[Freesurfer] FW: [All] Postdoctoral position at the Multicultural Alzheimer's Prevention Program

[Fischl, Bruce]

Contact Dr. Quiroz If you are interested in the postdoc opportunity below

Bruce

From: all-boun...@nmr.mgh.harvard.edu  On 
Behalf Of Quiroz, Yakeel T.,Ph.D.
Sent: Tuesday, June 1, 2021 8:44 PM
To: a...@nmr.mgh.harvard.edu
Subject: [All] Postdoctoral position at the Multicultural Alzheimer's 
Prevention Program

Dear all,

I hope everyone is doing well,

I recently received another grant to use multimodal imaging and biomarkers to 
study cognitive decline in older Latinos, and I'm currently looking to recruit 
1-2 postdoctoral fellows to join my group.

I'd appreciate any help sharing this info with your colleagues!

Any interested parties can contact me directly,

Thanks in advance for the help!


Yakeel T. Quiroz, PhD

Associate Professor | Harvard Medical School

MGH Research Scholar | Massachusetts General Hospital

Departments of Psychiatry and Neurology

Director, Familial Dementia Neuroimaging Lab

Director, Multicultural Alzheimer's Prevention Program-MAPP

Email: yqui...@mgh.harvard.edu

Phone: (617) 643-5944

@ytquiroz
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Re: [Freesurfer] mris_fix_topology taking ages

[Fischl, Bruce]

Or the ?h.inflated.nofix can be helpful as well

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, June 1, 2021 5:57 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_fix_topology taking ages

I mean mris_fix_topology. Try loading the ?h.smoothwm.nofix in surface viewing 
(not in the volume). You can often see defects better on this surface (they 
look likes holes or handles; you should at least see some)
On 6/1/2021 4:55 PM, Ellen Ji wrote:

External Email - Use Caution
Hi Doug, when you say it did not finish, could you clarify what process "it" 
refers to?
I loaded the files you suggested and nothing popped out to me aside from the 
fact that the wm.mgz didn't seem to cover all the white matter.
Is it possible that topology error labels don't necessarily suggest that 
something went wrong and I can trust the results?
Thanks.
On 6/1/2021 2:51 AM, Douglas N. Greve wrote:
The topology error labels might be be created if it did not finish. YOu can try 
just loading the brain.mgz, the wm.mgz, and the orig.nofix and see if you can 
find a big topo error
On 5/31/2021 11:16 AM, Ellen Ji wrote:
   External Email - Use Caution
Dear experts,

mris_fix_topology has been running for several hours now and the log suggests 
many more defects than normal. I tried to follow Bruce's advice from the thread 
here 
https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html,
 but wasn't able to load the _labels as I received the error below.

Attached is part of the recon-all.log (starting from mris_fix_topology). Is 
there any other way to check/visualize what might have gone wrong?
FYI, I'm running recon-all thru the HCP Pipeline. Thanks!

tksurfer avoss_01 lh defect_labels

subject is avoss_01
hemiis lh
surface is defect_labels
surfer: current subjects dir: 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf
checking for nofix files in 'defect_labels'
Reading image info 
(/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01)
Reading 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
surfer: Reading header info from 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
nquads=4063237,  nvertices=664
ERROR: MRISread: file 
'/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels'
 has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

No such file or directory



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Re: [Freesurfer] Freesurfer- subcortical group analysis

[Douglas N. Greve]

Not easily. You can do something in matlab, eg,

aseg = MRIread('fsaverage/mri/aseg.mgz');
out = aseg;
out.vol = zeros(out.volsize);
ind = find(aseg.vol==17); % 17 = left hippo
out.vol(ind) = YourValueForLeftHippoFromTheGLMAnalysis;
% same thing for other ROIs
MRIwrite(out,'sig.aseg.mgz');
Then visualize on the fsaverage volume


On 6/1/2021 6:14 PM, Francisca Ferreira wrote:


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I see, thanks. Is there a way in Freesurfer to obtain a visual 
representation of these results-  like in other modalities of group 
analysis? (eg. surface based)


Many thanks

On Tue, 1 Jun 2021 at 17:44, Douglas N. Greve > wrote:


There are not results to visualize, there is just a table. There
should be a sig table in the output folder

On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote:


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So so sorry to bother you again - hopefully the last time...

I have followed your suggestion and that has worked, having used
this command

mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd
dods \--C groupdiff.mtx \--glmdir aseg.glmdir

I am now trying to visualise the results according to FSwiki,
used this command

freeview -f

/usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50
-viewport 3d

I get the following error

ERROR: reading /usr/local/freesurfer/subjects
Read 0 bytes, expected 1
Read 0 bytes, expected 1
/freesurfer/subjects
MRISread failed

I wonder is this means there is something wrong with the GLM I
created or if it is something wrong with my Freeview?

Thanks a lot in advance!
Kind regards,
Francisca


*From:* Douglas N. Greve 

*Sent:* 27 May 2021 21:05
*To:* Aldinhas De Freitas Ferreira, Francisca


*Subject:* Re: Freesurfer- subcortical group analysis
Hi Francisca, if you run asegstats2table on your group to create
a group table (subjects on the rows, structures on the columns,
each element being the structure volume for that subject), then
you can use mri_glmfit with the --table option (instead of --y).
You may want to correct for intracranial volume by adding --etiv
to the asegstats2table command.
doug


On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote:


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Dear Dr Greve,

My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging
PhD student at the FIL in UCL. I have recently contacted Eugenio
Iglesias, who kindly pointed me in your direction. Sorry to
bother you, I have been working with Freesurfer and I was hoping
you would kindly give me your opinion?

I am looking to compare responders vs non responders to deep
brain stimulation of a subcortical structure called ventral
tegmental area. I ran recon-all, and thought Freesurfer could be
useful for this task as it now has a brainstem segmenting module
that I’ve installed.

I thought I could use brainstem or subcortical volumes/surfaces
to do the glm group analysis? (in my case regressing out age and
gender). It seems that all the options i found on mri_glm only
allow surface-based analysis? (the flags available being - -
cortex or - -non-cortex) is there any way around this?

I am sorry for any lack of background knowledge- which stems
from the fact that I am primarily a clinician...
I’d be most grateful for any suggestions!

Kind regards,
Francisca


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Re: [Freesurfer] Freesurfer- subcortical group analysis

[Francisca Ferreira]

External Email - Use Caution

I see, thanks. Is there a way in Freesurfer to obtain a visual
representation of these results-  like in other modalities of group
analysis? (eg. surface based)

Many thanks

On Tue, 1 Jun 2021 at 17:44, Douglas N. Greve 
wrote:

> There are not results to visualize, there is just a table. There should be
> a sig table in the output folder
>
> On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
>
> External Email - Use Caution
> So so sorry to bother you again - hopefully the last time...
>
> I have followed your suggestion and that has worked, having used this
> command
>
> mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd dods \--C
> groupdiff.mtx \--glmdir aseg.glmdir
>
> I am now trying to visualise the results according to FSwiki, used this
> command
>
> freeview -f
> /usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50
> -viewport 3d
>
> I get the following error
>
> ERROR: reading /usr/local/freesurfer/subjects
> Read 0 bytes, expected 1
> Read 0 bytes, expected 1
> /freesurfer/subjects
> MRISread failed
>
> I wonder is this means there is something wrong with the GLM I created or
> if it is something wrong with my Freeview?
>
> Thanks a lot in advance!
> Kind regards,
> Francisca
>
> --
> *From:* Douglas N. Greve  
> *Sent:* 27 May 2021 21:05
> *To:* Aldinhas De Freitas Ferreira, Francisca
>  
> *Subject:* Re: Freesurfer- subcortical group analysis
>
> Hi Francisca, if you run asegstats2table on your group to create a group
> table (subjects on the rows, structures on the columns, each element being
> the structure volume for that subject), then you can use mri_glmfit with
> the --table option (instead of --y). You may want to correct for
> intracranial volume by adding --etiv to the asegstats2table command.
> doug
>
>
> On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote:
>
> External Email - Use Caution
> Dear Dr Greve,
>
> My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging PhD
> student at the FIL in UCL. I have recently contacted Eugenio Iglesias, who
> kindly pointed me in your direction. Sorry to bother you, I have been
> working with Freesurfer and I was hoping you would kindly give me your
> opinion?
>
> I am looking to compare responders vs non responders to deep brain
> stimulation of a subcortical structure called ventral tegmental area. I ran
> recon-all, and thought Freesurfer could be useful for this task as it now
> has a brainstem segmenting module that I’ve installed.
>
> I thought I could use brainstem or subcortical volumes/surfaces to do the
> glm group analysis? (in my case regressing out age and gender). It seems
> that all the options i found on mri_glm only allow surface-based analysis?
> (the flags available being - - cortex or - -non-cortex) is there any way
> around this?
>
> I am sorry for any lack of background knowledge- which stems from the fact
> that I am primarily a clinician...
> I’d be most grateful for any suggestions!
>
> Kind regards,
> Francisca
>
>
> 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 Mass General
> Brigham Compliance HelpLine at
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> 

Re: [Freesurfer] recon-all errors

[Douglas N. Greve]

OK, I'll have to take a look at the data. Someone will be in touch about 
getting it.



On 6/1/2021 11:02 AM, Mark Wagshul wrote:


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External Email - Use Caution

It works fine in 6.0, was in 7.1. The registration looks fine (the 
FLAIR is brain extracted, while the orig.mgz is not, is this expected, 
or was that my error, I don’t recall which FLAIR image I fed in).


Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email:_mark.wags...@einsteinmed.org _

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*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *Douglas N. Greve

*Sent:* Thursday, May 27, 2021 6:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta 
--targ orig.mgz



On 5/20/2021 4:33 PM, Mark Wagshul wrote:

*External Email - Use Caution *

*External Email - Use Caution *

Hi. I’m trying to run recon-all, with T1 and FLAIR images and
running into errors, which seem to be associated with the FLAIR
refinement of the pial surface.

recon-all -s 2019-10049-045-SP –FLAIR
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz
-FLAIRpial -all

1.Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2.cat /proc/version:  Linux version
2.6.32-696.6.3.el6.694g.x86_64
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur
) (gcc
version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul
12 02:19:57 UTC 2017

3.uname –a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1
SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email:_mark.wags...@einsteinmed.org
_

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Re: [Freesurfer] mris_fix_topology taking ages

[Douglas N. Greve]

I mean mris_fix_topology. Try loading the ?h.smoothwm.nofix in surface 
viewing (not in the volume). You can often see defects better on this 
surface (they look likes holes or handles; you should at least see some)


On 6/1/2021 4:55 PM, Ellen Ji wrote:


External Email - Use Caution

Hi Doug, when you say it did not finish, could you clarify what 
process "it" refers to?
I loaded the files you suggested and nothing popped out to me aside 
from the fact that the wm.mgz didn't seem to cover all the white matter.
Is it possible that topology error labels don't necessarily suggest 
that something went wrong and I can trust the results?

Thanks.

On 6/1/2021 2:51 AM, Douglas N. Greve wrote:
The topology error labels might be be created if it did not finish. 
YOu can try just loading the brain.mgz, the wm.mgz, and the 
orig.nofix and see if you can find a big topo error


On 5/31/2021 11:16 AM, Ellen Ji wrote:

External Email - Use Caution
Dear experts,

mris_fix_topology has been running for several hours now and the log 
suggests many more defects than normal. I tried to follow Bruce's 
advice from the thread here 
https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html, 
but wasn't able to load the _labels as I received the error 
below.


Attached is part of the recon-all.log (starting from 
mris_fix_topology). Is there any other way to check/visualize what 
might have gone wrong?

FYI, I'm running recon-all thru the HCP Pipeline. Thanks!

tksurfer avoss_01 lh defect_labels

subject is avoss_01
hemi    is lh
surface is defect_labels
surfer: current subjects dir: 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w

surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: 
/mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf

checking for nofix files in 'defect_labels'
Reading image info 
(/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01)
Reading 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
surfer: Reading header info from 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz

nquads=4063237,  nvertices=664
ERROR: MRISread: file 
'/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' 
has many more faces than vertices!

Probably trying to use a scalar data file as a surface!

No such file or directory

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Re: [Freesurfer] PVC to calculate myelin maps

[Douglas N. Greve]

On 6/1/2021 10:19 AM, Marina Fernández wrote:


External Email - Use Caution

Thank you very much for your response Doug.

What PVC method is most recommended to use to calculate the T1 / T2 
ratio (RBV or MG)?
I've never done it before. I usually use MG (this will only work for 
gray matter). If you need white matter, then RBV I guess.


And what value of PSF should we specify to calculate this ratio? To my 
knowledge, this is an acquisition related parameter and if I set it to 
0 I will turn off PVC.
Yes, set psf to 0. It will still correct for the tissue fraction effect 
(unless you also add --no-tfe).



Best wishes,
Marina.


%%

Douglas N. Greve 
 
Mon, 31 May 2021 17:39:23 -0700 



Yes, you can use PETsurfer. I would apply it to the ratio
On 5/28/2021 10:25 AM, Marina Fernández wrote:

 External Email - Use Caution

Dear experts,

I want to calculate myelin maps using the ratio of T1w and T2w MRI
images. I saw that the correction of partial volume effects can be
used to create the maps (Shafee, Buckner & Fischl, 2015)*.Can I
use the PVC functions of PetSurfer for this purpose? And in case I
can:

Should I apply PVC only on T1? Or also in T2?

Which T1 should I use? The original T1 or the T1 with corrections
(for example, the nu.mgz file that is corrected for variations in
intensity)?

Any other advice for calculating myelin maps would be welcome.

Thank you in advance,

Marina


*Link:

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>



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Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[Douglas N. Greve]

Actually, I think I see what the problem is. You apparently have a 
command called "bc" in your path. mri_nu_correct.mni is trying to use 
the linux-native bc command (a simple calculator usually located in 
/bin). What do you get when you run

which bc


On 6/1/2021 9:59 AM, liub wrote:


External Email - Use Caution

Thank you for your help !


I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log


and got the nucor.log.



-原始邮件-
*发件人:*"Douglas N. Greve" 
*发送时间:*2021-06-01 08:35:38 (星期二)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Re: [Freesurfer] Recon-all error :Segmentation fault (core
dumped)

Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log




On 5/28/2021 7:51 AM, liub wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to recon-all my NIfTI-1 data ,while after a few
minutes of running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped)

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the
official data in */freesurfer/subjects/bert ,it raised the same
error. I googled this error,but there's still no answer.I've
attached the recon-all.log. The recon-all.log is belong to bert
and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP
Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1

Thank you for your kind help.

Best regards.


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Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[Douglas N. Greve]

What happens when you run the following two commands?
echo 5/6 | bc -l

echo "5/6" | bc -l


On 6/1/2021 9:59 AM, liub wrote:


External Email - Use Caution

Thank you for your help !


I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log


and got the nucor.log.



-原始邮件-
*发件人:*"Douglas N. Greve" 
*发送时间:*2021-06-01 08:35:38 (星期二)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Re: [Freesurfer] Recon-all error :Segmentation fault (core
dumped)

Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log




On 5/28/2021 7:51 AM, liub wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to recon-all my NIfTI-1 data ,while after a few
minutes of running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped)

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the
official data in */freesurfer/subjects/bert ,it raised the same
error. I googled this error,but there's still no answer.I've
attached the recon-all.log. The recon-all.log is belong to bert
and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP
Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1

Thank you for your kind help.

Best regards.


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Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

[Douglas N. Greve]

look at the tutorial

On 6/1/2021 12:00 AM, Diógenes Bispo wrote:


External Email - Use Caution

I would like to know what other modification I should make to my 
script to run --grf (volume analysis):


- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??

Thanks.

Diogenes Bispo
diogenesdi...@gmail.com 



Em sáb., 29 de mai. de 2021 às 03:14, Diógenes Bispo 
mailto:diogenesdi...@gmail.com>> escreveu:


Hi Freesurfer team.

I made the following command:

#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
  foreach smoothing (10)
    foreach meas (volume)
        mris_preproc --fsgd FSGD/{$study}.fsgd \
          --cache-in {$meas}.fwhm{$smoothing}.fsaverage \
          --target fsaverage \
          --hemi {$hemi} \
          --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
    end
  end
end

#!/bin/tcsh
set study = $argv[1]
foreach hemi (lh rh)
  foreach smoothness (10)
    foreach meas (volume)
        mri_glmfit \
        --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
        --fsgd FSGD/{$study}.fsgd dods \
        --C Contrasts/Contrast-1_group.diff.mtx \
        --C Contrasts/Contrast-2_group-x-age.mtx \
        --C Contrasts/Contrast-3_group-x-icv.mtx \
        --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
        --C Contrasts/Contrast-5_GCCV.intercept.mtx \
        --C Contrasts/Contrast-6_GCCV.age.mtx \
        --surf fsaverage {$hemi}  \
        --cortex  \
        --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
        --eres-save
    end
  end
end

#!/bin/tcsh
setenv study $argv[1]
foreach meas (volume)
  foreach hemi (lh rh)
    foreach smoothness (10)
      foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
          mri_glmfit-sim \
          --glmdir {$dir} \
          --grf 2.0 neg \
          --cwp 0.05  \
          --2spaces \
      end
    end
  end
end

I have the following error:
...

mri_surfcluster --in
rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask
rh.volume.covid.10.glmdir/mask.mgh --cwsig

rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh
--sum

rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary
--ocn
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh
--no-fixmni --csd-out
rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd
--fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign
neg --oannot
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot
--bonferroni 2 --surf white

ERROR: need --csd with --csd-out


How should I proceed to solve this problem?

Thanks

Diógenes Bispo
diogenesdi...@gmail.com 


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Re: [Freesurfer] mris_fix_topology taking ages

[Ellen Ji]

   External Email - Use Caution

Hi Doug, when you say it did not finish, could you clarify what process 
"it" refers to?
I loaded the files you suggested and nothing popped out to me aside from 
the fact that the wm.mgz didn't seem to cover all the white matter.
Is it possible that topology error labels don't necessarily suggest that 
something went wrong and I can trust the results?

Thanks.

On 6/1/2021 2:51 AM, Douglas N. Greve wrote:
The topology error labels might be be created if it did not finish. 
YOu can try just loading the brain.mgz, the wm.mgz, and the orig.nofix 
and see if you can find a big topo error


On 5/31/2021 11:16 AM, Ellen Ji wrote:

External Email - Use Caution
Dear experts,

mris_fix_topology has been running for several hours now and the log 
suggests many more defects than normal. I tried to follow Bruce's 
advice from the thread here 
https://secure-web.cisco.com/11N_pSFTUOEZsMU7wtMNfIhMmRNWqmvsxTQeTGxdl-E3X_FJ9XkuZNLzTomdCZZwiiC6gS9oiXPNWh-M2KVbb9fP-1Qt7J-woH5hdLFg1otls4745ZoOKkz_-HOcFhenNfrq2-hdM_aX4I_g63u4rUe-NJLArGfWzCA77LLGm4lm0GK5kbCLf4Y6EqC9wHUUa-pdXC-7yMwNoi3Ips7HILVXXSdMEYlu_BPlUFIyI78yqCt3CSo6lAnlXS7QmRQY6JMl9WsV56bEMNqz44Bdlkw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg03182.html, 
but wasn't able to load the _labels as I received the error 
below.


Attached is part of the recon-all.log (starting from 
mris_fix_topology). Is there any other way to check/visualize what 
might have gone wrong?

FYI, I'm running recon-all thru the HCP Pipeline. Thanks!

tksurfer avoss_01 lh defect_labels

subject is avoss_01
hemi    is lh
surface is defect_labels
surfer: current subjects dir: 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w

surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: 
/mnt/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf

checking for nofix files in 'defect_labels'
Reading image info 
(/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01)
Reading 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz
surfer: Reading header info from 
/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/mri/orig.mgz

nquads=4063237,  nvertices=664
ERROR: MRISread: file 
'/home/eji/newdata/projects/avoss/HCP/subjects/avoss_01/T1w/avoss_01/surf/lh.defect_labels' 
has many more faces than vertices!

Probably trying to use a scalar data file as a surface!

No such file or directory

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[Freesurfer] OHBM Brainhack 2021

[tibor.auer]

External Email - Use Caution

Dear all,

 

We are happy to announce the upcoming Organization for Human Brain Mapping
(OHBM) Brainhack 2021 happening June 16-18 around the clock around the
world! Join the party by registering here
  ($25
fee, or optional fee waiver; check out some project proposals here

 ).

 

We are also looking for volunteers to help spread the word and facilitate
Brainhack activities. We'd like to recruit around 100 volunteers-so any
contribution is more than welcome, no prerequisites needed! Volunteer by
filling out this form 

  (more
information about volunteer roles here
 ).

 

About Brainhack:

Brainhacks 

  (including OHBM Brainhack

 ) are events promoting
interdisciplinary neuroscience research; they bring researchers together
from a variety of subfields (e.g., neurobiology, psychology, computer
science, etc.) and research backgrounds (e.g., medical student, industry
professional, RA, etc.) to collaborate on projects and ideas and teach open
science-oriented technical skills. The focus on intensive community- and
skill-building opens doors to a number of professional opportunities (learn
more about these benefits here

 ).
Brainhacks are not your typical hackathon-they are actively inclusive rather
than competitive. To that end, even if you have never attended a hackathon
before or written a line of code, you are welcome! No need to work with
neuroimaging methods or be part of OHBM to attend. All you need is to come
along and share your ideas, expertise, contributions with whatever pace and
form you can make it happen while having a chance to collaborate and meet
with many other researchers all around the world!  

 

We particularly welcome the contributions of groups traditionally
underrepresented in neuroscience, including women, BIPOC, LGBTQ+,
individuals with disabilities, and more. Brainhacks are safe spaces, with a
policy of zero tolerance for harassment. OHBM Brainhack 2021 is intended for
everyone to feel safe, learn from each other and share knowledge. Our event
would be enriched by your involvement and contributions. To support our
mission, please share this widely-we'd especially love your help translating
and sharing this message in your local language to reach as many people
around the world as we can! Events will take place across 

Re: [Freesurfer] Freesurfer- subcortical group analysis

[Douglas N. Greve]

There are not results to visualize, there is just a table. There should 
be a sig table in the output folder


On 5/28/2021 9:37 AM, Aldinhas De Freitas Ferreira, Francisca wrote:


External Email - Use Caution

So so sorry to bother you again - hopefully the last time...

I have followed your suggestion and that has worked, having used this 
command


mri_glmfit \--table aseg_stats.txt \--fsgd newCH_deblank3.fsgd dods 
\--C groupdiff.mtx \--glmdir aseg.glmdir


I am now trying to visualise the results according to FSwiki, used 
this command


freeview -f 
/usr/local/freesurfer/subjects:annot=aparc.annot:annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/F.mgh:overlay_threshold=20,50 
-viewport 3d


I get the following error

ERROR: reading /usr/local/freesurfer/subjects
Read 0 bytes, expected 1
Read 0 bytes, expected 1
/freesurfer/subjects
MRISread failed

I wonder is this means there is something wrong with the GLM I created 
or if it is something wrong with my Freeview?


Thanks a lot in advance!
Kind regards,
Francisca


*From:* Douglas N. Greve 
*Sent:* 27 May 2021 21:05
*To:* Aldinhas De Freitas Ferreira, Francisca 


*Subject:* Re: Freesurfer- subcortical group analysis
Hi Francisca, if you run asegstats2table on your group to create a 
group table (subjects on the rows, structures on the columns, each 
element being the structure volume for that subject), then you can use 
mri_glmfit with the --table option (instead of --y). You may want to 
correct for intracranial volume by adding --etiv to the 
asegstats2table command.

doug


On 5/27/2021 7:13 AM, Aldinhas De Freitas Ferreira, Francisca wrote:


External Email - Use Caution

Dear Dr Greve,

My name is Francisca Ferreira, I am a neurosurgeon/neuroimaging PhD 
student at the FIL in UCL. I have recently contacted Eugenio 
Iglesias, who kindly pointed me in your direction. Sorry to bother 
you, I have been working with Freesurfer and I was hoping you would 
kindly give me your opinion?


I am looking to compare responders vs non responders to deep brain 
stimulation of a subcortical structure called ventral tegmental area. 
I ran recon-all, and thought Freesurfer could be useful for this task 
as it now has a brainstem segmenting module that I’ve installed.


I thought I could use brainstem or subcortical volumes/surfaces to do 
the glm group analysis? (in my case regressing out age and gender). 
It seems that all the options i found on mri_glm only allow 
surface-based analysis? (the flags available being - - cortex or - 
-non-cortex) is there any way around this?


I am sorry for any lack of background knowledge- which stems from the 
fact that I am primarily a clinician...

I’d be most grateful for any suggestions!

Kind regards,
Francisca


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Re: [Freesurfer] recon-all errors

[Mark Wagshul]

External Email - Use Caution

It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is 
brain extracted, while the orig.mgz is not, is this expected, or was that my 
error, I don't recall which FLAIR image I fed in).

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

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This email message and any accompanying attachments may contain privileged 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz


On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


1.   Freesurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

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Re: [Freesurfer] PVC to calculate myelin maps

[Marina Fernández]

External Email - Use Caution

Thank you very much for your response Doug.

What PVC method is most recommended to use to calculate the T1 / T2 ratio
(RBV or MG)?
And what value of PSF should we specify to calculate this ratio? To my
knowledge, this is an acquisition related parameter and if I set it to 0 I
will turn off PVC.


Best wishes,
Marina.


%%

Douglas N. Greve

 Mon, 31 May 2021 17:39:23 -0700


Yes, you can use PETsurfer. I would apply it to the ratio


On 5/28/2021 10:25 AM, Marina Fernández wrote:

External Email - Use Caution

Dear experts,


I want to calculate myelin maps using the ratio of T1w and T2w MRI images.
I saw that the correction of partial volume effects can be used to create
the maps (Shafee, Buckner & Fischl, 2015)*.

Can I use the PVC functions of PetSurfer for this purpose? And in case I
can:

Should I apply PVC only on T1? Or also in T2?


Which T1 should I use? The original T1 or the T1 with corrections (for example,
the nu.mgz file that is corrected for variations in intensity)?

Any other advice for calculating myelin maps would be welcome.

Thank you in advance,

Marina


*Link:


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Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

[liub]

External Email - Use Caution

Thank you for your help !





I have run the command:

mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log

and got the nucor.log.







-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2021-06-01 08:35:38 (星期二)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Recon-all error :Segmentation fault (core dumped)

Not sure, can you try this
cd /home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
mri_nu_correct.mni --debug --i orig.mgz --o nu.mgz --uchar 
transforms/talairach.xfm --n 2 --ants-n4 >& nucor.log
and send the file nucor.log





On 5/28/2021 7:51 AM, liub wrote:


External Email - Use Caution

Hello FreeSurfer Developers,




I'm attempting to recon-all my NIfTI-1 data ,while after a few minutes of 
running,there was an error:

mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz 
/dev/shm/tmp.mri_nu_correct.mni.897826/nu0.mgz mul

Segmentation fault (core dumped) 

Command exited with non-zero status 1

Also when I ran the command "recon-all -all -s bert" using the official data in 
*/freesurfer/subjects/bert ,it raised the same error. I googled this error,but 
there's still no answer.I've attached the recon-all.log. The recon-all.log is 
belong to bert and recon-all(1).log is belong to my data.

Here is my operating system info :

uname -a: Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 
00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Platform: CentOS Linux release 8.3.2011

FreeSurfer version: freesurfer-Linux-centos8_x86_64-7.1.1




Thank you for your kind help.




Best regards.



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set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 9 != 0 )

set flag = $argv[1] ; shift ;
set flag = --i
shift

switch ( $flag )
switch ( --i )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
set InVol = $argv[1] ; shift ;
set InVol = orig.mgz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 7 != 0 )

set flag = $argv[1] ; shift ;
set flag = --o
shift

switch ( $flag )
switch ( --o )
if ( $#argv == 0 ) goto arg1err ;
if ( 6 == 0 ) goto arg1err
set OutVol = $argv[1] ; shift ;
set OutVol = nu.mgz
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;
set flag = --uchar
shift

switch ( $flag )
switch ( --uchar )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set talxfm = $argv[1] ; shift ;
set talxfm = transforms/talairach.xfm
shift
if ( ! -e $talxfm ) then
if ( ! -e transforms/talairach.xfm ) then
set DoUchar = 1 ;
set DoUchar = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 3 != 0 )

set flag = $argv[1] ; shift ;
set flag = --n
shift

switch ( $flag )
switch ( --n )
if ( $#argv == 0 ) goto arg1err ;
if ( 2 == 0 ) goto arg1err
set nIters = $argv[1] ; shift ;
set nIters = 2
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 1 != 0 )

set flag = $argv[1] ; shift ;
set flag = --ants-n4
shift

switch ( $flag )
switch ( --ants-n4 )
set DoAntsN4 = 1 ;
set DoAntsN4 = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return


goto check_params ;
goto check_params
if ( $#InVol == 0 ) then
if ( 1 == 0 ) then
if ( ! -e $InVol ) then
if ( ! -e orig.mgz ) then
if ( $#OutVol == 0 ) then
if ( 1 == 0 ) then
if ( $DoAntsN3 && $DoAntsN4 ) then
if ( 0 && 1 ) then
if ( $DoAntsN3 ) then
if ( 0 ) then
if ( $DoAntsN4 ) then
if ( 1 ) then
which AntsN4BiasFieldCorrectionFs > & /dev/null
which AntsN4BiasFieldCorrectionFs
if ( $status ) then
if ( 0 ) then
endif
endif



set cmd = ( which bc )
set cmd = ( which bc )
$cmd
which bc
/usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc
if ( $status ) then
if ( 0 ) then

goto check_params_return ;
goto check_params_return

set OutDir = `dirname $OutVol` ;
set OutDir = `dirname $OutVol`
dirname nu.mgz
mkdir -p $OutDir ;
mkdir -p .

if ( $#LF == 0 ) set LF = $OutDir/mri_nu_correct.mni.log
if ( 0 == 0 ) set LF = ./mri_nu_correct.mni.log
set LF = ./mri_nu_correct.mni.log
if ( -e $LF ) mv $LF $LF.bak
if ( -e ./mri_nu_correct.mni.log ) mv ./mri_nu_correct.mni.log 
./mri_nu_correct.mni.log.bak
mv ./mri_nu_correct.mni.log ./mri_nu_correct.mni.log.bak

pwd | tee -a $LF
pwd
tee -a ./mri_nu_correct.mni.log
/home/liubing/FreeSurfer/data/test_recon/ANDI1/mri
which mri_nu_correct.mni | tee -a $LF
which mri_nu_correct.mni
tee -a ./mri_nu_correct.mni.log
/home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni
echo $cmdargs | tee -a $LF
echo --debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 
--ants-n4
tee -a ./mri_nu_correct.mni.log
--debug --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4
echo "nIters $nIters" | tee -a $LF
echo nIters 2
tee 

Re: [Freesurfer] recon-all errors

[Mark Wagshul]

External Email - Use Caution

Thanks. I've never used this command before to register the FLAIR, but I'm 
getting the following error:

[mwagshul@loginnode2 mri]$ tkregisterfv --mov orig/FLAIRraw.mgz --reg 
transforms/FLAIRraw.lta --targ orig.mgz
cd 
/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri
freeview -transform-volume -viewport cor -v 
orig.mgz:visible=1:name=orig.mgz(targ) 
/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri/orig/FLAIRraw.mgz:name=FLAIRraw.mgz(mov):reg=/gs/gsfs0/users/mrrc-all/PROJECTS/HOLTZER/MSAGING/MS_PROCESSING/2019-10049-044/mri/transforms/FLAIRraw.lta
/public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: conditional binary 
operator expected
/public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: syntax error near 
`FS_ALLOW_VGLRUN'
/public/apps/freesurfer/7.1.0/bin/fsvglrun: line 20: `if [[ ! -v 
FS_ALLOW_VGLRUN ]]; then'
[mwagshul@loginnode2 mri]$

Thanks for any advice on the issue here.

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

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This email message and any accompanying attachments may contain privileged 
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receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz


On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


1.   Freesurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

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This email message and any accompanying attachments may contain privileged 
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distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
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[Freesurfer] Error/shifting in cortical parcellation

[Helena-Céline Stevelt]

   External Email - Use Caution


Dear Freesurfer Community,

I wish to manually reassign/edit cortical parcellation performed by FS.

We use the cortical parcellation done by FS and it has worked very well 
for most of our subjects. However, we have two subjects where the 
parcellation has not been done correctly. It seems that the central 
sulcus has been mis-classified to be one sulcus too far posterior in the 
brain - this has resulted in incorrect labeling of surrounding gyri. 
Curiously, it is only one hemisphere for both subjects (rh for one and 
lh for the other), where the other hemisphere is correctly parcellated.


In our two mis-parcellated subjects, how might we manually reassign or 
guide FS to correctly classify the central sulcus and thus correctly 
label the surrounding gyri?


I have attached a picture of an erroneous parcellation.
Freesurfer version: freesurfer-linux-centos6_x86_64-dev-20201011-4d2b06a
Platform: Ubuntu 16.04

Best,
Helena-Céline Stevelt
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Re: [Freesurfer] (no subject)

[Francisca Ferreira]

External Email - Use Caution

Hi Doug,

I ran
mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
groupdiff.mtx \--glmdir aseg.glmdir

this created a folder aseg.glmdir which contains another folder groupdiff,
where sig.ghm is,

I then tried to visualise results using

freeview -f
/usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5
-viewport 3d

Many thanks in advance!

Francisca


On Tue, Jun 1, 2021 at 1:40 AM Douglas N. Greve 
wrote:

> How did you create the sig.mgh that you are trying to overlay?
>
> On 5/28/2021 11:16 AM, Francisca Ferreira wrote:
>
> External Email - Use Caution
> Dear Experts,
>
> I have extracted subcortical vols corrected for intracranial vols using
> asegstats2table and I  ran mri_glmfit using the following command
>
> mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C
> groupdiff.mtx \--glmdir aseg.glmdir
>
> this seems to have worked.
> I am now trying to visualise my results adapting the recommended wiki
> command
>
> freeview -f
> /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:annot=aparc.annot_outline=1:overlay=/usr/local/freesurfer/subjects/aseg.glmdir/groupdiff/sig.mgh:overlay_threshold=4,5
> -viewport 3d
>
> Freeview crashes and I'm getting the following error
>
> Number of vertices in overlay data (64 or 64) does not match with surface
> (163842).
> Number of vertices in overlay data (64 or 64) does not match with surface
> (163842).
>
> Is there something wrong with the commands priot  to this step?
>
>
>
>
>
>
>
>
> ___
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