Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

[Chris Vriend]

External Email - Use Caution

Dear Eugenio,

Douglas referred me to you for this question. Do you have an
explanation for the difference in asymmetry between the native (aseg) and
ThalamicNuclei.v12 segmentation?

kind regards, Chris


*I'm not sure about this. The FS segmentation atlas was not created to be
symmetrical, so interpreting the asymmetry of aseg results can be tricky. I
know that Eugenio often creates his atlases to be symmetric; unfortunately,
he's away until next week. Thalamus is also quite tricky because the
contrast with WM is so low it can make finding the border quite variable.
You are right about LGN/MGN. So, try re-sending this next week and see what
Eugenio has to say.*

Op ma 31 aug. 2020 om 17:21 schreef Chris Vriend :

> Dear freesurfer experts,
>
>
>
> I’m currently using FreeSurfer 7.1 with the thalamus subsegmentation from
> Iglesias et al (version 12) to subsegment the thalamus. Something we
> noticed is that the asymmetry between the left and right whole thalamus is
> reversed when comparing the native thalamus segmentation by FreeSurfer
> itself and the Iglesias method. This is exemplified by the values below
> where we calculated the Asymmetry Index [ (Left – right)/(left + right) *
> 100 ] and shows that for some subjects the left thalamus is larger when
> looking at the results of the Iglesias method, but smaller with the native
> method.
>
> To allow comparison between the two methods we subtracted the LGN and MGN
> volumes from the whole thalamus volume, because –  if I’m not mistaken –
>  these nuclei are not segmented by the standard recon-all pipeline?
>
> We don’t know why we observe this and not just in one dataset or one
> subject but in multiple. Do you have any words of wisdom or explanation for
> this phenomenon?
>
>
>
> Your advice is much appreciated.
>
>
>
> Kind regards,
>
>
>
> Chris Vriend
>
>
> Whole_thalamus_lh_Iglesias
>
> whole_thalamus_rh_Iglesias
>
> AI
>
> Fsnative_Left-Thal
>
> Fsnative_Right-Thal
>
> AI
>
> 4913.391
>
> 5129.889
>
> -2.155650345
>
> 5987.2
>
> 5764.6
>
> 1.894177913
>
> 6019.185
>
> 6235.017
>
> -1.761289719
>
> 6793.9
>
> 6732.4
>
> 0.454669791
>
> 6374.575
>
> 6574.893
>
> -1.546920692
>
> 7543.9
>
> 7592.1
>
> -0.318446089
>
> 6974.051
>
> 6983.314
>
> -0.066366395
>
> 7661.3
>
> 7624.8
>
> 0.238779021
>
> 5907.853
>
> 5798.037
>
> 0.93812602
>
> 6756.4
>
> 6485.2
>
> 2.048090865
>
> 6316.792
>
> 6382.639
>
> -0.518503546
>
> 7191.2
>
> 6959.7
>
> 1.63593835
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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[Freesurfer] Log transformation vertex-wise

[Jose Graterol]

External Email - Use Caution

Hello FreeSurfer Developers,

I have a technical question for which I have not yet found the answer.
First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on CentOS 7.

Now to the question: is there a way to apply, say, a logarithmic
transformation vertex-wise? For example, while doing a whole-brain analysis
for cortical thickness with mri_glmfit it would calculate everything with
the logarithmic value instead of mm.

If this is not implemented, do you have an idea of how I could achieve
this? Perhaps extracting the matrix with the values of each vertex and
reading it in Matlab?

Thanks in advance.

José
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Re: [Freesurfer] Log transformation vertex-wise

[Tim Schäfer]

External Email - Use Caution

Hi José,

most likely there is an easier way to do this with some FreeSurfer command that 
others can suggest (and I am not aware of), but I would do it in R with this 
script: https://gist.github.com/dfsp-spirit/ccdc8c5efb0cff2ba5b139190bbfb397

Best,

Tim

> On September 8, 2020 at 10:25 AM Jose Graterol  
> wrote:
> 
> 
> External Email - Use Caution
> 
> Hello FreeSurfer Developers,
> 
> I have a technical question for which I have not yet found the answer.
> First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on CentOS 7.
> 
> Now to the question: is there a way to apply, say, a logarithmic
> transformation vertex-wise? For example, while doing a whole-brain analysis
> for cortical thickness with mri_glmfit it would calculate everything with
> the logarithmic value instead of mm.
> 
> If this is not implemented, do you have an idea of how I could achieve
> this? Perhaps extracting the matrix with the values of each vertex and
> reading it in Matlab?
> 
> Thanks in advance.
> 
> José
> ___
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Log transformation vertex-wise

[Jose Graterol]

External Email - Use Caution

Hey Tim,

thanks for the quick response and for the script. I will try that.


Best,

José

On Tue, Sep 8, 2020 at 11:07 AM Tim Schäfer  wrote:

> External Email - Use Caution
>
> Hi José,
>
> most likely there is an easier way to do this with some FreeSurfer command
> that others can suggest (and I am not aware of), but I would do it in R
> with this script:
> https://gist.github.com/dfsp-spirit/ccdc8c5efb0cff2ba5b139190bbfb397
>
> Best,
>
> Tim
>
> > On September 8, 2020 at 10:25 AM Jose Graterol <
> gpjosealbert...@gmail.com> wrote:
> >
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> > I have a technical question for which I have not yet found the answer.
> > First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on CentOS 7.
> >
> > Now to the question: is there a way to apply, say, a logarithmic
> > transformation vertex-wise? For example, while doing a whole-brain
> analysis
> > for cortical thickness with mri_glmfit it would calculate everything with
> > the logarithmic value instead of mm.
> >
> > If this is not implemented, do you have an idea of how I could achieve
> > this? Perhaps extracting the matrix with the values of each vertex and
> > reading it in Matlab?
> >
> > Thanks in advance.
> >
> > José
> > ___
> > 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
>
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Re: [Freesurfer] Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"

[fsbuild]

External Email - Use Caution

Hi Alex,
I see via a search for,
ubuntu 16 Failed to initialize XRandr
- that what you report happens when trying to connect remotely, e.g., via VNC, 
to something running X windows/graphics (for other flavors of linux as well). 
 This 
thread,https://serverfault.com/questions/788503/xrandr-error-when-accessing-debian-vm-over-vnc-
 seems to indicate the version of libGL.so could be an issue.  One take 
away is if you are trying do run X remotely, then you can test to see if a 
simple X program like glxgears can be run remotely (before trying to run 
freeview).
I don’t think this one is much help as it reads like you already have these 
installed,https://askubuntu.com/questions/1039129/randr-extension-missing
There could be interactions going on w.r.t what you have installed, and then 
having to set/configure some things so X can work remotely thru the google 
cloud.  I don’t know how/if Goggle cloud supports X forwarding etc., but I 
do know that other ways of doing cloud virtualization, e.g., thru docker 
containers, needs some work to run X applications remotely.   Maybe google 
cloud taking your virtual machine image and turning it into some kind of 
“container” to run (which can be done with docker I believe).
If possible, I would first test the Ubuntu 16 virtual machine by running it 
directly on a local machine and check that glxgears and freeview work.. 
 Then I would try running it in the cloud and see what happens with 
respect to trying to run those programs remotely.   If you don’t have to 
use Ubuntu 16, we have an Ubuntu 18 virtual disk image you can download and run 
that already has everything installed to run 7.1.0 (and you could update it to 
7.1.1), https://drive.google.com/file/d/1bPvF9m2z4yRDIOv51B5bihU1VN_o2J5x/view?usp=sharing
- R.

On Sep 7, 2020, at 14:22, Alex White  
wrote:External Email - Use 
CautionHi Thanks for the 
quit reply. I followed those instructions, it seemed that all those libraries 
were already installed. Freeview still won’t launch (even after 
rebooting). Here’s the output of the second command you 
suggested: alexlw@alexs:~$ sudo apt-get install libx11-dev 
 libxext-dev  libxrandr2  libxrender-devReading package lists... 
DoneBuilding dependency tree       Reading state 
information... Donelibxext-dev is already the newest version 
(2:1.3.3-1).libxext-dev set to manually installed.libxrandr2 is already the 
newest version (2:1.5.0-1).libxrender-dev is already the newest version 
(1:0.9.9-0ubuntu1).libxrender-dev set to manually installed.libx11-dev is 
already the newest version (2:1.6.3-1ubuntu2.2).The following packages were 
automatically installed and are no longer required:  guile-2.0-libs 
hdf5-helpers libaec-dev libavcodec-dev libavformat-dev  libavutil-dev 
libfontconfig1-dev libgc1c2 libgl2ps-dev libgsasl7  libhwloc-dev 
libibverbs-dev libjbig-dev libkyotocabinet16v5 libllvm5.0  liblzma-dev 
libmailutils4 libnetcdf-cxx-legacy-dev libntlm0 libnuma-dev  libopenjp2-7 
libopenmpi-dev libswresample-dev libswscale-dev libtiffxx5  libxft-dev 
libxss-dev mailutils-common mpi-default-dev python3-boto tcl-dev  
tcl8.6-dev tk-dev tk8.6-devUse 'sudo apt autoremove' to remove them.0 upgraded, 
0 newly installed, 0 to remove and 41 not upgraded.Any other ideas? Thanks 
a million AlexOn Sep 7, 2020, at 12:21 AM, fsbuild 
 wrote:Hello Alex,I’m not sure Ubuntu 16.04 LTS has 
everything installed by default that the Qt graphics framework is looking to 
run in the X windows server.  You could try installing, $ sudo 
apt-get update$ sudo apt-get install libx11-dev  libxext-dev 
 libxrandr2  libxrender-dev- R.On Sep 7, 2020, at 01:52, Alex White 
 wrote:Qt: 
XKEYBOARD​___Freesurfer mailing 
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[Freesurfer] lobe annotation and stats file

[Marina Fernández]

External Email - Use Caution

Dear experts,

I would like to get a .stats file this the volume and thickness of lobe
annotation, so I am following the steps indicated in this link
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.
Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot
cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a
s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh

The output file that I get (lh.lobe.stats) seems normal and contains the
measurements that I need (volume and thickness). The problem is that the
terminal output contains this error message:
ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot
(below you can find the full terminal output)

What I have to do to obtain the lh.lobe.stats file (with the same or
similar stucture) without the error message?

Best regards,
Marina


  % *TERMINAL OUTPUT * %















































*subject = s_001annotation = aparchemi = rhsurface   = whiteReading surface
 /usr/local/freesurfer/subjects/s_001/surf/rh.whiteLoading annotations from
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annotreading colortable
from annotation file...colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)Seg
base 2000MRISmergeAnnotations: parcCount=11,
newparcname=frontalmri_annotation2 supposed to be reproducible but seed not
setMRISmergeAnnotations: parcCount=9,
newparcname=temporalMRISmergeAnnotations: parcCount=5,
newparcname=parietalMRISmergeAnnotations: parcCount=4,
newparcname=occipitalMRISmergeAnnotations: parcCount=4,
newparcname=cingulatecomputing statistics for each annotation in
s_001/label/rh.lobe.annot.reading volume
/usr/local/freesurfer/subjects/s_001/mri/wm.mgz...reading input surface
/usr/local/freesurfer/subjects/s_001/surf/rh.white...Using TH3 vertex
volume calcTotal face volume 176610Total vertex volume 173305
(mask=0)reading input pial surface
/usr/local/freesurfer/subjects/s_001/surf/rh.pial...reading input white
surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...reading
colortable from annotation file...colortable with 8 entries read
(originally none)table columns are:number of verticestotal surface
area (mm^2)total gray matter volume (mm^3)average cortical
thickness +- standard deviation (mm)integrated rectified mean
curvatureintegrated rectified Gaussian curvaturefolding index
intrinsic curvature indexstructure nameERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annotatlas_icv
(eTIV) = 1198953 mm^3(det: 1.624839 )37262  24668  63218  2.363 0.474
  0.124 0.029  41443.8  frontal 3602   2412   6370  2.374 0.615
0.137 0.027   54 3.8  cingulate12917   8443  18251  2.024
0.428 0.134 0.030  17115.6  occipital19235  12890  36112
 2.488 0.535 0.119 0.028  21121.0  temporal26568  17417
 41499  2.204 0.466 0.119 0.024  28725.6  parietal 2510
1617   4741  3.018 0.820 0.126 0.036   28 3.9  insula*
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Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

[Iglesias Gonzalez, Juan E.]

Very interesting, Chris! The atlas is indeed designed to be symmetric, such 
that left-right differences arise from the data rather than the prior.
Did you try on a larger sample? Are these differences in asymmetry significant?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Chris Vriend 

Reply-To: Freesurfer support list 
Date: Tuesday, September 8, 2020 at 03:07
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Asymmetry whole thalamus with native vs Iglesias 
method


External Email - Use Caution
Dear Eugenio,

Douglas referred me to you for this question. Do you have an explanation for 
the difference in asymmetry between the native (aseg) and ThalamicNuclei.v12 
segmentation?

kind regards, Chris


I'm not sure about this. The FS segmentation atlas was not created to be 
symmetrical, so interpreting the asymmetry of aseg results can be tricky. I 
know that Eugenio often creates his atlases to be symmetric; unfortunately, 
he's away until next week. Thalamus is also quite tricky because the contrast 
with WM is so low it can make finding the border quite variable. You are right 
about LGN/MGN. So, try re-sending this next week and see what Eugenio has to 
say.

Op ma 31 aug. 2020 om 17:21 schreef Chris Vriend 
mailto:chrisvri...@gmail.com>>:
Dear freesurfer experts,

I’m currently using FreeSurfer 7.1 with the thalamus subsegmentation from 
Iglesias et al (version 12) to subsegment the thalamus. Something we noticed is 
that the asymmetry between the left and right whole thalamus is reversed when 
comparing the native thalamus segmentation by FreeSurfer itself and the 
Iglesias method. This is exemplified by the values below where we calculated 
the Asymmetry Index [ (Left – right)/(left + right) * 100 ] and shows that for 
some subjects the left thalamus is larger when looking at the results of the 
Iglesias method, but smaller with the native method.
To allow comparison between the two methods we subtracted the LGN and MGN 
volumes from the whole thalamus volume, because –  if I’m not mistaken –  these 
nuclei are not segmented by the standard recon-all pipeline?
We don’t know why we observe this and not just in one dataset or one subject 
but in multiple. Do you have any words of wisdom or explanation for this 
phenomenon?

Your advice is much appreciated.

Kind regards,

Chris Vriend


Whole_thalamus_lh_Iglesias
whole_thalamus_rh_Iglesias
AI
Fsnative_Left-Thal
Fsnative_Right-Thal
AI
4913.391
5129.889
-2.155650345
5987.2
5764.6
1.894177913
6019.185
6235.017
-1.761289719
6793.9
6732.4
0.454669791
6374.575
6574.893
-1.546920692
7543.9
7592.1
-0.318446089
6974.051
6983.314
-0.066366395
7661.3
7624.8
0.238779021
5907.853
5798.037
0.93812602
6756.4
6485.2
2.048090865
6316.792
6382.639
-0.518503546
7191.2
6959.7
1.63593835








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

[Douglas N. Greve]

Yes, you just need a registration file. You can use mri_label2vol 
passing the aal atlas with the --seg option


On 9/6/2020 1:30 PM, Diógenes Bispo wrote:


External Email - Use Caution

Dear,

Can I use Freesurfer to convert aal atlas 3 from the MNI space to the 
native space of the T1 sequence?


Thanks.

Diógenes Bispo
Neuroradiologist
diogenesdi...@gmail.com 



Em sáb., 29 de ago. de 2020 às 12:22, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> escreveu:


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

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Diógenes Bispo
*Sent:* Saturday, August 29, 2020 6:10 AM
*To:* Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*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 

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Re: [Freesurfer] recon-all error

[Douglas N. Greve]

This is  not something we do. I have seen it done before, so do a search 
online and/or talk to the authros


On 9/6/2020 11:43 PM, Jie Zhao wrote:

 External Email - Use Caution

Hi, Bruce and all

The paper attached quoted "A semiautomated process was implemented to convert 
FreeSurfer generated
macaque surfaces into Caret file formats and to register the individual hemispheres 
to the F99 atlas."
Is the freesurfer have the function to generate macaque surface and how make it 
?

Best,
Jie


-原始邮件-
发件人: "Fischl, Bruce" 
发送时间: 2020-09-04 22:27:48 (星期五)
收件人: "Freesurfer support list" 
抄送:
主题: Re: [Freesurfer] recon-all error

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


-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" 
 wrote:

 External Email - Use Caution
 
 Hi Andrew
 
 Thanks fro your response.

 I have soruced the Freesurfer.
 Attached is the recon-all log.
 
   

Re: [Freesurfer] Results summary in QDEC

[Douglas N. Greve]

Run mri_glmfit-sim --help to get details on the output

On 9/7/2020 12:35 PM, Steve Petersen wrote:


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Dear Freesurfer experts,

I performed group analysis in QDEC in order to compare cortical 
thickness between two groups using the Monte Carlo Z simulation 
correction. My question is, where is located the z-score of each 
significant cluster? Maybe in the second column named as Max?. Below 
you can find an example. In this case z-scores of the precuneus and 
the inferior parietal would be 3.422 and 3.926 respectively?



Input 
 /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-HC-ad_plus-Intercept-thickness/sig.mgh

# Frame Number      0
# srcsubj fsaverage
# hemi lh
# surface white
# group_avg_surface_area 82220
# group_avg_vtxarea_loaded 1
# annot aparc
# SUBJECTS_DIR /usr/local/freesurfer/subjects
# SearchSpace_mm2 75146
# SearchSpace_vtx 146493
# Bonferroni 0
# Minimum Threshold 2.3
# Maximum Threshold infinity
# Threshold Sign    abs
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold    0 mm^2
# CSD thresh  2.30
# CSD nreps    1
# CSD simtype  null-z
# CSD contrast NA
# CSD confint  90.00
# Overall max 4.16102 at vertex 61133
# Overall min -1.24867 at vertex 155746
# NClusters          2
# FixMNI = 1
#
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ  CWP   
 CWPLow    CWPHi   NVtxs    WghtVtx   Annot
   1        3.422   78695    820.44    -11.2  -54.8   49.4  0.00250 
 0.00190  0.00310   1664     4553.35  precuneus
   2        3.926   52042    733.99    -30.8  -66.6   40.7  0.00410 
 0.00330  0.00490   1190     3620.13  inferiorparietal


Simulation complete.



Thanks in advance.

Best regards,


Steve.


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Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

[Douglas N. Greve]

The noise properties depends on the sequence, but the MP2RAGE sequence I 
use is a little noisier than the MEMPRAGE. The B0 distortion is 
different. Since it is a different sequence, there will be systematic 
differences between the acqs. Generally, this is nothing to be done 
about it. The bias will probably affect all groups the same, so it will 
not affect your final group stats much.


On 9/7/2020 3:09 PM, Fischl, Bruce wrote:


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 > 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>>

*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





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Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

[Douglas N. Greve]

On 9/7/2020 10:52 PM, Paul wrote:


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Dear Freesurfer Experts,
I have few questions regarding CWP values from mri_glmfit-sim using 
--cwp 0.05, --cwp 0.1, --cwp 0.999.

Using the 3 three commands below (A, B and C):
A. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs 
--cwp 0.05 --2spaces --bg 1
B. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs 
--cwp 0.1 --2spaces --bg 1
C. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs 
--cwp 0.999 --2spaces --bg 1
I end up with the same significant ClusterNo 1.  (in terms of Max, 
VtxMax, Size(mm^2), MNIX, MNIY, MNIZ, NVtxs, WghtVtx, Annot)
However, the CWP is 0.00040, 0.00140, and 0.00020 for A, B and C 
respetively.
I was expected after 10,000 iterations, the CWP would be more closely 
matched or even convergent.
Could you please let me know if this result is typical after 10,000 
iterations?
Also, should I be using more iterations (say 20k or more 100k?) to 
reach convergence across A, B, and C or is it usual to just report

A, B or C?
I don't understand. All you are changing is the CWP threshold? The final 
CWP value for a cluster should not be changing at all. If this is the 
case, can you send me the summary file for each?

Kind regards,
Paul

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Re: [Freesurfer] Log transformation vertex-wise

[Douglas N. Greve]

you just want to compute the log of the voxel values in a volume? You 
can use fscalc


On 9/8/2020 6:30 AM, Jose Graterol wrote:


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Hey Tim,

thanks for the quick response and for the script. I will try that.


Best,

José

On Tue, Sep 8, 2020 at 11:07 AM Tim Schäfer > wrote:


      External Email - Use Caution

Hi José,

most likely there is an easier way to do this with some FreeSurfer
command that others can suggest (and I am not aware of), but I
would do it in R with this script:
https://gist.github.com/dfsp-spirit/ccdc8c5efb0cff2ba5b139190bbfb397

Best,

Tim

> On September 8, 2020 at 10:25 AM Jose Graterol
mailto:gpjosealbert...@gmail.com>> wrote:
>
>
>         External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I have a technical question for which I have not yet found the
answer.
> First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on
CentOS 7.
>
> Now to the question: is there a way to apply, say, a logarithmic
> transformation vertex-wise? For example, while doing a
whole-brain analysis
> for cortical thickness with mri_glmfit it would calculate
everything with
> the logarithmic value instead of mm.
>
> If this is not implemented, do you have an idea of how I could
achieve
> this? Perhaps extracting the matrix with the values of each
vertex and
> reading it in Matlab?
>
> Thanks in advance.
>
> José
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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and
Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am
Main, Germany

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Re: [Freesurfer] lobe annotation and stats file

[Douglas N. Greve]

Try something like this

mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white



On 9/8/2020 7:58 AM, Marina Fernández wrote:


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Dear experts,

I would like to get a .stats file this the volume and thickness of 
lobe annotation, so I am following the steps indicated in this link 
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.

Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot
cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a 
s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh


The output file that I get (lh.lobe.stats) seems normal and contains 
the measurements that I need (volume and thickness). The problem is 
that the terminal output contains this error message:
ERROR: stating file 
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

(below you can find the full terminal output)

What I have to do to obtain the lh.lobe.stats file (with the same or 
similar stucture) without the error message?


Best regards,
Marina


  % /TERMINAL OUTPUT / % /

subject = s_001
annotation = aparc
hemi = rh
surface   = white

Reading surface
 /usr/local/freesurfer/subjects/s_001/surf/rh.white
Loading annotations from 
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot

reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Seg base 2000
MRISmergeAnnotations: parcCount=11, newparcname=frontal
mri_annotation2 supposed to be reproducible but seed not set
MRISmergeAnnotations: parcCount=9, newparcname=temporal
MRISmergeAnnotations: parcCount=5, newparcname=parietal
MRISmergeAnnotations: parcCount=4, newparcname=occipital
MRISmergeAnnotations: parcCount=4, newparcname=cingulate
computing statistics for each annotation in s_001/label/rh.lobe.annot.
reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...
reading input surface 
/usr/local/freesurfer/subjects/s_001/surf/rh.white...

Using TH3 vertex volume calc
Total face volume 176610
Total vertex volume 173305 (mask=0)
reading input pial surface 
/usr/local/freesurfer/subjects/s_001/surf/rh.pial...
reading input white surface 
/usr/local/freesurfer/subjects/s_001/surf/rh.white...

reading colortable from annotation file...
colortable with 8 entries read (originally none)

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

ERROR: stating file 
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

atlas_icv (eTIV) = 1198953 mm^3    (det: 1.624839 )
37262  24668  63218  2.363 0.474     0.124     0.029  414    43.8  frontal
 3602   2412   6370  2.374 0.615     0.137     0.027 54     3.8  cingulate
12917   8443  18251  2.024 0.428     0.134     0.030  171    15.6 
 occipital
19235  12890  36112  2.488 0.535     0.119     0.028  211    21.0 
 temporal
26568  17417  41499  2.204 0.466     0.119     0.024  287    25.6 
 parietal

 2510   1617   4741  3.018 0.820     0.126     0.036 28     3.9  insula/

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Re: [Freesurfer] freeview Inflated image with mosaic

[Wang, Ruopeng]

Are you running freeview locally or remotely?

Ruopeng

On Sep 5, 2020, at 1:11 AM, Wei Shao 
mailto:ws...@research.baycrest.org>> wrote:


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Hi, Freesurfer Team

My name is Wei Shao,  as you can see, whenever I tried to Freeview Inflated 
image , it gives me the picture with mosaic. I was wondering this is because of 
hardware or the setting? Thanks

Best,
Wei

<3D freesurfer.PNG>
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Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Park, James]

External Email - Use Caution



Sincerely,
James Park

From: "Park, James" 
Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical 
ribbon mask stage during recon-all

Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze T1 MRI data 
and ran into an error specifically when utilizing the -parallel flag.

We specifically ran into errors at the cortical ribbon mask stage during the 
code we ran (shown below with some parts of the paths removed).

recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd 
“…/freesurfer_output" -all -parallel

When the same code was run without the -parallel flag, the recon-all line ran 
successfully.

This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

The recon-all.log file has been attached here as a reference.

Thank you for your help in advance.

Sincerely,
James Park
Willie Lab, Dpt. of Neurosurgery, Emory



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recon-all-status.log
Description: recon-all-status.log
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Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Douglas N. Greve]

The issue with the ribbon is something we recently became aware of. does 
it happen consistently for you? I can send you a recon-all that will fix 
this for you, just tell me which version you are running.



On 9/8/2020 11:49 AM, Park, James wrote:


External Email - Use Caution

Sincerely,

James Park

*From: *"Park, James" 
*Date: *Tuesday, September 8, 2020 at 11:48 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Troubleshooting -parallel flag for Freesurfer, error in the 
cortical ribbon mask stage during recon-all


Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze T1 
MRI data and ran into an error specifically when utilizing the 
-parallel flag.


We specifically ran into errors at the cortical ribbon mask stage 
during the code we ran (shown below with some parts of the paths removed).


recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd 
“…/freesurfer_output" -all -parallel


When the same code was run without the -parallel flag, the recon-all 
line ran successfully.


This was run on a Mac with macOS Catalina Version 10.15.6 using 
FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.


The recon-all.log file has been attached here as a reference.


Thank you for your help in advance.

Sincerely,

James Park

Willie Lab, Dpt. of Neurosurgery, Emory




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Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Park, James]

External Email - Use Caution

Hello,

Thank you for such a prompt response.

This has happened consistently and across multiple mac laptops that we utilize 
in our laboratory.

Below is the freesurfer version that we are utilizing as noted in the 
build-stamp.txt file:
freesurfer-darwin-macOS-7.1.1-20200811-8b40551

That would be great thank you so much.

Sincerely,
James Park

From:  on behalf of "Douglas N. Greve" 

Reply-To: Freesurfer support list 
Date: Tuesday, September 8, 2020 at 12:06 PM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [External] Re: [Freesurfer] Troubleshooting -parallel flag for 
Freesurfer, error in the cortical ribbon mask stage during recon-all

The issue with the ribbon is something we recently became aware of. does it 
happen consistently for you? I can send you a recon-all that will fix this for 
you, just tell me which version you are running.

On 9/8/2020 11:49 AM, Park, James wrote:

External Email - Use Caution


Sincerely,
James Park

From: "Park, James" 

Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical 
ribbon mask stage during recon-all

Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze T1 MRI data 
and ran into an error specifically when utilizing the -parallel flag.

We specifically ran into errors at the cortical ribbon mask stage during the 
code we ran (shown below with some parts of the paths removed).

recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd 
“…/freesurfer_output" -all -parallel

When the same code was run without the -parallel flag, the recon-all line ran 
successfully.

This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer 
version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

The recon-all.log file has been attached here as a reference.

Thank you for your help in advance.

Sincerely,
James Park
Willie Lab, Dpt. of Neurosurgery, Emory



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[Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis

[Rizvi, Batool]

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Hi FreeSurfer team,

After running longitudinal FS, and running mri_glmfit using files that measured 
spc, we found clusters associated with our continuous variable (WMH volume) 
after controlling for other covariates. I was wondering though, do the values 
found in cache.th13.abs.y.ocn.dat reflect the change in thickness (as measured 
by spc) for each subject of the cluster found to be significantly associated? I 
read other posts that it was a value of thickness of each cluster, but I wasn't 
sure if the same was true for a longitudinal analysis (spc), as the file 
contains both positive and negative numbers.

Thanks so much for your help!
Batool
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Re: [Freesurfer] lobe annotation and stats file

[Marina Fernández]

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Hi Doug,

I used the command that you sent me but I have the same error message
(ERROR: stating file /usr/local/freesurfer/...).

Do you know other options?

Thank you in advance.
Marina


-


Douglas N. Greve
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22>
 Tue, 08 Sep 2020 08:14:19 -0700
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Try something like this


mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.lobe.stats
-b -a ../label/lh.lobe.annot fsm010 lh white

On 9/8/2020 7:58 AM, Marina Fernández wrote:

External Email - Use Caution

Dear experts,


I would like to get a .stats file this the volume and thickness of lobe
annotation, so I am following the steps indicated in this link
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.

Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot

cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a
s_001/label/lh.lobe.annot
-f s_001/stats/lh.lobe.stats -b s_001 lh

The output file that I get (lh.lobe.stats) seems normal and contains the
measurements that I need (volume and thickness). The problem is that the
terminal output contains this error message: ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

(below you can find the full terminal output)


What I have to do to obtain the lh.lobe.stats file (with the same or similar
stucture) without the error message?

Best regards,
Marina


  % /TERMINAL OUTPUT / % /

subject = s_001
annotation = aparc
hemi = rh
surface   = white

Reading surface
 /usr/local/freesurfer/subjects/s_001/surf/rh.white

Loading annotations from
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)

Seg base 2000
MRISmergeAnnotations: parcCount=11, newparcname=frontal
mri_annotation2 supposed to be reproducible but seed not set
MRISmergeAnnotations: parcCount=9, newparcname=temporal
MRISmergeAnnotations: parcCount=5, newparcname=parietal
MRISmergeAnnotations: parcCount=4, newparcname=occipital
MRISmergeAnnotations: parcCount=4, newparcname=cingulate
computing statistics for each annotation in s_001/label/rh.lobe.annot.
reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...

reading input surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...

Using TH3 vertex volume calc
Total face volume 176610
Total vertex volume 173305 (mask=0)

reading input pial surface
/usr/local/freesurfer/subjects/s_001/surf/rh.pial... reading input white
surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...

reading colortable from annotation file...
colortable with 8 entries read (originally none)

table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name


ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

atlas_icv (eTIV) = 1198953 mm^3(det: 1.624839 )
37262  24668  63218  2.363 0.474 0.124 0.029  41443.8  frontal
 3602   2412   6370  2.374 0.615 0.137 0.027 54 3.8  cingulate

12917   8443  18251  2.024 0.428 0.134 0.030  17115.6
 occipital 19235  12890  36112  2.488 0.535 0.119 0.028  211
 21.0  temporal 26568  17417  41499  2.204 0.466 0.119 0.024  287
 25.6  parietal

 2510   1617   4741  3.018 0.820 0.126 0.036 28 3.9  insula/

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[Freesurfer] Freesurfer Licensing

[Rollo, Patrick]

External Email - Use Caution

Hi all,

My group is working on a software platform with the hopes of some level of 
commercialization. Our platform uses some freesurfer code. Is there a specific 
person or group I can contact and work with to figure out the specifics of what 
this situation requires?

Best,
Patrick Rollo

713-500-5475
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Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

[Douglas N. Greve]

Try using this version of recon-all
https://gate.nmr.mgh.harvard.edu/safelinks/greve/recon-all.711.parallel


On 9/8/2020 12:09 PM, Park, James wrote:


External Email - Use Caution

Hello,

Thank you for such a prompt response.

This has happened consistently and across multiple mac laptops that we 
utilize in our laboratory.


Below is the freesurfer version that we are utilizing as noted in the 
build-stamp.txt file:


freesurfer-darwin-macOS-7.1.1-20200811-8b40551

That would be great thank you so much.

Sincerely,

James Park

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Tuesday, September 8, 2020 at 12:06 PM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *[External] Re: [Freesurfer] Troubleshooting -parallel flag 
for Freesurfer, error in the cortical ribbon mask stage during recon-all


The issue with the ribbon is something we recently became aware of. 
does it happen consistently for you? I can send you a recon-all that 
will fix this for you, just tell me which version you are running.


On 9/8/2020 11:49 AM, Park, James wrote:

*External Email - Use Caution *

Sincerely,

James Park

*From: *"Park, James" 

*Date: *Tuesday, September 8, 2020 at 11:48 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Troubleshooting -parallel flag for Freesurfer, error in
the cortical ribbon mask stage during recon-all

Dear FreeSurfer Developers,

We have recently been exploring the recon -all option to analyze
T1 MRI data and ran into an error specifically when utilizing the
-parallel flag.

We specifically ran into errors at the cortical ribbon mask stage
during the code we ran (shown below with some parts of the paths
removed).

recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output"
-sd “…/freesurfer_output" -all -parallel

When the same code was run without the -parallel flag, the
recon-all line ran successfully.

This was run on a Mac with macOS Catalina Version 10.15.6 using
FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

The recon-all.log file has been attached here as a reference.


Thank you for your help in advance.

Sincerely,

James Park

Willie Lab, Dpt. of Neurosurgery, Emory




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Re: [Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis

[Douglas N. Greve]

The interpretation depends on what you pass mri_glmfit in the --y 
argument. If you passed it differences in thicknesses, then the .dat 
file will be differences


On 9/8/2020 12:29 PM, Rizvi, Batool wrote:


External Email - Use Caution

Hi FreeSurfer team,

After running longitudinal FS, and running mri_glmfit using files that 
measured spc, we found clusters associated with our continuous 
variable (WMH volume) after controlling for other covariates. I was 
wondering though, do the values found in cache.th13.abs.y.ocn.dat 
reflect the change in thickness (as measured by spc) for each subject 
of the cluster found to be significantly associated? I read other 
posts that it was a value of thickness of each cluster, but I wasn’t 
sure if the same was true for a longitudinal analysis (spc), as the 
file contains both positive and negative numbers.


Thanks so much for your help!

Batool


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Re: [Freesurfer] lobe annotation and stats file

[Douglas N. Greve]

I think you SUBJECTS_DIR is set to the wrong place. What happens if you run
ls $SUBJECTS_DIR/s_001
Do you see your subject there?

On 9/8/2020 12:33 PM, Marina Fernández wrote:


External Email - Use Caution

Hi Doug,

I used the command that you sent me but I have the same error message 
(ERROR: stating file /usr/local/freesurfer/...).


Do you know other options?

Thank you in advance.
Marina


-


Douglas N. Greve 
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22> 
Tue, 08 Sep 2020 08:14:19 -0700 
<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20200908>


Try something like this

mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white

On 9/8/2020 7:58 AM, Marina Fernández wrote:

 External Email - Use Caution

Dear experts,

I would like to get a .stats file this the volume and thickness of
lobe annotation, so I am following the steps indicated in this
link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation.

Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot

cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a
s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001
lhThe output file that I get (lh.lobe.stats) seems normal and
contains the measurements that I need (volume and thickness). The
problem is that the terminal output contains this error message:
ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

(below you can find the full terminal output)

What I have to do to obtain the lh.lobe.stats file (with the same
or similar stucture) without the error message?

Best regards,
Marina


   % /TERMINAL OUTPUT / % /

subject = s_001
annotation = aparc
hemi = rh
surface   = white

Reading surface
  /usr/local/freesurfer/subjects/s_001/surf/rh.white

Loading annotations from
/usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot

reading colortable from annotation file...

colortable with 36 entries read (originally

/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)


Seg base 2000
MRISmergeAnnotations: parcCount=11, newparcname=frontal
mri_annotation2 supposed to be reproducible but seed not set
MRISmergeAnnotations: parcCount=9, newparcname=temporal
MRISmergeAnnotations: parcCount=5, newparcname=parietal
MRISmergeAnnotations: parcCount=4, newparcname=occipital
MRISmergeAnnotations: parcCount=4, newparcname=cingulate
computing statistics for each annotation in s_001/label/rh.lobe.annot.
reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz...

reading input surface
/usr/local/freesurfer/subjects/s_001/surf/rh.white...

Using TH3 vertex volume calc
Total face volume 176610
Total vertex volume 173305 (mask=0)

reading input pial surface
/usr/local/freesurfer/subjects/s_001/surf/rh.pial... reading input
white surface /usr/local/freesurfer/subjects/s_001/surf/rh.white...

reading colortable from annotation file...
colortable with 8 entries read (originally none)

table columns are:
     number of vertices
     total surface area (mm^2)
     total gray matter volume (mm^3)
     average cortical thickness +- standard deviation (mm)
     integrated rectified mean curvature
     integrated rectified Gaussian curvature
     folding index
     intrinsic curvature index
     structure name

ERROR: stating file
/usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot

atlas_icv (eTIV) = 1198953 mm^3    (det: 1.624839 )
37262  24668  63218  2.363 0.474     0.124     0.029  414    43.8  frontal
  3602   2412   6370  2.374 0.615     0.137     0.027 54     3.8  cingulate

12917   8443  18251  2.024 0.428     0.134     0.030  171    15.6
 occipital 19235  12890  36112  2.488 0.535     0.119     0.028
 211    21.0  temporal 26568  17417  41499  2.204 0.466     0.119
    0.024  287    25.6  parietal

  2510   1617   4741  3.018 0.820     0.126     0.036 28     3.9  insula/

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Re: [Freesurfer] BrainSegNotVent {Disarmed}

[Douglas N. Greve]

That scan looks low res and T2 weighted, so you would not run recon-all 
on it. But even if it were the right contrast/resolution, I think it is 
too extensive. I don't know if there is going to be something that we 
have that is going to do that for you.


On 9/8/2020 1:44 PM, Harkey, Thomas Jarrott wrote:


External Email - Use Caution

Douglas,

We are conducting a study with stroke patients using DWI MRI. Image 
attached. Is Freesurfer capable of taking an MRI with an infarct (as 
you can see in the picture) and providing a volume for that 
hyperintense area?


Is there a command we can run do specify for that?

Would recon all do it?

Thanks

--

*Thomas Harkey **
University of Arkansas for Medical Sciences***

*College of Medicine, Class of 2022
501-553-6318*

*tjhar...@uams.edu *

*From: * on behalf of "Douglas 
N. Greve" 

*Reply-To: *Freesurfer support list 
*Date: *Thursday, September 3, 2020 at 8:17 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] BrainSegNotVent {Disarmed}

Not really, since it requires having the surfaces. You can add them up 
yourself, or you can binarize aseg.presurf.mgz to just the regions you 
want (mri_binarize --match id1 id2 ...), then run mri_segstats on that


On 9/2/2020 2:04 PM, Harkey, Thomas Jarrott wrote:

*External Email - Use Caution *

Hello,

Two final questions: when I did autorecon1 and autorecon2-volonly,
I then ran the following command:

mri_segstats –brain-vol-from-seg –seg aseg.presurf.mgz –sum stats

However, it is just printing the volumes of each segmentation and
not adding them up. I want the BrainSegNotVent measurement without
having to do the entire recon all. What am I doing wrong?

Is there a way to obtain the aseg.stats file or brainvol.stats
file without using recon-all?

Just trying to save time.

Thanks for your help.



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


 on behalf of
Douglas N. Greve 

*Sent:* Monday, August 24, 2020 9:12 AM
*To:* freesurfer@nmr.mgh.harvard.edu

*Subject:* Re: [Freesurfer] BrainSegNotVent {Disarmed}

Right, you will actually need to run both autorecon1 and
-autorecon2-volonly
-autorecon2-volonly will take a few hours

On 8/23/2020 7:35 PM, Harkey, Thomas Jarrott wrote:

*External Email - Use Caution *

Ok, I tried that command and it didn’t work because
aseg.presurf.mgz doesn’t exist in that directory

I don’t think that file was generated with autorecon1.

So do you think I need to run reconall -all to get the
BrainSegNotVent?

If there were a more efficient way to obtain this volume, I
would be open to learning it.

-- 


*Thomas Harkey **
University of Arkansas for Medical Sciences*

*College of Medicine, Class of 2022
501-553-6318*

*tjhar...@uams.edu *

*From: *
 on behalf of
"Douglas N. Greve" 

*Reply-To: *Freesurfer support list


*Date: *Sunday, August 23, 2020 at 2:03 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"



*Subject: *Re: [Freesurfer] BrainSegNotVent

Actually, that file won't be there either because it does not
get created until all processing is done (not just
autorecon1). You can run mri_segststats like
mri_segstats --seg subject/mri/aseg.presurf.mgz --ctab-default
--sum subject/stats/aseg.presurf.stats
Then add up all the segmentations you want to get BrainSegNotVent

On 8/23/2020 11:42 AM, Douglas N. Greve wrote:

Are you using v7? If so, look in subject/stats/brainvol.stats

On 8/22/2020 5:39 PM, Harkey, Thomas Jarrott wrote:

*External Email - Use Caution *

Hello,
I am a student learning free surfer. I was able to
obtain intracranial volume by running

recon-all –i  file.dcm   –subject  bert –autorecon1

and then

mri_segstats --subject bert --etiv-only

How can I obtain the BrainSegNotVent volume? I have tried

mri_segstats --subject bert --brain-vol-from-seg

however, “ERROR: must specify a segmentation volume”

Can this be calculated using the data from autorecon1,
or do I

Re: [Freesurfer] G_subcallosal region is missing

[Douglas N. Greve]

OK, I see what you mean now, I'm just not sure how to fix it. What 
version of FS are you using?


On 9/3/2020 12:07 PM, Marina Fernández wrote:


External Email - Use Caution

Hi Doug,

I sent you the images attached to the email and also through FTP File 
Exchange.


Thank you for your attention.
Best regards,

Marina





  Douglas N. Greve
I'm still not understanding what is happening. Can you send three
pics of the inflated surface of same location, one with
cortex.label, one with aparc.annot, and one with
aparc.a2009s.annot? Also, please remember to include previous
emails so that I have context, thanks


On 9/3/2020 9:55 AM, Marina Fernández wrote:

 External Email - Use Caution

Sorry for the misunderstanding Doug . I have checked
the lh.aparc.annot on the surface and there is no G_subcallosal
label in these subjects. In that region are the G_and_S_cingul-Ant
label / S_pericallosal labels. On the other hand,  the surface
appears normal.

What do you recommend us to do?

Thank you in advance.
Marina.


Douglas N. Greve


Wed, 02 Sep 2020 10:31:13 -0700



Sorry, I meant to look on the surface and see if the label is
there and what the lh.aparc.annot looks like there

On 9/2/2020 11:05 AM, Marina Fernández wrote:

 External Email - Use Caution

Hi Doug,

When I load the volume aparc.a2009s+aseg.mgz in a subject
without the G_subcallosal region in the lh.aparc.a2009s.stats
file, I can see that in the other hemisphere (right in this
case) there is G_subcallosal while in the left hemisphere this
contralateral region is filled by the lh_S_suborbital region.
So, it's covered by another label.

What should we do?

Best wishes,
Marina





Douglas N. Greve


Wed, 02 Sep 2020 07:23:58 -0700

Does
the cortex label cover it? What does the aparc look like in
that area?

On 9/2/2020 6:09 AM, Marina Fernández wrote:

 External Email - Use Caution Dear experts,

 I have noticed that some subjects don't show the G_subcallosal
 region in the *h.aparc.a2009s.stats file. Do you know why is this
 happening? Is there a way to fix it?

 Thank you in advance. Best regards, Marina
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Re: [Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis

[Rizvi, Batool]

External Email - Use Caution

Thanks for the info, Dr. Greve!

So for the files I used for the --y argument were stacked files of this file: 
lh.long.thickness-spc.fwhm10.fsaverage.mgh or 
rh.long.thickness-spc.fwhm10.fsaverage.mgh.
So would my interpretation of the ocn.dat file be that each value is the 
symmetrized percent change in thickness of the significant cluster for each 
subject?

Thanks again,
Batool
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Re: [Freesurfer] mri_vol2vol with --inv-morph producing unexpected results

[Noriana Jakopin]

External Email - Use Caution

Hello,
I just wanted to follow up on this and see if anyone had any suggestions,
as I still have not resolved the issue.

Best,
Noriana Jakopin

On Tue, Aug 18, 2020 at 12:54 PM Noriana Jakopin 
wrote:

> Hello FreeSurfer Developers,
> I am attempting to use the inverse of the final m3z registration file
> produced by mri_cvs_register to take files in mni152 space back into my
> subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish
> this. However, the resulting outputs produce images with abnormal warpings
> to the brain. Using mri_vol2vol to take subject files into mni152 space
> with the same m3z file works fine, it seems to be the inverse that is the
> problem. Does anyone have thoughts on how I can remedy this issue?
>
> FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1
> Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS
>
> Thank you!
> Noriana Jakopin
>
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Re: [Freesurfer] interpreting file (cache.th13.abs.y.ocn.dat) from longitudinal vertex-wise analysis

[Douglas N. Greve]

Correct

On 9/8/2020 7:26 PM, Rizvi, Batool wrote:


External Email - Use Caution

Thanks for the info, Dr. Greve!

So for the files I used for the --y argument were stacked files of 
this file: lh.long.thickness-spc.fwhm10.fsaverage.mgh or 
rh.long.thickness-spc.fwhm10.fsaverage.mgh.


So would my interpretation of the ocn.dat file be that each value is 
the symmetrized percent change in thickness of the significant cluster 
for each subject?


Thanks again,

Batool



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[Freesurfer] -hires vs -conf2hires in 7.1.1.

[Alexopoulos, Dimitrios]

External Email - Use Caution

Does the hires flag still generate segs at the native hi resolution and place 
surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but 
places surfaces on the hires images?

Which option is recommended and why?

Jim


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[Freesurfer] outputs from step of trac- all prep

[Zeng, Qi]

External Email - Use Caution

Hi,

Where is the nifti output stored from running trac-all preprocess? Is
it dmri/dwi.nii.gz? Is there an additional step segment this nifti file
into the grey matter and white matter for later tensor-fitting?

Best,
Qi
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