Re: [Freesurfer] Cortical thickness

[Joshua deSouza]

Hi Doug,

I did not specify anything in the mris_preproc, so it would be using the
unsmoothed data. I only specify smoothing during the mri_surf2surf, which
is 15 and then run glmfit. So what could be the reasons why i'm getting a
residual fwhm of 47?

Regards,

Joshua

On Thu, Jun 6, 2013 at 12:16 AM, Douglas N Greve
wrote:

> Unless you specify otherwise, mris_preproc will use unsmoothed data. If
> you then smooth it with mri_surf2surf and run run mri_glmfit with --fwhm
> then you will be smoothing it twice.
> doug
>
>
>
>
> On 06/04/2013 09:49 PM, Joshua deSouza wrote:
>
>> Hello Doug,
>>
>> Each individuals subject data has already been smoothed by 5 10 15 20 and
>> 25 through the qache function during the initial processing.
>>
>> I'm a little confused now. I thought that the mri_preproc would use the
>> non-smoothed values of the subjects and create an mgh file. After which I
>> smooth the mgh file and then use mri_glmfit to analyse it according to the
>> contrasts.
>>
>> If the above is not the case and the subject data has already been
>> smoothed, then what should I do if I wish my final mgh file to have a
>> smoothing value of 15 before doing a glmfit on it?
>>
>> Thank you,
>>
>> Joshua
>>
>>
>> On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza <
>> desouzajoshu...@gmail.com 
>> >
>> wrote:
>>
>> Hello Doug,
>>
>> Each individuals subject data has already been smoothed by 5 10 15
>> 20 and 25 through the qache function during the initial processing.
>>
>> I'm a little confused now. I thought that the mri_preproc would
>> use the non-smoothed values of the subjects and create an mgh
>> file. After which I smooth the mgh file and then use mri_glmfit to
>> analyse it according to the contrasts.
>>
>> If the above is not the case and the subject data has already been
>> smoothed, then what should I do if I wish my final mgh file to
>> have a smoothing value of 15 before doing a glmfit on it?
>>
>> Thank you,
>>
>> Joshua
>>
>> On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve
>> > >
>> wrote:
>>
>>
>> Hi Joshua, when you add --fwhm 15 to the command line you are
>> instructing mri_glmfit to smooth by 15mm. Is this what you
>> want?  Or is the data already smoothed?
>> doug
>>
>>
>>
>> On 6/3/13 12:26 AM, Joshua deSouza wrote:
>>
>>> Hi Doug,
>>>
>>> The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt
>>> dods --C t1.txt --surface fsaverage lh --cortex --fwhm 15
>>> --glmdir lh.t.15.glmdir
>>>
>>> I am doing a whole hemisphere analysis and am measuring
>>> cortical thickness. I do not have my own mask but I have
>>> doubts about the mask that has been produced because from
>>> previous studies, there has been significant thinning in the
>>> area around the hippocampus and parts of it are being left
>>> out in the mask, such as the para-hippocampal region.
>>>
>>> Regards
>>>
>>> Joshua
>>>
>>> On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve
>>> >> >
>>> wrote:
>>>
>>>
>>> The residual FWHM is measured from the data itself. You
>>> apply a certain amount of smoothing, but there is already
>>> some smoothness to the data, so the final fwhm is a
>>> combination of what is already there and what you apply.
>>> A fwhm of 47 is huge and may indicate that something is
>>> wrong. What is the input? cortical thickness? Are you
>>> using your own mask or is this a whole hemisphere analysis?
>>>
>>> doug
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 6/2/13 10:29 PM, Joshua deSouza wrote:
>>>
 Hello Doug,

 Thank you for your quick replies to my queries. Really
 appreciate it.

 I have found the files containing the cortical thickness
 values. Thank you. I assume that the order in which they
 follow are based on the fsgd file and the cluster
 annotation numbers.

 I was just slightly confused about the residual fwhm. I
 have already done a smoothing of 15 on the file and have
 recieved a residual value of 47, which I assume is
 extremely large. Since I'm finding out values for the
 entire cortex I cannot do a glmfit-sim as there are no
 fwhm cache values of 47. Could you please tell me what
 the residual values mean?  What do you recommend I do?
 Is there anything I can read up on to find out more
 about this? (Please pardon my questions if they seem a
 little trivial)

 Thank you

Re: [Freesurfer] max thickness value

[Colin Reveley]

I just found mris_thickness. which has a setting to override the default
5mm. you just run it.

whoops. I'm very tired. apologies. I just assumed it would be hard.
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[Freesurfer] averaging tracts?

[Hoptman, Matthew]

Hi all,
Thanks for tracula , which I think is a terrific tool.  Is there any way to 
average tracts across subjects for viewing purposes?  I have in mind somehting 
along the line of a group average merged_avg33_mni_bbi.mgz.
Thanks,
Matt

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research
Research Associate Professor in Psychiatry
NYU School of Medicine

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[Freesurfer] Group analysis

[Tudor Popescu]

>
> Under fsaverage/surf there is both an lh.white and an lh.white_avg file,
>> while under average/surf there's only lh.white_avg. I repeated the
>> mri_surf2surf command above with "--s fsaverage" instead of "--s average"
>> (since I understand in this case it's the same thing), and then it ran to
>> completion.
>>
> It should be close but probably not exact.

So if I want to use the study-specific "average" subject surface with
mri_surf2surf, rather than the generic "fsaverage" one, how can this be
done given that the required ls.white file only exists in the latter but
not in the former? Can I just rename (or duplicate) ls.white into
ls.white_avg?

Also,

1) Doesn't mri_surf2surf also need to be applied to surface of individual
study subjects, or only to the (fs)average subject?

2) Shouldn't the input to mri_glmfit be the output of mri_surf2surf?
In the group
tutorial,
the former is "lh.gender_age.thickness.*10*.mgh" while the latter is
"lh.gender_age.thickness.*10B*.mgh". Or should it just be the unsmoothed
output of mris_preproc?

3) Assuming the label files (corresponding to my ROI, and extracted from
the Destrieux atlas) are different for each subject, and given mri_glmfit
is called just once, for all subjects, which label file (corresponding to
what subject) should I point it to?

Thanks!
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Re: [Freesurfer] maximum thickness value?

[Bruce Fischl]

Hi Colin

you can use

mris_thickness -max 100 ...

to change the saturation point of the thickness measures.

cheers
Bruce

On Thu, 6 Jun 2013, Colin Reveley wrote:


I'm using data that's 0.35mm isotropic (and lower, but I've just noticed
this). to do that I alter the header so that the voxels claim to be 1mm.
it's a small brain so this works. Everything in general is fine.
the only thing is I'm having touble with the cortical thickness output of
mris_make_surfaces. I can't remember if this is a new problem, or has just
never mattered to me before.

when I run mris_make_surfaces, the ?h.thickness data seems to top out at 5.
So that most of the brain has a thickness of 5.

I wonder does freesurfer top out the thickness metric data at 5mm, since
humans (or monkeys) don't normally have GM that is more than 5mm thick?

if that's the case, can I change the behavior? 

I hope it is my error, and the thickness is topping at 5 for some reason I
can control.

attahced: pial surface with metric on it and scale bar
sagittal slice with little measurements drawn to estimate thickness.

if you multiply the meaurements by 0.35 they are roughly what you'd expect.

but many are >5mm before scaling. they all report as 5mm.

I really need just anyway to calculate the thickness. that would be great.
It needs to be quite accurate.

maybe I could change the volume back to 0.35 conformed, then scale the
surfaces as well, and use mris-refine or something like that? the data would
be the same but freesurfer would now know the true dimensions when it ran
mris_refine. or anything that generates ?h.thickness.

many thanks, 

Colin

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Re: [Freesurfer] Saving subjects

[Bruce Fischl]

Hi Gari

I took a quick look at the images and the surfaces look reasonable. What 
are the problems you are having? There's a lot of dropoff at the vertex in 
the data, probably because of your coil geometry. Is this the problem you 
are referring to, that superior wm/gm is not captured by the surfaces? A 
couple of control points in the WM up there should help a lot.


cheers
Bruce


On Thu, 6 Jun 2013, Garikoitz 
Lerma-Usabiaga wrote:



Hi list,we have some subjects with acquisition problems. 

Do you think it is possible to save this two subjects, and if so, how?

They have been run with:
recon-all -i (file) -s (subject) -qcache -hippo-subfields -all

They have been acquired with 3T, MPRAGE (but I didn't add the flags). 
I've read in the list about -washu-mprage , but I don't know how to use,
couldn't find the documentation. 

Should it be enough adding wm control points?


Many thanks in advance!
Gari

(sorry to post that many images, they belong to only two different subjects)

Inline image 5 Inline image 4 Inline image 3 Inline image 2 Inline image 1

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Re: [Freesurfer] Saving subjects

[Garikoitz Lerma-Usabiaga]

Thanks Bruce,
yes, the problem was that the box wasn't set up properly and we lost
several subjects because of that (head cut at the top).

I'll just try with the control points then, thanks!

Gari


On Thu, Jun 6, 2013 at 3:23 PM, Bruce Fischl wrote:

> Hi Gari
>
> I took a quick look at the images and the surfaces look reasonable. What
> are the problems you are having? There's a lot of dropoff at the vertex in
> the data, probably because of your coil geometry. Is this the problem you
> are referring to, that superior wm/gm is not captured by the surfaces? A
> couple of control points in the WM up there should help a lot.
>
> cheers
> Bruce
>
>
> On Thu, 6 Jun 2013, Garikoitz Lerma-Usabiaga wrote:
>
>  Hi list,we have some subjects with acquisition problems.
>>
>>
>> Do you think it is possible to save this two subjects, and if so, how?
>>
>> They have been run with:
>> recon-all -i (file) -s (subject) -qcache -hippo-subfields -all
>>
>> They have been acquired with 3T, MPRAGE (but I didn't add the flags).
>> I've read in the list about -washu-mprage , but I don't know how to use,
>> couldn't find the documentation.
>>
>> Should it be enough adding wm control points?
>>
>>
>> Many thanks in advance!
>> Gari
>>
>> (sorry to post that many images, they belong to only two different
>> subjects)
>>
>> Inline image 5 Inline image 4 Inline image 3 Inline image 2 Inline image 1
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] SPM ROI to Cortical Thickness

[McMains, Stephanie]

I am wondering why you didn't tell them to go through fsvarege space?  I 
thought that was an easy way to go from SPM MNI to freesurfer land.


tksurfer fsaverage lh inflated -aparc -mni152reg -overlay 
/pathname/to/spm/roi/yourfile.img


I am wondering because when I look at the segmentation for fsaverage, it seems 
like it is missing a lot of the gray matter, particularly in the big sulci, 
most likely from the 'smoothing' that comes with averaging subjects together.  
And therefore I wonder if this is the best thing to use as an intermediate 
step.  Are you instead suggesting (as it seemed like in this thread), to put 
the SPM roi into individual subject space and then somehow project it to the 
surface in free surfer?

Thanks,
Stephanie


+

Stephanie McMains
Neuroimaging Staff Scientist
Center for Brain Science
Harvard University
52 Oxford Street
Cambridge, MA 02138

+
For answers to frequently asked questions:
http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/faq







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[Freesurfer] (no subject)

[David Dalton]

Hello,

I am currently attempting to download the freesurfer software onto my mac
device from the website, but I am having trouble.  None of the links will
open, and when I tried typing the wget (curl-O for me) command into my
command line, nothing happened.  Any suggestions?

Thanks,
David
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Re: [Freesurfer] SPM ROI to Cortical Thickness

[Douglas N Greve]

Hi Stephanie, I don't know which recommendation you are referring to. We 
get a lot of emails, and I can't remember each one. Can you repost with 
the full thread?
doug


On 06/06/2013 10:40 AM, McMains, Stephanie wrote:
> I am wondering why you didn't tell them to go through fsvarege space? 
>  I thought that was an easy way to go from SPM MNI to freesurfer land.
>
>> /tksurfer fsaverage lh inflated -aparc -mni152reg -overlay 
>> /pathname/to/spm/roi/yourfile.img/
>
>
> I am wondering because when I look at the segmentation for fsaverage, 
> it seems like it is missing a lot of the gray matter, particularly in 
> the big sulci, most likely from the 'smoothing' that comes with 
> averaging subjects together.  And therefore I wonder if this is the 
> best thing to use as an intermediate step.  Are you instead suggesting 
> (as it seemed like in this thread), to put the SPM roi into individual 
> subject space and then somehow project it to the surface in free surfer?
>
> Thanks,
> Stephanie
>
>
> +
>
> Stephanie McMains
> Neuroimaging Staff Scientist
> Center for Brain Science
> Harvard University
> 52 Oxford Street
> Cambridge, MA 02138
>
> +
> For answers to frequently asked questions:
> http://cbs.fas.harvard.edu/science/core-facilities/neuroimaging/information-investigators/faq
>
>
>
>
>
>
>
>
>
> ___
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] (no subject)

[Z K]

David,

Are you using the links from this page?

http://surfer.nmr.mgh.harvard.edu/fswiki/Download

I just tested the download from two different computers on two different 
networks and both were successful. There was another post to the 
freesurfer list a couple weeks ago claiming to have the same problem so 
Im open to attempting to diagnose the issue, but all tests on my end 
fail to replicate it. I have a couple questions:

1) Is it only the Mac downloads that dont work? What happens when you 
click the linux distibutions?

2) Can you provide a snapshot of the terminal after you type the "curl" 
command?

-Zeke


On 06/06/2013 11:03 AM, David Dalton wrote:
> Hello,
>
> I am currently attempting to download the freesurfer software onto my
> mac device from the website, but I am having trouble.  None of the links
> will open, and when I tried typing the wget (curl-O for me) command into
> my command line, nothing happened.  Any suggestions?
>
> Thanks,
> David
>
>
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Re: [Freesurfer] averaging tracts?

[Anastasia Yendiki]

Hi Matt - Thanks for your kind words!

The merged_*.mgz file is just a 4D mgz file where each frame corresponds 
to one of the 18 tracts. The only special thing about this mgz file is 
that it has some special fields in its header that tell freeview how to 
display each tract (color, name, and threshold). I haven't tried this, but 
I would guess that if you performed any operation on that mgz file, those 
header fields would be preserved. And if they're not they should be, so we 
should know about it.


You can try to map each mgz file from individual DWI space to a common 
space with mri_vol2vol and then average them with mri_concat. Let us know 
if this ends up working or if you have any questions about these steps.


Thanks!
a.y

On Thu, 6 Jun 2013, Hoptman, Matthew wrote:



Hi all,

Thanks for tracula , which I think is a terrific tool.  Is there any way to
average tracts across subjects for viewing purposes?  I have in mind
somehting along the line of a group average merged_avg33_mni_bbi.mgz.

Thanks,

Matt

 

Matthew J. Hoptman, PhD
Research Scientist V
Nathan S. Kline Institute for Psychiatric Research

Research Associate Professor in Psychiatry
NYU School of Medicine

 

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[Freesurfer] Enquire about running FreeSurfer {Disarmed}

[pablo najt]

Hello I have a question regarding the installation/running FreeSurfer.I have 
just completed the installation and got the confirmation that Free surfer was 
installed. Please see snapshot.However when I follow the steps for testing 
(https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer), I always get 
"command not found". I was wondering if you would be able to help 
me.Thanks,Pablo   <>___
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Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

[Douglas N Greve]

what command is not found?
On 06/06/2013 11:58 AM, pablo najt wrote:
> Hello I have a question regarding the installation/running FreeSurfer.
> I have just completed the installation and got the confirmation that 
> Free surfer was installed. Please see snapshot.
> However when I follow the steps for testing (*MailScanner has detected 
> a possible fraud attempt from "connect.yale.edu" claiming to be* 
> https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer 
> ),
>  
> I always get "command not found". I was wondering if you would be able 
> to help me.
> Thanks,
> Pablo
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] autorecon3 error

[Gabriel Gonzalez Escamilla]

Dear Freesurfers

I am running an autorecon3 to the same subject that Rafa sent you (the name 
looks different but is exactly the same subject), with the command to fix the 
ribbon.mgz the autorecon-2 has finished, so I continued with -autorecon3, but 
now is encountering the following error, this time seems to be something with 
the seg.mgz. 



#-
#@# Cortical Parc lh Thu Jun  6 17:01:26 CEST 2013
/root/trabajo/freesurfer/subjects/qsm1_17/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 
qsm1_17 lh ../surf/lh.sphere.reg 
/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
 ../label/lh.aparc.annot

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
f[113526]->v[1] = 539832625 - out of range!

reading atlas from 
/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs...
reading color table from GCSA file
average std = 1.0   using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s qsm1_17 exited with ERRORS at Thu Jun  6 17:01:33 CEST 2013

For more details, see the log file 
/root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Any ideas how to fix this?

Bests,
Gabriel

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Re: [Freesurfer] autorecon3 error

[Bruce Fischl]

Hi Gabriel

seems like something is wrong with that surface file. Can you load the 
lh.sphere.reg in tksurfer and see if it looks ok?

Bruce


On Thu, 6 Jun 2013, 
Gabriel Gonzalez Escamilla wrote:



Dear Freesurfers

I am running an autorecon3 to the same subject that Rafa sent you (the name
looks different but is exactly the same subject), with the command to fix
the ribbon.mgz the autorecon-2 has finished, so I continued with
-autorecon3, but now is encountering the following error, this time seems to
be something with the seg.mgz.



#-
#@# Cortical Parc lh Thu Jun  6 17:01:26 CEST 2013
/root/trabajo/freesurfer/subjects/qsm1_17/scripts

 mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234
qsm1_17 lh 
../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_kill
iany.2010-03-25.gcs ../label/lh.aparc.annot

setting seed for random number generator to 1234
using ../mri/aseg.mgz aseg volume to correct midline
$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
f[113526]->v[1] = 539832625 - out of range!

reading atlas 
from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_kill
iany.2010-03-25.gcs...
reading color table from GCSA file
average std = 1.0   using min determinant for regularization = 0.011
0 singular and 384 ill-conditioned covariance matrices regularized
Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT
2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s qsm1_17 exited with ERRORS at Thu Jun  6 17:01:33 CEST 2013

For more details, see the log file
/root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Any ideas how to fix this?

Bests,
Gabriel
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[Freesurfer] mri_convert

[Ray, Siddharth]

Hi free-surfer folks,

I have some subjects with L-R header flipped in nifti's. Is it possible to flip 
the header using mri_convert so that I can have the right orientation 
information for subjects.

Please let me know.

Thanks,
-Siddharth


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[Freesurfer] The feasibility of this procedure

[淼]

Dear FS,
I want to do an analysis with freesurfer but this is relatively complicated. I 
would like to know whether this is doable by freesurfer.
I first want to create a custom template based on my subjects and I have seen 
the SurfaceRegAndTemplate page and this should be the place where I should 
start.
Then I should use mris_register to register all my subjects to the new template.
Then I want to export volume data of each region of interest and total 
intracranial volume of subjects to SPSS for further analysis and I don't have a 
clue on how to do that yet.
Do you think this is feasible? Any problems there? Thanks for any help in 
advance.
Miao

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Re: [Freesurfer] mri_convert

[Douglas N Greve]

You will be much better off if you can convert properly from DICOM. If 
that is not possible, you can use --left-right-reverse with mri_convert 
to change the header (put not pixel data) or --left-right-reverse-pix to 
change the pixel data (but not head).
doug

On 06/06/2013 12:27 PM, Ray, Siddharth wrote:
>
> Hi free-surfer folks,
>
> I have some subjects with L-R header flipped in nifti’s. Is it 
> possible to flip the header using mri_convert so that I can have the 
> right orientation information for subjects.
>
> Please let me know.
>
> Thanks,
>
> -Siddharth
>
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] The feasibility of this procedure

[Bruce Fischl]

Hi Miao

yes, it should be. Why do you need to create your own template? That makes 
it a lot more complex (and computationally intensive)


cheers
Bruce

On Thu, 6 Jun 2013, 淼 wrote:

Dear FS, I want to do an analysis with freesurfer but this is relatively 
complicated. I would like to know whether this is doable by freesurfer. I 
first want to create a custom template based on my subjects and I have 
seen the SurfaceRegAndTemplate page and this should be the place where I 
should start. Then I should use mris_register to register all my subjects 
to the new template. Then I want to export volume data of each region of 
interest and total intracranial volume of subjects to SPSS for further 
analysis and I don't have a clue on how to do that yet. Do you think this 
is feasible? Any problems there? Thanks for any help in advance. Miao


Sent from my iPhone
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Re: [Freesurfer] Freesurfer Digest, Vol 112, Issue 17

[Douglas N Greve]

> > command. I have a volumetric mask with voxels of interest
> based on a VBM
> > > analysis  in SPM. I would like to extract the cortical
> thickness measurements
> > > based on these voxels.  I am not clear what specifications I
> need to include
> > > when using vol2surf. For example, what do I use as my
> registration matrix?
> > >
> > > Thank you for your help!
> > > Ola
> > >
> > > Ola Ozranov-Palchik M.S.
> > > Research Coordinator, Gaab Lab
> > > Laboratories of Cognitive Neuroscience
> > > Children's Hospital Boston
> > > 1 Autumn Street, Mailbox # 713
> > > Boston, MA 02115
> > > olga.ozra...@childrens.harvard.edu
> <mailto:olga.ozra...@childrens.harvard.edu>
>  <http://childrens.harvard.edu>
> > > phone: (617) 334-5046 
> > > main lab: (617) 355-0400 
> > > fax: (617) 730-0518 
> > >http://www.childrenshospital.org/research/gaablab
> > >
> > >
> > > -Original Message-
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>  <http://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, June 04, 2013 1:48 PM
> > > To:freesurfer@nmr.mgh.harvard.edu
> <mailto:to%3afreesur...@nmr.mgh.harvard.edu>
>  <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > Subject: Re: [Freesurfer] SPM ROI to Cortical Thickness
> > >
> > >
> > > Make sure that your SPM volume is registered to the
> anatomical, then use
> > > mri_vol2surf to map the volume to the surface, then
> mri_segstats to extract
> > > the mean of the thickness
> > >
> > > doug
> > >
> > >
> > >
> > >
> > > On 06/04/2013 01:45 PM, Ozranov-Palchik, Ola wrote:
> > >> main lab: (617) 355-0400 
> > > Dear FreeSurfer Experts,
> > >
> > > I was wondering if anyone can advise on the best way to use an
> ROI mask
> > > created in SPM (XjView) to extract cortical thickness values
> in freesurfer.
> > >
> > > Thank you in advance for your help!
> > >
> > > Ola
> > >
> > > Ola Ozranov-Palchik M.S.
> > > Research Coordinator, Gaab Lab
> > > Laboratories of Cognitive Neuroscience
> > >
> > > Children's Hospital Boston
> > > 1 Autumn Street, Mailbox # 713
> > > Boston, MA 02115
> > > olga.ozra...@childrens.harvard.edu
> <mailto:olga.ozra...@childrens.harvard.edu>
>  <http://childrens.harvard.edu>
> > > <mailto:olga.ozra...@childrens.harvard.edu
> <mailto:olga.ozra...@childrens.harvard.edu>>
> > > phone: (617) 334-5046 
> > > main lab: (617) 355-0400 
> > > fax: (617) 730-0518 
> > >http://www.childrenshospital.org/research/gaablab
> > >
> >
> >
> >
> >
> > Then it goes on:
> >
> > Hi Ola, this probably will not work. The tal coordinate is
> notoriously
> > inaccurate in cortex. You are verylikely to totally miss the
> area you
> > are looking for. A better way is to run the MNI template through
> > recon-all, map your VBM result to the surface of that, then use
> > mri_surf2surf to map the effect to each individual.
> > doug
> >
> >
> > On 06/05/2013 02:58 PM, Ozranov-Palchik, Ola wrote:
> > > Hi Doug,
> > >
> > > Thank you, again! I decided to try to use the Talairach
> coordinates from my
> > > analysis for ROI extraction. I created an average  subject and
> preprocessed
> > > the data (mris_preproc). I obtained the vertex index based on
> the coordinates
> > > from the average subject.  Any ideas on how I can now find the
> corresponding
> > > vertices in all my subjects?
> > >
> > > Thanks very much!
> > > Ola
> > >
> > >
> >
> > --
> > Douglas N. Greve, Ph.D.
&

[Freesurfer] Base Pial Surface Edits

[David Tate]

We have recently run a set of longitudinal data (FreeSurfer5.3) and are making 
edits to the base pial surfaces.  It is clear that there are two different ways 
of doing pial edits including: 1. editing the brainmask.mgz and 2. the 
brain.finalsurfs.mgz.  I recognize that they are specific ways to deal with 
different issues in the surface reconstruction.

My question is will the following command (recon-all -base  
-autorecon2-pial -autorecon3) pick up both edits in the -base rerun 

or

will you need to make the brainmask.mgz edits, rerun the -base recon command 
the make brain.finalsufs.mgz edits, rerun the -base command?

Thanks,

David



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Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

[pablo najt]

HelloMy previous problem seemed to be fixed by reinstalling xquartz.However, 
the strange thing that I get it that I can perfectly run the following and 
display the images.This is what I have done. (commands in yellow)
* setenv FREESURFER_HOME /Applications/freesurfer/* *source 
$FREESURFER_HOME/SetUpFreeSurfer.csh*
 freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Setting 
up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   
/Applications/freesurfer/FSFAST_HOME   
/Applications/freesurfer//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR  
/Applications/freesurfer/subjects/MNI_DIR   
/Applications/freesurfer//mni[Pablo-Najts-MacBook-Pro:/Applications/freesurfer] 
pablonajt% 
* setenv SUBJECTS_DIR /Applications/freesurfer/subjects/*
(After this I am able to run)
*freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v 
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f 
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f 
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red*
2013-06-06 14:07:11.155 Freeview[624:903] invalid drawable2013-06-06 
14:07:11.160 Freeview[624:903] invalid drawable2013-06-06 14:07:11.183 
Freeview[624:903] invalid drawable2013-06-06 14:07:11.186 Freeview[624:903] 
invalid drawable2013-06-06 14:07:11.209 Freeview[624:903] invalid 
drawable2013-06-06 14:07:11.212 Freeview[624:903] invalid drawable2013-06-06 
14:07:11.235 Freeview[624:903] invalid drawable2013-06-06 14:07:11.237 
Freeview[624:903] invalid drawablereading colortable from annotation 
file...colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)colortable
 with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)reading
 colortable from annotation file...colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)colortable
 with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
*However, eerytime I want to open the display I have to repeat all the commands 
(setenv FRESURFER... ; source...; setenv SUBJECTS_DIR)
The other problem is that commands such as qdec, tkmedit bert orig.mgz, give 
"me command not found".
Please let me know if I need to provide you with further information.Many 
thanks,Pablo

> Date: Thu, 6 Jun 2013 13:45:42 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: pablon...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
> 
> 
> Hi Pablo, please respond to the list and not to us directly. Please just 
> cut and paste  the text of the error into the email.
> thanks
> doug
> 
> On 06/06/2013 12:30 PM, pablo najt wrote:
> > Thank you for your quick response. I have re run the installation but 
> > I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer 
> > bert rh pial_ commands.
> > Please see attach for the detailed errors.
> > Best,
> > Pablo
> >
> >
> > > Date: Thu, 6 Jun 2013 12:01:22 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
> > >
> > > what command is not found?
> > > On 06/06/2013 11:58 AM, pablo najt wrote:
> > > > Hello I have a question regarding the installation/running FreeSurfer.
> > > > I have just completed the installation and got the confirmation that
> > > > Free surfer was installed. Please see snapshot.
> > > > However when I follow the steps for testing (*MailScanner has 
> > detected
> > > > a possible fraud attempt from "connect.yale.edu" claiming to be*
> > > > https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
> > > > 
> > ),
> >  
> >
> > > > I always get "command not found". I was wondering if you would be 
> > able
> > > > to help me.
> > > > Thanks,
> > > > Pablo
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > 

[Freesurfer] AR2 Error

[Erin Browning]

Hi everyone--

I emailed the other day about hyperintensity after running motioncor. We've
skipped motioncor in our processing now, but we keep getting this error
while running AR2.

\n mri_ca_register -invert-and-save transforms/talairach.m3z \n
mri passed volume size is different from the one used to create M3D data
Loading, Inverting, Saving, Exiting ...
Reading transforms/talairach.m3z
gunzip -c transforms/talairach.m3z
Inverting GCAM
ERROR: mri_ca_register with non-zero status 0
Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7
16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s freesurfer exited with ERRORS at Wed Jun  5 19:32:56 CDT 2013

I tried rerunning recon-all -s freesurfer -talairach before running AR2,
and that didn't fix the error. What's going wrong?

Thanks,
Erin Browning
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Re: [Freesurfer] AR2 Error

[Douglas N Greve]

Hi Erin, thanks for reposting. Can you post the recon-all.log file?
doug


On 06/06/2013 02:37 PM, Erin Browning wrote:
> Hi everyone--
>
> I emailed the other day about hyperintensity after running motioncor. 
> We've skipped motioncor in our processing now, but we keep getting 
> this error while running AR2.
>
> \n mri_ca_register -invert-and-save transforms/talairach.m3z \n
> mri passed volume size is different from the one used to create M3D data
> Loading, Inverting, Saving, Exiting ...
> Reading transforms/talairach.m3z
> gunzip -c transforms/talairach.m3z
> Inverting GCAM
> ERROR: mri_ca_register with non-zero status 0
> Darwin cerebrum.uwm.edu  10.8.0 Darwin Kernel 
> Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; 
> root:xnu-1504.15.3~1/RELEASE_I386 i386
> recon-all -s freesurfer exited with ERRORS at Wed Jun  5 19:32:56 CDT 2013
>
> I tried rerunning recon-all -s freesurfer -talairach before running 
> AR2, and that didn't fix the error. What's going wrong?
>
> Thanks,
> Erin Browning
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
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http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] AR2 Error

[Erin Browning]

The log file for recon-all is too large. How should I send it?


On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve
wrote:

> Hi Erin, thanks for reposting. Can you post the recon-all.log file?
> doug
>
>
> On 06/06/2013 02:37 PM, Erin Browning wrote:
> > Hi everyone--
> >
> > I emailed the other day about hyperintensity after running motioncor.
> > We've skipped motioncor in our processing now, but we keep getting
> > this error while running AR2.
> >
> > \n mri_ca_register -invert-and-save transforms/talairach.m3z \n
> > mri passed volume size is different from the one used to create M3D data
> > Loading, Inverting, Saving, Exiting ...
> > Reading transforms/talairach.m3z
> > gunzip -c transforms/talairach.m3z
> > Inverting GCAM
> > ERROR: mri_ca_register with non-zero status 0
> > Darwin cerebrum.uwm.edu  10.8.0 Darwin Kernel
> > Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
> > root:xnu-1504.15.3~1/RELEASE_I386 i386
> > recon-all -s freesurfer exited with ERRORS at Wed Jun  5 19:32:56 CDT
> 2013
> >
> > I tried rerunning recon-all -s freesurfer -talairach before running
> > AR2, and that didn't fix the error. What's going wrong?
> >
> > Thanks,
> > Erin Browning
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] AR2 Error

[Erin Browning]

Yes, it was. I tried copy and pasting it and just attaching the log file.
Can I paste urls here? I'll just upload it to pastebin or something like
that.


On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve
wrote:

> That's weird, people upload their recon-all.log files all the time. Was
> the email kicked back to you?
>
> On 06/06/2013 03:27 PM, Erin Browning wrote:
> > The log file for recon-all is too large. How should I send it?
> >
> >
> > On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Erin, thanks for reposting. Can you post the recon-all.log file?
> > doug
> >
> >
> > On 06/06/2013 02:37 PM, Erin Browning wrote:
> > > Hi everyone--
> > >
> > > I emailed the other day about hyperintensity after running
> > motioncor.
> > > We've skipped motioncor in our processing now, but we keep getting
> > > this error while running AR2.
> > >
> > > \n mri_ca_register -invert-and-save transforms/talairach.m3z \n
> > > mri passed volume size is different from the one used to create
> > M3D data
> > > Loading, Inverting, Saving, Exiting ...
> > > Reading transforms/talairach.m3z
> > > gunzip -c transforms/talairach.m3z
> > > Inverting GCAM
> > > ERROR: mri_ca_register with non-zero status 0
> > > Darwin cerebrum.uwm.edu 
> >  10.8.0 Darwin Kernel
> > > Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
> > > root:xnu-1504.15.3~1/RELEASE_I386 i386
> > > recon-all -s freesurfer exited with ERRORS at Wed Jun  5
> > 19:32:56 CDT 2013
> > >
> > > I tried rerunning recon-all -s freesurfer -talairach before running
> > > AR2, and that didn't fix the error. What's going wrong?
> > >
> > > Thanks,
> > > Erin Browning
> > >
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu 
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > Outgoing:
> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > The information in this e-mail is intended only for the person to
> > whom it is
> > addressed. If you believe this e-mail was sent to you in error and
> > the e-mail
> > contains patient information, please contact the Partners
> > Compliance HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to
> > you in error
> > but does not contain patient information, please contact the
> > sender and properly
> > dispose of the e-mail.
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] AR2 Error

[Erin Browning]

Here is the log file.

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9>

Thank you!


On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning  wrote:

> Yes, it was. I tried copy and pasting it and just attaching the log file.
> Can I paste urls here? I'll just upload it to pastebin or something like
> that.
>
>
> On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve  > wrote:
>
>> That's weird, people upload their recon-all.log files all the time. Was
>> the email kicked back to you?
>>
>> On 06/06/2013 03:27 PM, Erin Browning wrote:
>> > The log file for recon-all is too large. How should I send it?
>> >
>> >
>> > On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>> >
>> > Hi Erin, thanks for reposting. Can you post the recon-all.log file?
>> > doug
>> >
>> >
>> > On 06/06/2013 02:37 PM, Erin Browning wrote:
>> > > Hi everyone--
>> > >
>> > > I emailed the other day about hyperintensity after running
>> > motioncor.
>> > > We've skipped motioncor in our processing now, but we keep getting
>> > > this error while running AR2.
>> > >
>> > > \n mri_ca_register -invert-and-save transforms/talairach.m3z \n
>> > > mri passed volume size is different from the one used to create
>> > M3D data
>> > > Loading, Inverting, Saving, Exiting ...
>> > > Reading transforms/talairach.m3z
>> > > gunzip -c transforms/talairach.m3z
>> > > Inverting GCAM
>> > > ERROR: mri_ca_register with non-zero status 0
>> > > Darwin cerebrum.uwm.edu 
>> >  10.8.0 Darwin Kernel
>> > > Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
>> > > root:xnu-1504.15.3~1/RELEASE_I386 i386
>> > > recon-all -s freesurfer exited with ERRORS at Wed Jun  5
>> > 19:32:56 CDT 2013
>> > >
>> > > I tried rerunning recon-all -s freesurfer -talairach before
>> running
>> > > AR2, and that didn't fix the error. What's going wrong?
>> > >
>> > > Thanks,
>> > > Erin Browning
>> > >
>> > >
>> > >
>> > > ___
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu 
>> > Phone Number: 617-724-2358
>> > Fax: 617-726-7422
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > 
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > 
>> > Outgoing:
>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu > Freesurfer@nmr.mgh.harvard.edu>
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to
>> > whom it is
>> > addressed. If you believe this e-mail was sent to you in error and
>> > the e-mail
>> > contains patient information, please contact the Partners
>> > Compliance HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to
>> > you in error
>> > but does not contain patient information, please contact the
>> > sender and properly
>> > dispose of the e-mail.
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not 

Re: [Freesurfer] AR2 Error

[Erin Browning]

Thanks Doug! I'll run it with AR2+AR3 from now on.


On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve
wrote:

>
> OK, this is a known problem when running recon-all with -autorecon1
> -autorecon2 but not autorecon3. If you run it with -autorecon3, then it
> should run all the way through without a problem. Alternatively, I can
> give you a new version of the offending program (mri_segstats) that will
> allow you to use just ar1 and ar2.
>
> doug
>
>
>
>
> On 06/06/2013 03:46 PM, Erin Browning wrote:
> > Here is the log file.
> >
> > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=zrh2oi9>
> >
> > Thank you!
> >
> >
> > On Thu, Jun 6, 2013 at 2:43 PM, Erin Browning  > > wrote:
> >
> > Yes, it was. I tried copy and pasting it and just attaching the
> > log file. Can I paste urls here? I'll just upload it to pastebin
> > or something like that.
> >
> >
> > On Thu, Jun 6, 2013 at 2:38 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>>
> wrote:
> >
> > That's weird, people upload their recon-all.log files all the
> > time. Was
> > the email kicked back to you?
> >
> > On 06/06/2013 03:27 PM, Erin Browning wrote:
> > > The log file for recon-all is too large. How should I send it?
> > >
> > >
> > > On Thu, Jun 6, 2013 at 1:48 PM, Douglas N Greve
> > >  > 
> >  > >> wrote:
> > >
> > > Hi Erin, thanks for reposting. Can you post the
> > recon-all.log file?
> > > doug
> > >
> > >
> > > On 06/06/2013 02:37 PM, Erin Browning wrote:
> > > > Hi everyone--
> > > >
> > > > I emailed the other day about hyperintensity after
> running
> > > motioncor.
> > > > We've skipped motioncor in our processing now, but we
> > keep getting
> > > > this error while running AR2.
> > > >
> > > > \n mri_ca_register -invert-and-save
> > transforms/talairach.m3z \n
> > > > mri passed volume size is different from the one used
> > to create
> > > M3D data
> > > > Loading, Inverting, Saving, Exiting ...
> > > > Reading transforms/talairach.m3z
> > > > gunzip -c transforms/talairach.m3z
> > > > Inverting GCAM
> > > > ERROR: mri_ca_register with non-zero status 0
> > > > Darwin cerebrum.uwm.edu 
> > 
> > >  10.8.0 Darwin Kernel
> > > > Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
> > > > root:xnu-1504.15.3~1/RELEASE_I386 i386
> > > > recon-all -s freesurfer exited with ERRORS at Wed Jun  5
> > > 19:32:56 CDT 2013
> > > >
> > > > I tried rerunning recon-all -s freesurfer -talairach
> > before running
> > > > AR2, and that didn't fix the error. What's going wrong?
> > > >
> > > > Thanks,
> > > > Erin Browning
> > > >
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu 
> >  > >
> > > Phone Number: 617-724-2358
> > > Fax: 617-726-7422
> > >
> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> > > 
> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > 
> > >
> > 
> > > Outgoing:
> > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > 

Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}

[pablo najt]

As suggested, I have modified the .csh file (since the last version does not 
have a .cshrc file).I have edited according with my current directories, but 
when I try
source $FREESURFER_HOME/SetUpFreeSurfer.csh
I get the following:
 freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 Setting 
up environment for FreeSurfer/FS-FAST (and FSL)WARNING: 
/Application/freesurfer//Applications/freesurfer/subjects does not 
existFREESURFER_HOME   /Applications/freesurfer/FSFAST_HOME   
/Applications/freesurfer//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR  
/Application/freesurfer//Applications/freesurfer/subjectsMNI_DIR   
/Applications/freesurfer//mni
The editing I made to the .csh file are the following: 
 setenv FREESURFER_HOME  /usr/local/freesurfer/stable5-pub CHANGED TO:setenv 
FREESURFER_HOME /Applications/freesurfer/endif

setenv SUBJECTS_DIR $FREESURFER_HOME/subjectsendifCHANGED TO:setenv 
SUBJECTS_DIR $FREESURFER_HOME/subjectsendif
Many thanks,Pablo
> Date: Thu, 6 Jun 2013 14:22:07 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
> 
> 
> You will need to put the FreeSurfer environment variables into your 
> .cshrc file to have it be in effect every time you open a new shell.
> doug
> 
> 
> 
> 
> On 06/06/2013 02:14 PM, pablo najt wrote:
> > Hello
> > My previous problem seemed to be fixed by reinstalling xquartz.
> > However, the strange thing that I get it that I can perfectly run the 
> > following and display the images.
> > This is what I have done. (commands in yellow)
> >
> > * setenv FREESURFER_HOME /Applications/freesurfer/*
> > *source $FREESURFER_HOME/SetUpFreeSurfer.csh*
> >
> >  freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME   /Applications/freesurfer/
> > FSFAST_HOME   /Applications/freesurfer//fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR  /Applications/freesurfer/subjects/
> > MNI_DIR   /Applications/freesurfer//mni
> > [Pablo-Najts-MacBook-Pro:/Applications/freesurfer] pablonajt%
> >
> > * setenv SUBJECTS_DIR /Applications/freesurfer/subjects/*
> >
> > (After this I am able to run)
> >
> > *freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v 
> > $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f 
> > $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f 
> > $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f 
> > $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f 
> > $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red*
> >
> > 2013-06-06 14:07:11.155 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.160 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.183 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.186 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.209 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.212 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.235 Freeview[624:903] invalid drawable
> > 2013-06-06 14:07:11.237 Freeview[624:903] invalid drawable
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally 
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > colortable with 36 entries read (originally 
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally 
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> > colortable with 36 entries read (originally 
> > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
> >
> > *However, eerytime I want to open the display I have to repeat all the 
> > commands (setenv FRESURFER... ; source
> > ...; setenv SUBJECTS_DIR)
> >
> > The other problem is that commands such asqdec, tkmedit bert orig.mgz, 
> > give
> > "me command not found".
> >
> > Please let me know if I need to provide you with further information.
> > Many thanks,
> > Pablo
> >
> >
> > > Date: Thu, 6 Jun 2013 13:45:42 -0400
> > > From: gr...@nmr.mgh.harvard.edu
> > > To: pablon...@hotmail.com; Freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
> > >
> > >
> > > Hi Pablo, please respond to the list and not to us directly. Please 
> > just
> > > cut and paste the text of the error into the email.
> > > thanks
> > > doug
> > >
> > > On 06/06/2013 12:30 PM, pablo najt wrote:
> > > > Thank you for your quick response. I have re run the installation but
> > > > I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer
> > > > bert rh pial_ commands.
> > > > Please see attach for the detailed errors.
> > > > Best,
> > > > Pablo
> > > >
> > > >
> > > > > Date: Thu, 6 Jun 2013 12:01:22 -0400
>

Re: [Freesurfer] Still confused by group analysis..

[Tudor Popescu]

Thanks Doug,



> So if I want to use the study-specific "average" subject surface with
>> mri_surf2surf, rather than the generic "fsaverage" one, how can this be
>> done given that the required ls.white file only exists in the latter but
>> not in the former? Can I just rename (or duplicate) ls.white into
>> ls.white_avg?
>>
>>  You can copy it or create a symbolic link.

So it is OK to copy the required lh.white file from the generic average
subject "fsaverage" and apply mri_surf2surf upon the study-specific average
subject ("average")? It still seems to me that "average" should have its
own (different) lh.white...



>
>> Shouldn't the input to mri_glmfit be the output of mri_surf2surf? In the
>> group tutorial, the former is "lh.gender_age.thickness.10.**mgh" while
>> the latter is "lh.gender_age.thickness.10B.**mgh". Or should it just be
>> the unsmoothed output of mris_preproc?
>>
>>  Yes, I can't remember why I put the "B" there, maybe to keep people from
> overwriting  lh.gender_age.thickness.10.mgh during the tutorial and having
> to wait the 10min or so for it to get recreated.

But if all these commands transform the same file (output of mris_preproc
becomes input of mri_surf2surf, which then feeds into mri_glmfit), then why
is it still necessary to keep intact the original
lh.gender_age.thickness.10.mgh, when all you need for the group analysis is
the mri_surf2surf'd version?



>
>> Assuming the label files (corresponding to my ROI, and extracted from the
>> Destrieux atlas) are different for each subject, and given mri_glmfit is
>> called just once, for all subjects, which label file (corresponding to what
>> subject) should I point it to?
>>
>>  You need to create the label in the average subject. There is a
> Destrieux atlas there.

Again, by "average subject" do you mean here the generic one (fsaverage) or
the study-specific one (average)? Should the former be used at any point of
a group analysis, if the latter exists?
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[Freesurfer] field of value too small, wrap-around

[Maria Kharitonova]

Hello,

We have a relatively small FOV in our study because we mostly scan kids. 
Sometimes we scan adults with the same protocol, though, and after looking 
through the adults' reconned brains, I've noticed wrap-around on some brains. 
For one subject it's particularly bad; it affects aparc labels, where the very 
back of the brain gets labeled as orbitofrontal cortex. Is there a way to 
remedy this (other than increasing the FOV for subsequent subjects)? E.g. 
manually relabeling the affected regions? 

I'm pretty new to FreeSurfer, so I apologize in advance if this questions is 
naive.

Thanks!

Maria Kharitonova, Ph.D.
Postdoctoral Research Fellow
Laboratories of Cognitive Neuroscience
Boston Children's Hospital


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[Freesurfer] R: R: Re: R: Re: Tracula

[stdp82]

Hi Anastasia,
I have resolved the previous problem by writing configuration file with sudo 
nano in command line.
Now I'm running trac-all -prep but I have this error:

writing registered surface to 
/Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding
 nbhd size to 1mris_resample: Command not found.
What's happened?
Thanks,

Stefano




Messaggio originale

Da: std...@virgilio.it

Data: 6-giu-2013 0.51

A: 

Cc: 

Ogg: [Freesurfer] R: Re:  R: Re: Tracula



I obtain /Applications/freesurfer/subjects/subject_prova
my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.
Thanks,

Stefano



Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-giu-2013 0.42
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re: Tracula


What do you get when you run "echo $SUBJECTS_DIR"?

On Thu, 6 Jun 2013, std...@virgilio.it wrote:

> Hi Anastasia,
> 
> yes, I have check the SUBJECTS_DIR. I do not understand why all previous
> configuration file start normally and this no.
> Do you note some line that might be wrong additionally to setenv
> SUBJECTS_DIR line.
> 
> 
> Stefano
> 
> 
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-giu-2013 16.09
> A: 
> Cc: 
> Ogg: Re: Tracula
> 
> 
> Is the "setenv SUBJECTS_DIR" line really commented out? You must set
> SUBJECTS_DIR, see the example configuration file on the wiki and under
> $FREESURFER_HOME/bin/dmrirc.example.
> 
> On Wed, 5 Jun 2013, std...@virgilio.it wrote:
> 
> > Hi list and Anastasia,
> > I'm performing a set of data with tracula version 3.0. I have change my
> > dmrirc file respect to previous analyses and now I have one problem 
> >
> > "set: Variable name must begin with a letter.
> > ERROR: must specify as many DWI dicoms as subjects".
> >
> > I do not find the line that is wrong. I think to have approximately used
> the
> > same lines of previous and correct analysis.
> >
> > I have attached the configuration file. Note that I'm using nii.gz.
> >
> > Thanks and best regards.
> >
> >
> > Stefano
> >
> >
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
> 
> 
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Re: [Freesurfer] field of value too small, wrap-around

[Bruce Fischl]

Hi Maria

if the brain wraps from back to front then it can't be recovered. Nothing 
to do with the analysis - the imaging data itself is corrupted.

sorry
Bruce
On Thu, 6 
Jun 2013, Maria Kharitonova wrote:

> Hello,
>
> We have a relatively small FOV in our study because we mostly scan kids. 
> Sometimes we scan adults with the same protocol, though, and after looking 
> through the adults' reconned brains, I've noticed wrap-around on some brains. 
> For one subject it's particularly bad; it affects aparc labels, where the 
> very back of the brain gets labeled as orbitofrontal cortex. Is there a way 
> to remedy this (other than increasing the FOV for subsequent subjects)? E.g. 
> manually relabeling the affected regions?
>
> I'm pretty new to FreeSurfer, so I apologize in advance if this questions is 
> naive.
>
> Thanks!
>
> Maria Kharitonova, Ph.D.
> Postdoctoral Research Fellow
> Laboratories of Cognitive Neuroscience
> Boston Children's Hospital
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] R: R: Re: R: Re: Tracula

[Lilla Zollei]

HI,

A patch is now available for the "mris_resample : Command not found"
error you encountered.

Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample

--Lilla

On Thu, 6 Jun 2013, std...@virgilio.it wrote:


Hi Anastasia,

I have resolved the previous problem by writing configuration file with sudo 
nano in command line.

Now I'm running trac-all -prep but I have this error:


writing registered surface to 
/Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...
expanding nbhd size to 1
mris_resample: Command not found.

What's happened?

Thanks,


Stefano



Messaggio originale
Da: std...@virgilio.it
Data: 6-giu-2013 0.51
A: 
Cc: 
Ogg: [Freesurfer] R: Re: R: Re: Tracula

I obtain /Applications/freesurfer/subjects/subject_prova
my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.

Thanks,


Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-giu-2013 0.42
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re: Tracula


What do you get when you run "echo $SUBJECTS_DIR"?

On Thu, 6 Jun 2013, std...@virgilio.it wrote:

> Hi Anastasia,
>
> yes, I have check the SUBJECTS_DIR. I do not understand why all previous
> configuration file start normally and this no.
> Do you note some line that might be wrong additionally to setenv
> SUBJECTS_DIR line.
>
>
> Stefano
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-giu-2013 16.09
> A: 
> Cc: 
> Ogg: Re: Tracula
>
>
> Is the "setenv SUBJECTS_DIR" line really commented out? You must set
> SUBJECTS_DIR, see the example configuration file on the wiki and under
> $FREESURFER_HOME/bin/dmrirc.example.
>
> On Wed, 5 Jun 2013, std...@virgilio.it wrote:
>
> > Hi list and Anastasia,
> > I'm performing a set of data with tracula version 3.0. I have change my
> > dmrirc file respect to previous analyses and now I have one problem 
> >
> > "set: Variable name must begin with a letter.
> > ERROR: must specify as many DWI dicoms as subjects".
> >
> > I do not find the line that is wrong. I think to have approximately used
> the
> > same lines of previous and correct analysis.
> >
> > I have attached the configuration file. Note that I'm using nii.gz.
> >
> > Thanks and best regards.
> >
> >
> > Stefano
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
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Re: [Freesurfer] R: R: Re: R: Re: Tracula

[Anastasia Yendiki]

This issue has come up on the list a few times recently. Please search for 
your error in the email archives before posting to the list. Thanks.


On Thu, 6 Jun 2013, std...@virgilio.it wrote:


Hi Anastasia,

I have resolved the previous problem by writing configuration file with sudo
nano in command line.

Now I'm running trac-all -prep but I have this error:


writing registered surface 
to/Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_av
g35.sphere.reg...
expanding nbhd size to 1
mris_resample: Command not found.

What's happened?

Thanks,


Stefano



Messaggio originale
Da: std...@virgilio.it
Data: 6-giu-2013 0.51
A: 
Cc: 
Ogg: [Freesurfer] R: Re: R: Re: Tracula

I obtain /Applications/freesurfer/subjects/subject_prova
my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.

Thanks,


Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 6-giu-2013 0.42
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re: Tracula


What do you get when you run "echo $SUBJECTS_DIR"?

On Thu, 6 Jun 2013, std...@virgilio.it wrote:

> Hi Anastasia,
>
> yes, I have check the SUBJECTS_DIR. I do not understand why all previous
> configuration file start normally and this no.
> Do you note some line that might be wrong additionally to setenv
> SUBJECTS_DIR line.
>
>
> Stefano
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 5-giu-2013 16.09
> A: 
> Cc: 
> Ogg: Re: Tracula
>
>
> Is the "setenv SUBJECTS_DIR" line really commented out? You must set
> SUBJECTS_DIR, see the example configuration file on the wiki and under
> $FREESURFER_HOME/bin/dmrirc.example.
>
> On Wed, 5 Jun 2013, std...@virgilio.it wrote:
>
> > Hi list and Anastasia,
> > I'm performing a set of data with tracula version 3.0. I have change my
> > dmrirc file respect to previous analyses and now I have one problem 
> >
> > "set: Variable name must begin with a letter.
> > ERROR: must specify as many DWI dicoms as subjects".
> >
> > I do not find the line that is wrong. I think to have approximately used
> the
> > same lines of previous and correct analysis.
> >
> > I have attached the configuration file. Note that I'm using nii.gz.
> >
> > Thanks and best regards.
> >
> >
> > Stefano
> >
> >
>
>
> The information in this e-mail is intended only for the person to whom it
is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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but does not contain patient information, please contact the sender and
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dispose of the e-mail.





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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] field of value too small, wrap-around

[Caspar M. Schwiedrzik]

Hi Maria,
if the warp around is such that the wrapped part of the brain ends up
outside the brain but on the other side of the FOV, you can maybe fix it
partially (e.g., if the frontal cortex is wrapped to the back but not into
the occipital cortex). You would just need to copy the respective rows from
the back to the front of the image before any processing of the data (use
MRIread in Matlab). However, the data will be unreliable; this may only
help with alignment of images etc., but I wouldn't try to analyze the data
in any way.
Caspar

2013/6/6 Bruce Fischl 

> Hi Maria
>
> if the brain wraps from back to front then it can't be recovered. Nothing
> to do with the analysis - the imaging data itself is corrupted.
>
> sorry
> Bruce
> On Thu, 6
> Jun 2013, Maria Kharitonova wrote:
>
> > Hello,
> >
> > We have a relatively small FOV in our study because we mostly scan kids.
> Sometimes we scan adults with the same protocol, though, and after looking
> through the adults' reconned brains, I've noticed wrap-around on some
> brains. For one subject it's particularly bad; it affects aparc labels,
> where the very back of the brain gets labeled as orbitofrontal cortex. Is
> there a way to remedy this (other than increasing the FOV for subsequent
> subjects)? E.g. manually relabeling the affected regions?
> >
> > I'm pretty new to FreeSurfer, so I apologize in advance if this
> questions is naive.
> >
> > Thanks!
> >
> > Maria Kharitonova, Ph.D.
> > Postdoctoral Research Fellow
> > Laboratories of Cognitive Neuroscience
> > Boston Children's Hospital
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] Yeo_JNeurophysiol11_FreeSurfer.zip

[Peter Savadjiev]

Hello,

I'm trying to download

ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip

(as linked from 
http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011),

however, the file doesn't seem to be available, or the server is not 
responsive.

Is there another location from where I could download this file?

Thank you,

Peter
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[Freesurfer] R: Re: R: R: Re: R: Re: Tracula

[stdp82]

The file that I have downloaded is named "unKnow" and it is of 7.6 MB.
I have placed it in $FREESURFER_HOME/bin directory but the error persist.
Anastasia, I apologize. Please, have patience with me :-)
but .. when I search for "mris_resample" in mail list I did not found any 
indication.
I found my previous mail and first Zeke response.
Thanks,

Stefano





Messaggio originale
Da: lzol...@nmr.mgh.harvard.edu
Data: 6-giu-2013 23.20
A: 
Cc: 
Ogg: Re: [Freesurfer] R:  R: Re:  R: Re: Tracula


HI,

A patch is now available for the "mris_resample : Command not found"
error you encountered.

Simply download the file from the following link and place it in your
$FREESURFER_HOME/bin directory:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample

--Lilla

On Thu, 6 Jun 2013, std...@virgilio.it wrote:

> Hi Anastasia,
> 
> I have resolved the previous problem by writing configuration file with sudo 
> nano in command line.
> 
> Now I'm running trac-all -prep but I have this error:
> 
> 
> writing registered surface to 
> /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...
> expanding nbhd size to 1
> mris_resample: Command not found.
> 
> What's happened?
> 
> Thanks,
> 
> 
> Stefano
> 
> 
> 
> Messaggio originale
> Da: std...@virgilio.it
> Data: 6-giu-2013 0.51
> A: 
> Cc: 
> Ogg: [Freesurfer] R: Re: R: Re: Tracula
> 
> I obtain /Applications/freesurfer/subjects/subject_prova
> my DWI file is in Diff01, Diff02 ... that are in subject_prova folder.
> 
> Thanks,
> 
> 
> Stefano
> 
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 6-giu-2013 0.42
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re: Tracula
> 
> 
> What do you get when you run "echo $SUBJECTS_DIR"?
> 
> On Thu, 6 Jun 2013, std...@virgilio.it wrote:
> 
> > Hi Anastasia,
> >
> > yes, I have check the SUBJECTS_DIR. I do not understand why all previous
> > configuration file start normally and this no.
> > Do you note some line that might be wrong additionally to setenv
> > SUBJECTS_DIR line.
> >
> >
> > Stefano
> >
> >
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 5-giu-2013 16.09
> > A: 
> > Cc: 
> > Ogg: Re: Tracula
> >
> >
> > Is the "setenv SUBJECTS_DIR" line really commented out? You must set
> > SUBJECTS_DIR, see the example configuration file on the wiki and under
> > $FREESURFER_HOME/bin/dmrirc.example.
> >
> > On Wed, 5 Jun 2013, std...@virgilio.it wrote:
> >
> > > Hi list and Anastasia,
> > > I'm performing a set of data with tracula version 3.0. I have change my
> > > dmrirc file respect to previous analyses and now I have one problem 
> > >
> > > "set: Variable name must begin with a letter.
> > > ERROR: must specify as many DWI dicoms as subjects".
> > >
> > > I do not find the line that is wrong. I think to have approximately used
> > the
> > > same lines of previous and correct analysis.
> > >
> > > I have attached the configuration file. Note that I'm using nii.gz.
> > >
> > > Thanks and best regards.
> > >
> > >
> > > Stefano
> > >
> > >
> >
> >
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