, and it is possible to visually display the 
non-wm hypointensity regions in freeview?

Appreciate your guidance in advance.

Lihong

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Make BEM with corrected brainmask

[Fischl, Bruce]

Try:

mris_expand lh.brainmask.surf 3 inner_skull

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kadwani, Manorama
Sent: Friday, September 18, 2020 6:16 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Make BEM with corrected brainmask

I read that the option "-thickness" expands the surface by a fraction of its 
thickness.
https://miykael.github.io/nipype/interfaces/generated/interfaces.freesurfer/utils.html#mrisexpand

How to expand by distance in mm? I want to expand using distance. But when I 
use the option "-distance" I get an error that it was an unknown option.

If that's not possible I tried using thickness and got this output:
< $ mris_expand -thickness lh.brainmask.surf 3 inner_skull
using distance as a % of thickness
expanding surface lh.brainmask.surf by 300.0% of thickness and writing it to 
inner_skull
reading thickness...
MRISreadNewCurvature: incompatible vertex number in file ./lh.thickness
No such file or directory
mris_expand: could not load thickness file
No such file or directory >

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Friday, September 18, 2020 11:01 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Make BEM with corrected brainmask

Try mris_expand
On 9/16/20 10:24 PM, Kadwani, Manorama wrote:
Thank you, I got a brain surface using the mri_binarize function.
Is there a function for expanding the surface radially by a few millimeters? I 
want to create the inner skull surface as an expansion of the brain surface.

Thanks,
Manorama

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, September 9, 2020 6:25 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] Make BEM with corrected brainmask

I'm not sure, but you might be able to just create a surface from the brain 
mask with
mri_binarize --i brainmask.mgz --min 0.5 --surf brainmask.surf
You can smooth it a bit if you add --surf-smooth 2
where 2 is the number of iterations (more for smoother)
Try that
On 9/9/2020 6:01 PM, Kadwani, Manorama wrote:
Hi,

Why does the "mri_watershed" function create a new brainmask? Is there a way to 
create BEM surfaces from an existing or already corrected brainmask?

I had manually edited the brainmask during recon-all process. After the 
recon-all process completed, the pial surfaces looked good.
But when I ran 'make_watershed_bem', the BEM surfaces came out incorrect. The 
function 'mri_watershed' re-created a brainmask with the same errors that I had 
corrected earlier.

I saw there was a question on this topic already, but couldn't find answers: 
https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+mri_watershed%22&o=newest&f=1

Thanks,
Manorama



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

[Fischl, Bruce]

Hi Mason

mri_mask takes volumes as inputs, not label files. If you bring up your volumes 
and the mask looks in the right place in freeview then it should work

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Tuesday, September 22, 2020 8:50 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations 
{Disarmed}


External Email - Use Caution
Hi Doug,

I did try to use mri_mask but could not get it to work. I have the mask both in 
label format (attached), and as an overlay in nii.gz format. The commands below 
results in this error.

mri_mask lh_zstats_EPI_space_5mm_surface_smoothing.mgh 
Atlas/lh_atlas_dilated.label test.mgh
mri_read(): couldn't determine type of file Atlas/lh_atlas_dilated.label

When I try to use the nii.gz as the mask, activation outside of the mask 
remains (attached).

I would like to compute a correlation coeffeident between the atlas regions 
(1-25) and all the output ICA maps on the surface (0-~250).

Thanks for all your help.
Mason


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University 
webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau'r Golwg

& Canolfan Ymchwil Delweddu'r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Monday, September 21, 2020 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations


On 9/19/2020 10:31 AM, Mason Wells wrote:

External Email - Use Caution
Hi Experts,

I wonder if anyone can give me any advice on a couple of things.
1) I have some ICA spatial maps which I have resampled to the surface using 
bbregister and vol2surf. I can load this data in Freeview as a generic overlay 
(see attched). I also have a label file which is a combination of several 
visual areas. What I want to do is use this label as a mask and remove any 
activation from the ICA map overlay which falls outside of the label/mask. Is 
this possible using Freesurfer? In FSL I have been using fslmaths with -mas 
flag.
What form are your labels in? If they are just binary masks, then you can use 
mri_mask


2) My next question is whether it is possible to run spatial correlations on 
the surface. For example, I would like to know how well my ICA component maps 
match with some visual areas labels I have created in Freesurfer. In FSL i have 
been using fslcc to run these correlations between my ROIs and the spatial maps 
in the volume.
You want to compute a correlation coefficient? Or a dice score?


Thanks in advance,
Mason


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk

Tel: 02920 879628

Web: Cardiff University 
webpage

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau'r Golwg

& Canolfan Ymchwil Delweddu'r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk

Ffôn: 02920 879628




___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

MailScanner has detected a possible fraud attempt from 
"eur03.safelinks.protection.outlook.com" claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

[Fischl, Bruce]

Hi Mason

mri_mask runs in the volume, not the surface. Are these volumes? There is a 
masking function in freeview I think for surface overlays - maybe Ruopeng can 
comment?

Thanks
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mason Wells
Sent: Wednesday, September 23, 2020 10:50 AM
To: Freesurfer support list 
Cc: Greve, Douglas N.,Ph.D. 
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations 
{Disarmed}


External Email - Use Caution
Hi Bruce and Doug,

Thanks for the advice. I have the mask as a volume 
(atlas_dilated.label.nii.gz), which loads fine as a generic overlay on the 
inflated surface.
However, when I run this command

mri_mask lh_zstats_EPI_space_5mm_surface_smoothing.mgh 
Atlas/atlas_dilated.nii.gz masked_func.mgh

The output still has activation outside of the mask (see attached). Am I doing 
something wrong here?

Also, I wondered if yourself or Doug could help with my other question in my 
original email? Is there a Freesurfer equivalent of fslcc? I want to run 
spatial cross-correlations between a probabilistic atlas (Wang 15 atlas) and my 
functional data.

Cheers,
Mason


Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>

Tel: 02920 879628

Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau'r Golwg

& Canolfan Ymchwil Delweddu'r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>

Ffôn: 02920 879628


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Tuesday, September 22, 2020 5:50 PM
To: 'Freesurfer support list' 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations 
{Disarmed}


Hi Mason



mri_mask takes volumes as inputs, not label files. If you bring up your volumes 
and the mask looks in the right place in freeview then it should work



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Mason Wells
Sent: Tuesday, September 22, 2020 8:50 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations 
{Disarmed}



External Email - Use Caution

Hi Doug,



I did try to use mri_mask but could not get it to work. I have the mask both in 
label format (attached), and as an overlay in nii.gz format. The commands below 
results in this error.



mri_mask lh_zstats_EPI_space_5mm_surface_smoothing.mgh 
Atlas/lh_atlas_dilated.label test.mgh

mri_read(): couldn't determine type of file Atlas/lh_atlas_dilated.label



When I try to use the nii.gz as the mask, activation outside of the mask 
remains (attached).



I would like to compute a correlation coeffeident between the atlas regions 
(1-25) and all the output ICA maps on the surface (0-~250).



Thanks for all your help.

Mason



Mason T Wells, MSc

PhD student

School of Optometry and Vision Sciences

& Cardiff University Brain Research

Imaging Centre (CUBRIC), School of Psychology

Cardiff University

Cardiff

CF24 4HQ

UK



Email: wells...@cardiff.ac.uk<mailto:wells...@cardiff.ac.uk>

Tel: 02920 879628

Web: Cardiff University 
webpage<https://www.cardiff.ac.uk/people/research-students/view/974214->

Mason T Wells, MSc

Myfyriwr PhD

Yr Ysgol Optometreg a Gwyddorau'r Golwg

& Canolfan Ymchwil Delweddu'r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol 
Seicoleg

Prifysgol Caerdydd

Heol Maindy

Caerdydd

CF24 4HQ

DU



E-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk>

Ffôn: 02920 879628





From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>>
Sent: Monday, September 21, 2020 3:34 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Masking surface overlays and spatial correlations





On 9/19/2020 10:31 AM, Mason Wells wrote:

External Email - Use Caution

Hi Experts,



I wonder if anyone can give me a

Re: [Freesurfer] parameterization template and the vertex correspondence in the pial surface

[Fischl, Bruce]

Hi Pam,


  1.  The variance downweights features that are variable across subject, and 
let’s the registration depend on more stable features like 
central/calcarine/sylvian in a smooth manner.
  2.  The surfaces for a given hemisphere all have the same topology (# of 
vertices,edges,faces) and vertex index is preserved, so it is trivial to look 
up the “same” vertex on the different surfaces.

Make sense?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Pam Garcia
Sent: Thursday, September 24, 2020 1:03 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] parameterization template and the vertex correspondence 
in the pial surface


External Email - Use Caution
Hi FreeSufer team.

I have some questions related to the parameterization template and the vertex 
correspondence in the pial surface.


1. In the parameterization template what is the reason for using the mean 
and variance of curvature for WM surface using the inflated and smoothed 
surface? What independent information do these measures supply?

2. Related to the vertex correspondence. How is the spherical surface 
mapped to the pial surface to achieve vertex correspondence between the WM and 
pial surfaces?

Thanks a lot for the responses

best
Pam
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] parameterization template and the vertex in the pial surface

[Fischl, Bruce]

Hi Pam

Yes, that’s pretty accurate.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Pam Garcia
Sent: Thursday, September 24, 2020 9:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] parameterization template and the vertex in the pial 
surface


External Email - Use Caution
Thanks for your response Bruce, just to clarify

If I understood, the wm surface is created using a surface deformation 
procedure that adaptively determined the MR intensity of the boundaries in 
question at each point in the cortex. Next a sphere from the wm inflated 
surface is computed, warps the sphere into a 2-D file containing the curvature 
and convexity patterns of the subject, and then registers the 2D file with a 
reference (parameterization template). This is executed to ensure that the 
curvature and convexity patterns are aligned with a generic reference template. 
The mean and the variance of curvature and convexity from the smooth and 
inflated surface are used in order to do more robust the register. Finally, the 
pial surface is created by expanding the white matter surface so that it 
closely follows the gray-CSF intensity gradient, keeping the same topology 
(number of vertex, edges, faces) and the vertex index is preserved. Finally, 
the vertex of the wm and pial surface are mapped in a common space and is here 
where we obtained vertex correspondence across the subjects.
Thanks
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] parameterization template and the vertex in the pial surface

[Fischl, Bruce]

Yes, that’s true. We compute the vertex correspondence across subjects, but 
don’t remap the surfaces as we like to keep uniform sampling in the subject 
space where we can

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, September 25, 2020 9:58 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] parameterization template and the vertex in the pial 
surface

You are right except for the last step. The surfaces are not retessellated to a 
common space. When it comes time for group analysis, overlays (eg, thickness) 
are sampled into the group space (not the surfaces themselves)
On 9/24/2020 9:40 PM, Pam Garcia wrote:

External Email - Use Caution
Thanks for your response Bruce, just to clarify

If I understood, the wm surface is created using a surface deformation 
procedure that adaptively determined the MR intensity of the boundaries in 
question at each point in the cortex. Next a sphere from the wm inflated 
surface is computed, warps the sphere into a 2-D file containing the curvature 
and convexity patterns of the subject, and then registers the 2D file with a 
reference (parameterization template). This is executed to ensure that the 
curvature and convexity patterns are aligned with a generic reference template. 
The mean and the variance of curvature and convexity from the smooth and 
inflated surface are used in order to do more robust the register. Finally, the 
pial surface is created by expanding the white matter surface so that it 
closely follows the gray-CSF intensity gradient, keeping the same topology 
(number of vertex, edges, faces) and the vertex index is preserved. Finally, 
the vertex of the wm and pial surface are mapped in a common space and is here 
where we obtained vertex correspondence across the subjects.
Thanks



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_extract issue

[Fischl, Bruce]

Hi Jie

Can you clarify what you mean by “head info. Disappeared in a sagittal slice”? 
Do you mean the head was cropped? If so, that probably just means you have to 
adjust the fov that you are cropping if you can.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Saturday, September 26, 2020 7:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_extract issue


External Email - Use Caution

Hi, Freesurfer Team



  My input volume dimension is 248*176*320, so I use mri_extract scale to 
256*256*256. However, the output volume lose some info. eg.some head info. 
disappeared in sagiital slice. How can scale my input voluem to 256*256*256, 
and also do not lose info.Thanks in advance!



All best,

Jie


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_extract issue

[Fischl, Bruce]

Hi Jie

Try using mri_extract.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Jie Zhao
Sent: Saturday, September 26, 2020 9:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_extract issue


External Email - Use Caution

Hi, Bruce



Yes, the head was cropped.How can I adjust the FOV?

My command line is: mri_convert -i orig.mgz -o origfinal.mgz --crop 160 160 160 
--conform –nc



Thanks!

Jie



-原始邮件-
发件人:"Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>>
发送时间:2020-09-26 23:31:33 (星期六)
收件人: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
抄送:
主题: Re: [Freesurfer] mri_extract issue
Hi Jie

Can you clarify what you mean by “head info. Disappeared in a sagittal slice”? 
Do you mean the head was cropped? If so, that probably just means you have to 
adjust the fov that you are cropping if you can.

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jie Zhao
Sent: Saturday, September 26, 2020 7:26 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_extract issue


External Email - Use Caution

Hi, Freesurfer Team



  My input volume dimension is 248*176*320, so I use mri_extract scale to 
256*256*256. However, the output volume lose some info. eg.some head info. 
disappeared in sagiital slice. How can scale my input voluem to 256*256*256, 
and also do not lose info.Thanks in advance!



All best,

Jie


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] postdoc opening with Thomas Yeo

[Fischl, Bruce]

Thomas Yeo is looking for a postdoc with a PhD in neuroscience, psychology or 
related field. Start date is any time in 2021. Topics are quite flexible. More 
details can be found here: https://sites.google.com/view/yeolab/jobs

Contact Thomas if you are interested.

Cheers
Bruce

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] License Management

[Fischl, Bruce]

Hi Paul

we don't really do much enforcement of the licenses, but it is important to our 
ability to get the resources to continue to maintain FreeSurfer that our 
license count reflects the size of our user base. So it would be great if you 
could request the number of licenses that accounts for your approximate number 
of users
cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pawletta, Paul 

Sent: Sunday, October 11, 2020 8:49 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] License Management


External Email - Use Caution

Hi,



we want to use Freesurfer in our “Virtual Research Environment”, where many 
users can process their neuroimaging data with prebuilt pipelines. Our question 
is about the license management for each user.

Would it be sufficient to obtain a general license that can be used by all 
users? - Similar to a central installation of Freesurfer.



Thank you,

Paul
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Regarding sMRI scans alignment

[Fischl, Bruce]

Hi Rahul

can you explain a bit more what you want? Is this the same subject imaged 
multiple times? Is it with the same sequence?

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Rahul Sharma 

Sent: Saturday, October 10, 2020 3:16 AM
To: Freesurfer support list 
Subject: [Freesurfer] Regarding sMRI scans alignment


External Email - Use Caution

Dear all,
Hope you all are in good health, I want to ask that how I can reslice the two 
different MRI scans so that when I extract the sagittal slices it all look 
same, can you help me out



Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
9827834360

"Manners Maketh Man"


On Sun, Oct 4, 2020 at 9:51 PM Didenur Sahin 
mailto:sahindide...@gmail.com>> wrote:

External Email - Use Caution

Dear All,

Brain Development And Psychosis Lab, is pleased to announce the opening of a 
postdoctoral fellowship position in clinical neuroscience and cognitive 
neuroimaging.  Please take a look at the attached advertisement.

Best,

Didenur Sahin

--
Didenur Şahin
Ph.D. Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM)

Bilkent University

Ankara, Turkey 06800

--
Didenur Şahin
Ph.D. Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM)

Bilkent University

Ankara, Turkey 06800

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Regarding sMRI scans alignment

[Fischl, Bruce]

Hi Rahul

That may just be an inevitable part of cross-subject anatomical variability. 
You could try explicitly registering them, or transform them all into Talairach 
coordinates which should help reduce the variability (e.g. mri_convert -at 
$SUBJECTS_DIR/$subject/mri/transforms/talairach.xm  

Cheers
Bruce

From: Rahul Sharma 
Sent: Sunday, October 11, 2020 3:59 PM
To: Freesurfer support list ; Fischl, Bruce 

Subject: Re: [Freesurfer] Regarding sMRI scans alignment


External Email - Use Caution
Dataset is taken from ADNI for Alzheimer's Disease Diagnosis.
Subjects are different. We want to extract slice between an exact range for all 
scans but when we are extracting we are facing issue, for ex. I want 80th slice 
in sagittal view to be extracted but for some images they are similar but for 
most of the images the extracted slice is different.


Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
9827834360

"Manners Maketh Man"


On Sun, Oct 11, 2020 at 8:46 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Rahul

can you explain a bit more what you want? Is this the same subject imaged 
multiple times? Is it with the same sequence?

cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Rahul Sharma 
mailto:sharmarahul.26...@gmail.com>>
Sent: Saturday, October 10, 2020 3:16 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Regarding sMRI scans alignment


External Email - Use Caution
Dear all,
Hope you all are in good health, I want to ask that how I can reslice the two 
different MRI scans so that when I extract the sagittal slices it all look 
same, can you help me out



Regards:
Rahul Sharma
Research Scholar
NIT Silchar
Assam
9827834360

"Manners Maketh Man"


On Sun, Oct 4, 2020 at 9:51 PM Didenur Sahin 
mailto:sahindide...@gmail.com>> wrote:

External Email - Use Caution
Dear All,

Brain Development And Psychosis Lab, is pleased to announce the opening of a 
postdoctoral fellowship position in clinical neuroscience and cognitive 
neuroimaging.  Please take a look at the attached advertisement.

Best,

Didenur Sahin
--
Didenur Şahin
Ph.D. Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM)

Bilkent University
Ankara, Turkey 06800

--
Didenur Şahin
Ph.D. Candidate
Neuroscience Graduate Program
National Magnetic Resonance Research Center (UMRAM)

Bilkent University
Ankara, Turkey 06800

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fixing error with pial surface

[Fischl, Bruce]

Hi Julie

It’s hard to tell from the single slice. Is there white matter in the wm.mgz 
that doesn’t have surface (?h.white) covering it? That would indicate a 
topological defect.

If you upload the entire gzipped and tarred subject’s directory we will take a 
look

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julie Ottoy
Sent: Sunday, October 11, 2020 3:51 PM
To: Freesurfer support list 
Subject: [Freesurfer] Fixing error with pial surface


External Email - Use Caution
Dear Freesurfer team,

I have a question related to fixing the pial surface when a part was missed 
(see attachment). On the freesurfer website, I only found how to erase the pial 
when there was too much (see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0 ), but I 
could not find what to do when there was too little.
As there is no white matter in this particular area, it is also not an option 
to place control points. Also the skull stripping did not change anything: I 
tried both the freesurfer skull stripping and an in-house skull stripping 
algorithm.

Thank you for your help.
Best regards
Julie


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fixing error with pial surface

[Fischl, Bruce]

Hi Julie

It’s really hard to diagnose this way. Are you able to upload the subject? If 
so, please send us the coordinates of the region where you think things are 
going wrong

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julie Ottoy
Sent: Monday, October 12, 2020 3:42 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Fixing error with pial surface


External Email - Use Caution
Hi Bruce,

Thanks for your answer. I have checked the wm.mgz but it does not seem to be a 
topological error I think.
I have added coronal, axial, and sag views in attachment (see the red cursor). 
Also I have added the first (coronal) slice that starts to show white matter 
(couple slices later).

Let me know if you still would like me to upload the data.

Best
Julie

On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Julie

It’s hard to tell from the single slice. Is there white matter in the wm.mgz 
that doesn’t have surface (?h.white) covering it? That would indicate a 
topological defect.

If you upload the entire gzipped and tarred subject’s directory we will take a 
look

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julie Ottoy
Sent: Sunday, October 11, 2020 3:51 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Fixing error with pial surface


External Email - Use Caution
Dear Freesurfer team,

I have a question related to fixing the pial surface when a part was missed 
(see attachment). On the freesurfer website, I only found how to erase the pial 
when there was too much (see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0 ), but I 
could not find what to do when there was too little.
As there is no white matter in this particular area, it is also not an option 
to place control points. Also the skull stripping did not change anything: I 
tried both the freesurfer skull stripping and an in-house skull stripping 
algorithm.

Thank you for your help.
Best regards
Julie


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Error during skullstripping: numerical result out of range

[Fischl, Bruce]

Hi Julia

Can you check the output of the skull stripping and see if it failed?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Hye Min Shin
Sent: Tuesday, October 20, 2020 1:13 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error during skullstripping: numerical result out of range


External Email - Use Caution
Hi experts,

While running recon-all on subjects with 3T T1 scans, I ran into an error with 
one subject during skullstripping stage. Recon-all was running with 3T flag.

The error message is the following:

register_mri: find_optimal_transform
find_optimal_transform: nsamples 3243, passno 0, spacing 8
GCAhistoScaleImageIntensities: could not find wm peak
resetting wm mean[0]: 100 --> 108
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=10.0
skull bounding box = (46, 56, 29) --> (216, 255, 255)
using (103, 122, 142) as brain centroid...
mean wm in atlas = 108, using box (82,97,114) --> (123, 146,169) to find MRI wm
before smoothing, mri peak at 73
robust fit to distribution - 72 +- 7.4
distribution too broad for accurate scaling - disabling
WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=100, mri_peak=108
after smoothing, mri peak at 0, scaling input intensities by inf
Numerical result out of range

I tried the following suggestion in 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12605.html but 
to no avail.

It's just strange because only one subject has this issue and the subject's 
scan looks fine- no part of the brain seems cutoff.

Any suggestions would be helpful.
Best,
Julia Shin
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Error running mris_ca_label

[Fischl, Bruce]

You are missing a switch before the ../label/lh.cortex.label parameter (-l I 
think? Read the help). That makes all the positional parameters apparently in 
the wrong place

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rollo, Patrick
Sent: Tuesday, October 20, 2020 11:06 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error running mris_ca_label


External Email - Use Caution

Experts,

My group runs an older version of Freesurfer so that when we run recon-all, it 
creates the 2005 FS atlas. I've installed the current version of FS on a new 
machine and I'm trying to go back and create DKT atlases for each of our 
previous patients. I use the following code, hoping to generate an .annot file 
but get the following output:


mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh 
../surf/lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs 
../label/lh/aparc.DKTatlas.annot

GCSAread(../surf/lh.sphere.reg): file magic #fe63 != GCSA_MAGIC (ababcdcd)
mris_ca_label: could not read classifier from ../surf/lh.sphere.reg


if I run it without the file path for the lh.sphere.reg file I get the 
following:

mris_ca_label ../label/lh.cortex.label -aseg aseg.presurf.mgz < subjid > lh 
lh.sphere.reg /Applications/freesurfer/average/lh.DKTatlas40.gcs 
../label/lh/aparc.DKTatlas.annot

GCSAread(lh.sphere.reg): could not open file

No such file or directory

mris_ca_label: could not read classifier from lh.sphere.reg

No such file or directory

Thank you for your help!






___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] please help me

[Fischl, Bruce]

Hi Saman

Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me


External Email - Use Caution
hi

I want to process MRI images to extract Morphology features.

I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).


Next I do not know what to do to extract morphological features?

My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?

Thank you


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] please help me

[Fischl, Bruce]

Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:


recon-all -i  -s  -sdir  -all

cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me


External Email - Use Caution
hi

Thank you for your response

I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.

According to what I said, what should I do?

If I have to use recon-all with what code can I do this? And what is the use of 
nifty?

On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:



Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] please help me



External Email - Use Caution

hi



I want to process MRI images to extract Morphology features.



I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).



Next I do not know what to do to extract morphological features?



My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?



Thank you




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

[Fischl, Bruce]

Where did you get the ct from?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of 1248742467
Sent: Thursday, October 22, 2020 7:25 AM
To: freesurfer 
Subject: [Freesurfer] The non-existent field'numEntries' is 
referenced.(write_annotation.m)


External Email - Use Caution

hello, fs

when i use the write_annotation.m, the error message occurs:
`The non-existent field'numEntries' is referenced.

Error write_annotation (line 62)
count = fwrite(fp, int32(ct.numEntries),'int');

Error test_1 (line 13)
write_annotation('rh.aparc.a2009s.annot', c, b, ct)`
How to solve the non-existent field'numEntries' is referenced？By the way, can 
ct change automatically according to the value of label?




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] please help me

[Fischl, Bruce]

You need a -s before the “subj1”

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 2:44 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me


External Email - Use Caution
hi

my code is:

recon-all -i /home/MRI/Training/99060003/T1-image/39501.dcm  subj1 -sdir  
/home/MRI4 -all

ERROR: Flag subj1 unrecognized.
-i /home/nbml-challenge/Training/99060003/T1-image/39501.dcm subj1 -sdir 
/home/team33/MRI4 -all

what is ??


On Thursday, October 22, 2020, 5:40:05 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:


hi Bruce

thank you very very much

On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:



Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:





recon-all -i  -s  -sdir  -all



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Thank you for your response



I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.



According to what I said, what should I do?



If I have to use recon-all with what code can I do this? And what is the use of 
nifty?



On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] please help me



External Email - Use Caution

hi



I want to process MRI images to extract Morphology features.



I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).



Next I do not know what to do to extract morphological features?



My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?



Thank you





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] please help me

[Fischl, Bruce]

It depends on your hardware. On a modern multi-core CPU you can get it down to 
3-4 hours I believe, and I think the final message is something like “recon-all 
finished in…”

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 4:12 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me


External Email - Use Caution
hi

How long does it take to execute a recon-all command?

and what message indicates that it finished?

Is there a way to speed it up?


thank you
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

[Fischl, Bruce]

Sorry, that is not a question for us but rather for your local sys admin

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 6:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] (no subject)


External Email - Use Caution
hi

I was running several  putty windows for recond-all MRI pictures.


Some putty were inactived during running.


How can I activate them?








___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] please help me

[Fischl, Bruce]

Hi Saman

That’s really a scientific question and up to you!
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 7:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me


External Email - Use Caution
hi

Which output can I use to predict age after recon-all?

On Friday, October 23, 2020, 11:46:09 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:


yes and replacing -sdir with -sd

thank you very much
On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:



You need a -s before the “subj1”



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 2:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



my code is:



recon-all -i /home/MRI/Training/99060003/T1-image/39501.dcm  subj1 -sdir  
/home/MRI4 -all



ERROR: Flag subj1 unrecognized.
-i /home/nbml-challenge/Training/99060003/T1-image/39501.dcm subj1 -sdir 
/home/team33/MRI4 -all



what is ??





On Thursday, October 22, 2020, 5:40:05 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





hi Bruce



thank you very very much



On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:





recon-all -i  -s  -sdir  -all



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Thank you for your response



I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.



According to what I said, what should I do?



If I have to use recon-all with what code can I do this? And what is the use of 
nifty?



On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] please help me



External Email - Use Caution

hi



I want to process MRI images to extract Morphology features.



I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).



Next I do not know what to do to extract morphological features?



My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?



Thank you





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] please help me

[Fischl, Bruce]

Not sure, cortical thickness maybe?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 11:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me


External Email - Use Caution
thank Bruce

I read several articles and got a little confused.

Can you help me a little if you have any information?

On Saturday, October 24, 2020, 6:04:07 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:



Hi Saman



That’s really a scientific question and up to you!
Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Saturday, October 24, 2020 7:17 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Which output can I use to predict age after recon-all?



On Friday, October 23, 2020, 11:46:09 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





yes and replacing -sdir with -sd



thank you very much

On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





You need a -s before the “subj1”



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Friday, October 23, 2020 2:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



my code is:



recon-all -i /home/MRI/Training/99060003/T1-image/39501.dcm  subj1 -sdir  
/home/MRI4 -all



ERROR: Flag subj1 unrecognized.
-i /home/nbml-challenge/Training/99060003/T1-image/39501.dcm subj1 -sdir 
/home/team33/MRI4 -all



what is ??





On Thursday, October 22, 2020, 5:40:05 PM GMT+3:30, saman fouladi 
mailto:smnfoul...@yahoo.com>> wrote:





hi Bruce



thank you very very much



On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:





recon-all -i  -s  -sdir  -all



cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] please help me



External Email - Use Caution

hi



Thank you for your response



I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.



According to what I said, what should I do?



If I have to use recon-all with what code can I do this? And what is the use of 
nifty?



On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:





Hi Saman



Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] please help me



External Email - Use Caution

hi



I want to process MRI images to extract Morphology features.



I convert my dcm file to nii format by mri-convert command and then  I used FSL 
software and BET(Best extraction Tool).



Next I do not know what to do to extract morphological features?



My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?



Thank you





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer

Re: [Freesurfer] Problem with pial and white matter segmentation

[Fischl, Bruce]

Hard to say for sure, but I would guess you have an incorrectly fixed 
topological defect in that region.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Edoardo Pinzuti
Sent: Wednesday, October 28, 2020 7:02 AM
To: Freesurfer support list 
Subject: [Freesurfer] Problem with pial and white matter segmentation


External Email - Use Caution
Dear Freesurfer team,

I am having trouble with the pial and white matter segmentation of one subject 
(you can see the picture attached), I tried to set control points but it did 
not work completely. The segmentation looks not good  at all for some slices, 
do you know what I could do ?

Thanks

Edoardo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

[Fischl, Bruce]

The segmentation nets typically output one-hot encoded values. So if you have 
30 labels, the output layer has 30 outputs, which can be loosely interpreted as 
p-values for each label (they will add to 1). To turn it into a segmentation 
you take the argmax over the 30-label dimension and toss the underlying 
probabilities

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, October 30, 2020 11:39 AM
To: 李梦君 ; Freesurfer support list 

Subject: Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned 
into No Statistic Difference after Mapping onto the Subjects

sorry, I don't understand your question. can you elaborate?
On 10/28/2020 11:57 PM, 李梦君 wrote:

External Email - Use Caution
Thanks for your help! I finished the -qcache for every subject before group 
analysis with Qdec/mri_label2label. I want to do the correlation analysis 
between the significant cortex area and the behavior score. Should I compare 
the group analysis without the -qcache before Qdec/mri_label2label?



-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-10-28 05:08:03 (星期三)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into 
No Statistic Difference after Mapping onto the Subjects


When you run your original analysis, you probably smoothed the map before doing 
the group analysis. This smoothing would not be in your ROI analysis, and the 
difference could be pretty big if the label is small. Also, the area map will 
have a jacobian correction that will not be in the raw data.
On 10/19/2020 11:29 PM, 李梦君 wrote:

External Email - Use Caution
Dear FreeSurfer Developers:

   I compared the thickness, area, volume in the mild traumatic brain injury 
patients with health control by FreeSurFer, and found a statistic difference 
region in the cortex area, I defined the statistic difference region as a label 
on the fsaverage and mapped this label to subjects by Qdec/mri_label2label. The 
label defined on the fsaverage was mapped onto all subjects successfully, and 
the label in subjects matched well with the inflated cortex of subjects in 
Freeview  Then the area value of the label in every single subjects was 
extracted, and I found that there is no statistic difference in the area value 
between the mild traumatic brain injury patients and health control. I have 
checked the segmentation of every subjects and it was a good job done by 
FreeSurFer.

FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.

Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University



___

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

[Fischl, Bruce]

Hmmm, did you log in as anonymous? I’ll cc Rob who should be able to help

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julie Ottoy
Sent: Tuesday, November 3, 2020 11:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Fixing error with pial surface {Disarmed}


External Email - Use Caution
Hi Bruce

Thank you!
Meanwhile, I tried to upload the subject on the server but I always get the 
following error:

230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> cd transfer/incoming
250 Directory successfully changed.
ftp> put subject_FS_upload.zip
local: subject_FS_upload.zip remote: subject_FS_upload.zip
421 Service not available, remote server has closed connection

Could you help me out with this?
Thanks
Julie

On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Julie

It’s really hard to diagnose this way. Are you able to upload the subject? If 
so, please send us the coordinates of the region where you think things are 
going wrong

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julie Ottoy
Sent: Monday, October 12, 2020 3:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Fixing error with pial surface


External Email - Use Caution
Hi Bruce,

Thanks for your answer. I have checked the wm.mgz but it does not seem to be a 
topological error I think.
I have added coronal, axial, and sag views in attachment (see the red cursor). 
Also I have added the first (coronal) slice that starts to show white matter 
(couple slices later).

Let me know if you still would like me to upload the data.

Best
Julie

On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Julie

It’s hard to tell from the single slice. Is there white matter in the wm.mgz 
that doesn’t have surface (?h.white) covering it? That would indicate a 
topological defect.

If you upload the entire gzipped and tarred subject’s directory we will take a 
look

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julie Ottoy
Sent: Sunday, October 11, 2020 3:51 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Fixing error with pial surface


External Email - Use Caution
Dear Freesurfer team,

I have a question related to fixing the pial surface when a part was missed 
(see attachment). On the freesurfer website, I only found how to erase the pial 
when there was too much (see MailScanner has detected a possible fraud attempt 
from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEditsV6.0<https://secure-web.cisco.com/1gpx46tpa8CTIUNay0UrrJ-gxsIj8Mag4YGO8J8nyhFBk_vUGzoIRj4Mcbd6QhCbXxxACP5NekTgpkwy1i_7hReP5AFQqNeKWbPlOKFgTdD71o6FOQEC25-2mLI9VIZ3DCCUILUIjSEHeA8PQm-jSQuf2Q35SRlvA0gE74LLqJnkql0Rs2lM9RWexhSh3jGixx7QPZFpX0y4nDvIsDFmhtQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FPialEditsV6.0>
 ), but I could not find what to do when there was too little.
As there is no white matter in this particular area, it is also not an option 
to place control points. Also the skull stripping did not change anything: I 
tried both the freesurfer skull stripping and an in-house skull stripping 
algorithm.

Thank you for your help.
Best regards
Julie


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1aSysztaOg72LTSrHZ8IMlAHyx36lqzh_mhacRbfU85DOTLuITwz3kWnasOayZnNZpzHZSWb5yin6dOCPVg41bA3XaEhUSmu2qLzGmwvcmvNrteWu-9Bq02pR9SPHPFq5coAaCcaqLAJPYFbqOglbTzBLSd3Jj0DTqAj7WlndHsL0y2Oth1Io1uSTzIyh1lgScLGMaZlhF10kZeZegItM5w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_

Re: [Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

[Fischl, Bruce]

Hi Lee

It's really hard to say. The change in voxel size might sound trivial, but it 
is a 30% change in volume (and hence SNR). The longer TE will counteract that 
by increasing T2* weighting.
Sorry I don't have anything more conclusive to say except that it is obviously 
not ideal
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Backhausen, Lea
Sent: Thursday, November 5, 2020 12:13 PM
To: 'freesurfer@nmr.mgh.harvard.edu' 
Subject: [Freesurfer] Different Sequences Longitudinal Stream {Disarmed}


External Email - Use Caution
Dear FreeSurfer experts,

I am currently working on a longitudinal data set with 4 time points, acquired 
at one site with the same Siemens Trio 3T scanner.
Unfourtunately, the T1 sequence differs slightly for one of these time points. 
These sequences have been measured:


  1.  repetition time (TR) = 2300 ms, echo time (TE) = 2.93 ms, inversion time 
(TI) = 900 ms, voxel size = 1.1 x 1.1 x 1.1mm, flip angle = 9°; matrix size = 
256 x 256 x 160 mm
  2.  repetition time (TR) = 1900 ms, echo time (TE) = 2.26 ms, inversion time 
(TI) = 900 ms, voxel size = 1.0 x 1.0 x 1.0mm, flip angle = 9°; matrix size = 
256 x 256 x 176 mm

Is it possible to process these different sequences in the longitudinal stream 
(if e.g. one participant would have 3 data sets of sequence 1 and one data set 
of sequence 2)?
Or would this cause too much bias?

Thank you very much, kind regards!
Lea Backhausen



--
Lea Backhausen
Ph.D. Student (M.Sc. Psychology/Neuroscience)
Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU 
Dresden, Germany
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.uniklinikum-dresden.de

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Recon1 command

[Fischl, Bruce]

HI Kelli

It sounds like you started running at some point but didn't get very far? Try 
something like:

mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234
recon-all -subjid 1234 -i 1234.nii -autorecon1

and see if that works (then you can probably delete the saved.1234 dir if you 
want)
cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Kelli Ann Nini
Sent: Saturday, November 7, 2020 5:28 PM
To: Freesurfer support list 
Subject: [Freesurfer] Recon1 command


External Email - Use Caution
Greetings, esteemed Surfers! I have a .nii file that I am trying to run through 
recon1 and I'm not sure I have my commands correct. At first I typed this 
command line and received this error: recon-all -subjid 1234 -i 1234.nii 
-autorecon1
ERROR: You are trying to re-run an existing subject with (possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then
 omit all -i flags.

However, if I omit the -i flag, I receive this message: recon-all -subjid 1234 
-autorecon1
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /home/scanlab1/Desktop/FSTraining_2020
Actual FREESURFER_HOME /usr/local/freesurfer
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 
17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' -> 
'/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.local-copy'
#
#@# MotionCor Tue Nov  3 17:46:26 CST 2020
ERROR: no run data found in /home/blah/blah/blah/1234/mri. Make sure to
have a volume called 001.mgz in  /home/blah/blah/blah/1234/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux SCANLab-Work1 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 
17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 2556 exited with ERRORS at Tue Nov  3 17:46:26 CST 2020

For more details, see the log file 
/home/scanlab1/Desktop/FSTraining_2020/2556/scripts/recon-all.log
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin

It's also been approx 1 year since FS was run on our machines. Perhaps an 
update is needed? Thank you so much!



NOTICE: This message, including all attachments transmitted with it, is 
intended solely for the use of the Addressee(s) and may contain information 
that is PRIVILEGED, CONFIDENTIAL, and/or EXEMPT FROM DISCLOSURE under 
applicable law. If you are not the intended recipient, you are hereby notified 
that any disclosure, copying, distribution, or use of the information contained 
herein is STRICTLY PROHIBITED. If you received this communication in error, 
please destroy all copies of the message, whether in electronic or hard copy 
format, as well as attachments and immediately contact the sender by replying 
to this email or contact the sender at the telephone numbers listed above. 
Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Subcortical Segmentation Atlas Question

[Fischl, Bruce]

Hi Tyler

The atlas is described in our 2002 (Neuron) and 2004 (NeuroImage) papers. It 
implements the anisitropic, nonstationary Markov Random Field segmentation. I 
think lots of people have compared their segmentations to it, although I would 
urge some caution as many of them are biased IMO (e.g. they use their own 
segmentation definitions or the MRI sequence they were trained on to drive the 
comparison).

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rooks, Tyler
Sent: Monday, November 9, 2020 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Subcortical Segmentation Atlas Question


External Email - Use Caution
Good Morning FreeSurfer Developers and Experts,

I hope all is well.  I am relatively new to the use of FreeSurfer and 
neuroimaging research in general.  I have been looking for any documentation or 
details regarding the probabilistic atlas used for subcortical segmentation 
tasks (RB_all_2008-03-26.gca) provided in the 'average' directory.  Is there 
any information available or that can be described about what this atlas was 
generated from or any additional details about the atlas?  I am looking for 
information relating to potential number of subjects used to develop the atlas 
if that is available or methods used to develop?  Additionally, are there any 
comparisons between this subcortical atlas and other subcortical atlases 
available?  I have found a few comparisons between FreeSurfer and other 
software/atlases, but nothing comparing the subcortical segmentation directly.

Any help or information would be greatly appreciated.

Thanks,
Tyler

Ph.D. Student
Medical College of Wisconsin

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Editing Issues

[Fischl, Bruce]

Hi Harriet

Do you know that it is a hole? More likely is that it only looks like one on a 
single slice and if you scroll back and forth or change to a different view you 
will find that it is not actually a hole.

As for the second question you only need to edit things if the nearby surfaces 
are in cortex and not accurate. If they are not accurate in the ventricles but 
fine in cortex it won't change any cortical results.

Cheers
Bruce

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Harriet Cornwell
Sent: Wednesday, November 11, 2020 5:37 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Editing Issues

External Email - Use Caution

Hi Jocelyn,

Many thanks for your response. I just wanted to confirm a couple of things:

1. Could you advise what specific edits need to be made to the brainmask.mgz 
volume to fix the hole in the WM, i.e., do we need to add GM, delete GM? We are 
used to only editing the brainmask.mgz volume when there is an issue with the 
GM so just want to make sure that we are fixing this hole in the WM correctly.
2. If we are only interested in cortical thickness, surface area, volume and 
gyrification, can you confirm that we do not need to spend time editing issues 
around the ventricles?

Thank you in advance.

Harriet
PhD Student | University of Bath

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: 10 November 2020 17:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 201, Issue 15

CAUTION:  This email came from outside of the University. To keep your account 
safe, only click on links and open attachments if you know the person who sent 
the email, or you expected to receive this communication.



Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit

https://secure-web.cisco.com/13lQ7nDnK-H3JJGsgcPOLKvh6e3uFroou_3nPyQucZyx16UAymXIF-fCEKzQWmk9LDsRvSlpm5ff5qvB2xF3Y5xWVVeUcbAQmDKs-g2MYTAaUedIPFxuPqBSatea-lhxnVHZkRVLqdDlyW_47eNs8k1abrQ0aFVzi17eifonf2TW2S4pbTLBQh4YzNMU9LZ7rQYhqtxjn4CaWJUryQWOh7Tht3lvdruPk6zOuxXfJVTgtnPyG2iFYzRy51pvBYfDVzQcMX00o27lV_-Yu84Ufeg/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Chgc36%2540bath.ac.uk%257C2d139b3addcf46cf338308d8859a5ceb%257C377e3d224ea1422db0ad8fcc89406b9e%257C0%257C0%257C637406245354469411%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C1000%26sdata%3DmhCvQG7jcfQiJ5uJNN4%252Bk7LYQOhjSuQnZxBw1zyn%252B4Q%253D%26reserved%3D0
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


Today's Topics:

   1. BIDS-ASL request for comments - closes THIS Friday(11/13)
  {Disarmed} (Franklin Feingold)
   2. Re: Editing Issues (Mora, Jocelyn S.)
   3. Create new .mgz from .annot (Hyon, Justin J.)
   4. eddy_correct with DTI {Disarmed} (Wei Shao)
   5. Correlation between thickness and csf_measures: vector
  (Steve Petersen)
   6. color and sign of sig.mgh data (Rovai Antonin)
   7. Postdoctoral Fellowship in advanced multi-parametric imaging
  in Parkinson?s disease, Alzheimer?s disease, and healthy aging
  (Maurizio Bergamino)
   8. Re: Freesurfer 7.1.0 on CentOS 8.1 {Disarmed} (Snedden, Ali)
   9. Re: trac-all -bedp error after successful -prep (Michele Valotti)
  10. Re: Help with mergecontrasts-sess function (Paula Maldonado)


--

Message: 1
Date: Mon, 9 Nov 2020 18:28:16 +
From: Franklin Feingold 
Subject: [Freesurfer] BIDS-ASL request for comments - closes THIS
Friday  (11/13) {Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: 
Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) 
extension. The updated draft is available for review at: 
https://secure-web.cisco.com/1ITF4bOtJJcQiVKXDz67qOkjGMsukmz9eyHDd76OIYTeEMNhcr-pqzFItqXqpDSSs15cEGSM-LrPij2uIMXaEUhiYM9VBUWlYHpl6CKp6ecnNL4nu6GxSu3B8ygb9a_NDvB6BrFIj_IjRi6Cs3Mx7WEkzrp1lreTbNG4d0dAIIai8uDUzrPdnbi3hvAu-RA3uranehnaBDwDX5YZPHc2h-JRIAht_14FygxKNlfjB34u2xmrgzL0_kqWzJs3Jue_Q2zA8ETOI13z51HTkNEjhDA/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F19iI4s--bs7Y_Tdzvgf_eO4rOWt7fabvAARvcNytKJYcOiFI6gGONKUG4ASQvypqsJms2A8I_a2oiLM9epfyjdHtyXW6CaNjs-zFsB_dB6GOFCZjkphCKIXh58QzBtMdlVxRojSk3ksyJJ0amn1AAmltb56n3xoeIneV_uYbxiR-mQaA9pzH2ocGhCflORlUq0kaNt

Re: [Freesurfer] Mean thickness estimation

[Fischl, Bruce]

Hi Stephanie

By using the average/std within region, then averaging those, you are weighting 
small regions more. I would just use the average/std across cortex.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Wednesday, November 18, 2020 12:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mean thickness estimation

[Fischl, Bruce]

Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Fischl, Bruce]

Hi Stephanie

Sorry, I think I misunderstood. If you have visually inspected the analysis 
results and think that they are accurate then you definitely should leave those 
subjects in

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 4:19 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

Is it also necessary to remove outliers (eg. 3 SD from the mean) for  
Freesurfer structural measures of MRI images that have been visually inspected 
as a further data cleaning step?

I really appreciate your help.

Thanks

On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://secure-web.cisco.com/1KPUR-tLJEURgzYmremNK46BwlQzhr2HuE-Vgj0d_IfX_gecAUGN6QjCWYLIn3brTZNmVndmFck4JXbECP-4ChBCCB9on11GCIcDXo_CeNsBG78TW3Un3dAkQZk9obRuWPnrYHXzp4kS7t-Y4GsaRBH04naRD0rppbxKez7XlIyHvl1NMwlQaEMRHOk6FqYoTIVHV6UrlC5oR6DZFRClnWLATwzWDCvj5zCYsdJ7pt7xmr1fz3Jml3iS6BjOivmfV4vWBZ-x-rpFZ_zoHRv07WA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Fischl, Bruce]

Hi Stephanie

I see. Yes, I guess this is ok, you just want to be careful when tossing 
datasets that you aren’t biasing your results. Always better to look at them if 
you can. Big errors are pretty obvious and can be found quite rapidly (e.g. by 
zipping through a bunch of snapshots with nmovie_qt)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Friday, November 20, 2020 6:25 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

No, I don’t think that you’ve misunderstood. I was asking about cohorts that 
had not been visually inspected in my first message and then in my last message 
I wanted to check that I didn’t need to also remove people from visually 
inspected data based on statistical outliers (as a further step). In 
conclusion, from what I’ve understood: if there is no visual inspection of 
data, it is best to remove statistical outliers (based on standard deviations) 
even for global measures such estimated intracranial volume, mean thickness 
from left and right hemispheres. When data is visually inspected, there is no 
need to remove any data based on statistical outliers even if those exist as 
these should be good quality.  For the visual inspected data, I have kept all 
participants (which have an acceptable cortical surface reconstruction rating)  
for the regional variables and I also retained all participants for global 
measures (thickness of mean hemisphere, estimated intracranial volume) as the 
data had been processed and removed from further Freesurfer processing if they 
had severe artifacts or irregularities.

Many thanks for your advice.

On Thursday, November 19, 2020, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

Sorry, I think I misunderstood. If you have visually inspected the analysis 
results and think that they are accurate then you definitely should leave those 
subjects in

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 4:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

Is it also necessary to remove outliers (eg. 3 SD from the mean) for  
Freesurfer structural measures of MRI images that have been visually inspected 
as a further data cleaning step?

I really appreciate your help.

Thanks

On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one r

Re: [Freesurfer] Mean Curvature for whole hemisphere

[Fischl, Bruce]

Hi Josue

No real reason. We provide maps of the mean curvature so it would be easy 
enough to average them. Not sure it will have much meaning. I guess it will 
loosely measure how much folding there is (since the less folding the more 
sphere-like the geometry will become)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Josue Luiz Dalboni Da 
Rocha
Sent: Wednesday, November 25, 2020 10:07 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Mean Curvature for whole hemisphere


External Email - Use Caution

Dear FreeSurfer,



Why an average whole hemispherical value for mean curvature is not provided by 
Qdec?

Is there geometrical reason?



Best regards,

Josue
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Mean Curvature

[Fischl, Bruce]

Hi Letitia

I wouldn't think so since mean curvature is a differential property and so 
should be pretty local, but I guess controlling for overall curvature would be 
a slightly different hypothesis

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Letitia Schneider
Sent: Friday, November 27, 2020 8:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Josue Luiz Dalboni Da Rocha 
Subject: [Freesurfer] Mean Curvature


External Email - Use Caution

Dear Freesurfer team,



When I analyse the mean curvature value of a particular ROI, do I have to 
control for overall brain curvature, to make sure the results are not driven by 
individual differences in overall brain curvature?



Best wishes,

Letitia Schneider
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Freesurfer skullstripping error

[Fischl, Bruce]

Hi Yezhe

It depends a lot on what your resolution, read out direction, bandwidth and 
field strength are. We generally fix these with T2 or FLASH scans at the same 
resolution/geometry/readout as the T1. Otherwise they are pretty tough as the 
dura is close enough to the gray matter that you can’t see any space between 
them

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of LIN, Yezhe
Sent: Monday, November 30, 2020 5:10 PM
To: freesurfer 
Subject: [Freesurfer] Freesurfer skullstripping error


External Email - Use Caution
Dear Freesurfer users,


Hope this finds you well.

I preprocessed our dataset with recon-all  -s  -all -qcache and 
found a number of our subjects had different levels of skullstrip errors. I 
tried fixing them by a couple of different approaches, such as -gcut and 
adjusted watershed threshold, but they both failed to fix the overlapping of 
dura mater (Fig1 and 2). I tried two methods on different subjects and received 
the same outcome. I wonder if you have any ideas to fix this error. At this 
point, for some who had less skullstripping, I can erase them manually and run 
-autorecon-pial or -make. But for the others with multiple locations of 
skullstripping (like Fig 3 and 4), do you have any ideas on how to approach to 
them at a systemic level? Also I found the skullstripping error in over half of 
our subjects, is it normal that we have a such proportion?



Thank you so much!

--

Best regards,

Yezhe

Yezhe Lin, MD MMed  (she/her/hers)

Postdoctoral Associate, Department of Psychiatry

University of Rochester Medical Center

yezhe.lin@gmail.com

Twitter:
 @LinYezhe | 
LinkedIn
 | 
Researchgate

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer