Re: [Freesurfer] Matlab Matlab Runtime issue

[Wei Shao]

External Email - Use Caution

HI, There

sorry for the late reply, I didn't see the reply due to the email setting
issues. I have tried the sudo command, but it still gave me the same error.


Best,
Wei

On Thu, Oct 1, 2020 at 2:56 PM Wei Shao  wrote:

> Hello, Freesurfer team
>
> My name is Wei Shao, FS user, I have a few questions regarding the Matlab
> package and the hippocampal subfield function with FS.
>
> I have followed the instruction from the website to install Matlab, sue
> the fs_install_mcr R2014b
>
> (Oct 01, 2020 14:41:05) Exiting with status 0
> (Oct 01, 2020 14:41:05) End - Successful.
> Finished
> MCR v84 (R2014b) already exists in /usr/local/freesurfer/7.1.0-1
> do you want to reinstall? [y/n]
> exiting without install
>
> *However*, when I try to use the hippocampal seg command:
>
> *segmentHA_T1.sh, it gives me this error*
>
> ERROR: cannot find Matlab 2014b runtime in location:
>
> /usr/local/freesurfer/7.1.0-1/MCRv84
>
> The hippocampal/amygdala and brainstem modules require the (free) Matlab
> runtime.
> You will need to download the Matlab Compiler Runtime (MCR) for Matlab
> 2014b.
> To do so, please run the following commands (you might need root
> permissions):
>
> LINUX:
>
> cd /usr/local/freesurfer/7.1.0-1
> curl "
> https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile=get=runtime2014bLinux.tar.gz;
> -o "runtime2014b.tar.gz"
> tar xvf runtime2014b.tar.gz
>
> Even after I did this as the following, it still gave me the same response
> when I tried segmentHA_T1.sh.
>
> Could you tell me how to fix this? Thanks!
>
> Best,
> Wei
>
>
>
>
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[Freesurfer] white matter surface extends too much into the cortex

[Caroline Chwiesko]

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Dear Freesurfer team,

when checking the output after recon-all i am having the issue that the
white matter surface extends too much into the cortex. I observe this in
most of my subjects (mostly in the posterior part of the brain) so it seems
to be a systematic issue.

I found in the archive that others had a similar problem and  were asked to
upload one subject to get a recommendation on how to change certain default
parameters in recon-all to fix this problem.

I was wondering if I could also upload a subject and get a recommendation
for my data set on how to fix this issue ?

Thank you very much in advance!
Carolin
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Re: [Freesurfer] extracting beta coefficients and p-values

[Batool Rizvi]

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Hi Dr. Greve,

Thank you for your response! Not sure if you already addressed this, but my
second question was whether there is a way to derive the (95%) confidence
intervals for my covariates that were included in the mri_glmfit analyses?

Thanks again!
Batool

On Wed, Oct 7, 2020 at 7:31 AM Douglas N. Greve 
wrote:

>
>
> On 10/6/2020 4:26 PM, Batool Rizvi wrote:
>
> External Email - Use Caution
> Hi,
>
> I had a couple additional questions related to this topic.
>
> 1. The beta-coefficients I derived from using the mri_segstats command
> with the input beta.mgh, are these values unstandardized?
>
> Yes, that have not been standarized
>
>
> 2. Just wondering, is there a possible way to also derive 95% confidence
> intervals for my covariates that were included in the mri_glmfit analyses?
>
> You can standardize them yourself. rvar.mgh is the residual variance and
> Xg is the design matrix. Between those and the beta values, you can
> standarize the betas
>
>
> Thanks so much for your help!
> Batool
>
>
> 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] Freesurfer 5.3.0 recon-all error

[Michele Valotti]

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Hi, thank you for getting back to me so quickly, I can confirm that it does
not run through on any scan and I have tried to run the command as you
suggested.
This is the error I am getting:

--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o
orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux ian-System-Product-Name 5.4.0-48-generic #52~18.04.1-Ubuntu SMP Thu
Sep 10 12:50:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Wed  7 Oct 16:46:17 BST 2020
nu_correct: Command not found.
tmpdir is ./tmp.mri_nu_correct.mni.1081
/home/michele/spd_processing/freesurfer2016/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.1081/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=7.92, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.22236e-09, 3.72529e-09)
j_ras = (-3.72529e-09, 4.65661e-10, -1)
k_ras = (7.82893e-09, 1, -4.65661e-10)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.1081/nu0.mnc...


Iteration 1 Wed  7 Oct 16:46:18 BST 2020
nu_correct -clobber ./tmp.mri_nu_correct.mni.1081/nu0.mnc
./tmp.mri_nu_correct.mni.1081/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.1081/0/ -iterations 1000 -distance 50
nu_correct: Command not found.
ERROR: nu_correct

I am assuming I am missing the MNI tools, so I have tried to download them
from http://bic-mni.github.io/ but all the downloads failed, do you have a
recommended way to download and install what I need to run my script?

Thank you again,
Michele

On Tue, 6 Oct 2020 at 15:59, Douglas N. Greve 
wrote:

>
> My guess is it is a problem with the install of the MNI tools. Does it run
> all the way through on other subjects? What happens when you run this
> command?
>
> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
>
> On 10/6/2020 9:16 AM, Michele Valotti wrote:
>
> External Email - Use Caution
> I am using freesurfer 5.3.0 (unfortunately this is the version I have to
> use) and I am encountering an error in the process. I have attached the
> recon-all.log file. Any pointers to identify the error would be very
> helpful,
>
> Thank you,
> Michele
>
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[Freesurfer] Issues with transferring edits from v6.0dev into v7.1

[Melanie Ganz]

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Dear FS list,

as soon as samseg was available in FS v6dev we used it to process some 
of our data. The plan was always to wait for v7 to use a stable version, 
but edits were made already on v6FSdev, while we waited last spring for 
v7 to come out.

Now I have been having issues with transferring edits from v6dev into 
v7.1, which I thought should be a straight forward thing to do.

The way I did it, is I ran v7.1 on the raw data, then I copied the files 
where edits where made, e.g. brainmask.mgz, wm.mgz as well as 
control.dat. Finally, at this point I reran recon-all -all ( since I 
actually couldn't get recon-all with the -make flag to work).

But I see my rerun fails with the error message:

Saving brainmask.auto.mgz
Command terminated by signal 11
@#@FSTIME  2020:10:06:14:45:45 mri_watershed N 10 e 20.81 S 1.93 U 22.55 
P 117% M 893740 F 0 R 330549 W 0 c 83 w 1353 I 22344 O 2312 L 3.35 3.67 2.94
@#@FSLOADPOST 2020:10:06:14:46:06 mri_watershed N 10 3.10 3.59 2.93
Linux krogh 4.12.14-lp151.28.59-default #1 SMP Wed Aug 5 10:58:34 UTC 
2020 (337e42e) x86_64 x86_64 x86_64 GNU/Linux

recon-all -s g612_GD exited with ERRORS at Tue Oct  6 14:46:06 CEST 2020

and I don't understand why. The earlier FSrun with v7.1 ran fine and I 
also tried copying to a separate directory to check file permissions and 
the same error appears again.

I have uploaded the subject to the ftp server at 
surfer.nmr.mgh.harvard.edu and it's called subject.tar.gz.

Kind regards,

Melanie


-- 

Yours sincerely


Melanie Ganz-Benjaminsen
Forsker


Direct: + 45 35 45 67 18
Mail: melanie.g...@nru.dk

Neurobiology Research Unit

Rigshospitalet, building 6931
Juliane Maries Vej 28, 3rd floor
DK-2100 Copenhagen, Denmark

Phone: +45 3545 6712
Fax: +45 3545 6713
URL:http://nru.dk


This e-mail and any attachment may contain confidential and privileged material 
intended for the addressee only. If you are not the addressee, you are notified 
that no part of the e-mail or any attachment may be disclosed, copied or 
distributed, and that any other action related to this e-mail or attachment is 
strictly prohibited, and may be unlawful. If you have received this e-mail by 
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[Freesurfer] Issues with transferring edits from v6.0dev into v7.1

[Melanie Ganz]

External Email - Use Caution

Dear FS list,

as soon as samseg was available in FS v6dev we used it to process some 
of our data. The plan was always to wait for v7 to use a stable version, 
but edits were made already on v6FSdev, while we waited last spring for 
v7 to come out.

Now I have been having issues with transferring edits from v6dev into 
v7.1, which I thought should be a straight forward thing to do.

The way I did it, is I ran v7.1 on the raw data, then I copied the files 
where edits where made, e.g. brainmask.mgz, wm.mgz as well as 
control.dat. Finally, at this point I reran recon-all -all ( since I 
actually couldn't get recon-all with the -make flag to work).

But I see my rerun fails with the error message:

Saving brainmask.auto.mgz
Command terminated by signal 11
@#@FSTIME  2020:10:06:14:45:45 mri_watershed N 10 e 20.81 S 1.93 U 22.55 
P 117% M 893740 F 0 R 330549 W 0 c 83 w 1353 I 22344 O 2312 L 3.35 3.67 
2.94
@#@FSLOADPOST 2020:10:06:14:46:06 mri_watershed N 10 3.10 3.59 2.93
Linux krogh 4.12.14-lp151.28.59-default #1 SMP Wed Aug 5 10:58:34 UTC 
2020 (337e42e) x86_64 x86_64 x86_64 GNU/Linux

recon-all -s g612_GD exited with ERRORS at Tue Oct  6 14:46:06 CEST 2020

and I don't understand why. The earlier FSrun with v7.1 ran fine and I 
also tried copying to a separate directory to check file permissions and 
the same error appears again.

I have uploaded the subject to the ftp server at 
surfer.nmr.mgh.harvard.edu and it's called subject.tar.gz.

Kind regards,

Melanie

-- 

Yours sincerely


Melanie Ganz-Benjaminsen
Forsker


Direct: + 45 35 45 67 18
Mail: melanie.g...@nru.dk

Neurobiology Research Unit

Rigshospitalet, building 6931
Juliane Maries Vej 28, 3rd floor
DK-2100 Copenhagen, Denmark

Phone: +45 3545 6712
Fax: +45 3545 6713
URL:http://nru.dk


This e-mail and any attachment may contain confidential and privileged material 
intended for the addressee only. If you are not the addressee, you are notified 
that no part of the e-mail or any attachment may be disclosed, copied or 
distributed, and that any other action related to this e-mail or attachment is 
strictly prohibited, and may be unlawful. If you have received this e-mail by 
error, please notify the sender immediately by return e-mail, and delete this 
message.


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Re: [Freesurfer] Resting state fMRI - volume analysis

[Douglas N. Greve]

Did you see the part about only analyzing subcortical gray matter 
earlier in our conversation?


On 10/7/2020 12:00 PM, Wenzhen Zhao wrote:


External Email - Use Caution

Hi,

I find it weird that it does not show full brain after smoothing 
(-fwhm 5). Is this normal?


Also, even with -no-subcort-mask, volume analysis does not do full 
brain analysis.


Best,
Wenzhen

On Wed, Oct 7, 2020 at 10:16 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


What is wrong?


On 10/6/2020 12:28 PM, Wenzhen Zhao wrote:


External Email - Use Caution

Thank you for your help.

The smoothing issue occurs only on volume. It works okay with
surface. When I smooth the volume by 5, the results look like
below. The command I used was $preproc-sess -s sess01 -fsd rest
-stc siemens -noreg  -mni305 -vol-fwhm 5 -no-subcort-mask
-per-run -update


Thanks,
Wenzhen


On Oct 6, 2020, at 11:53 AM, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:

Correct, we analyze the cortical surface using surface-based
analysis. If you want to have full volume analysis, you can add
-no-subcort-mask to preproc-sess. Not sure what the problem is
with smoothing.





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

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of
Wenzhen Zhao mailto:wenzhen.z...@yale.edu>>
*Sent:*Monday, October 5, 2020 3:22 PM
*To:*Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:*[Freesurfer] Resting state fMRI - volume analysis
External Email - Use Caution
Dear Freesurfer Developers,

I have a question regarding volume analysis of fMRI data. I
wanted to perform volume analysis in MNI305 space, and I used
following command after creating a seed;

$mkanalysis-sess -analysis lh.pcc.mni305.vol -mni305 2 -stc
siemens -fwhm 0 -notask -taskreg lh.pcc.dat 1 -nuisreg vcsf.dat
5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 10 -fsd rest
-hpf 0.01 -TR 3 -per-run

$selxavg3-sess -s sess01 -a lh.pcc.mni305.vol -no-preproc -overwrite

The resulting analysis seems only showing subcortical regions,
not the whole brain. (Shown in the attachment) I read on the
page that volume analysis is only for subcortical regions, is
this the reason that I only see subcortical regions?

Another problem is that in the preprocessing step, I could not
smooth the volume. If I do, it seems to distort the image and
only gives something similar to the picture shown. Could this be
the reason for the distorted analysis?

Thanks for your help.

Best,
Wenzhen


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Re: [Freesurfer] Recon-all Results for fMRI

[Douglas N. Greve]

Yes, you should. You must use the same platform though

On 10/7/2020 11:22 AM, goktekin.duru...@boun.edu.tr wrote:
>  External Email - Use Caution
>
> Hi Douglas,
>
> I am trying to understand the reproducibility of
> "aparc.a2009s+aseg.mgz" file. The main question is :
>
> If I use the same data as an input (T1, T2 images), should I get the
> "exactly" same result of   "aparc.a2009s+aseg.mgz" file for freesurfer
> version 5.3.0?
>
> Thanks
>
> Goktekin
>
>> not sure what you mean. can you elaborate?
>>
>> On 10/7/2020 2:59 AM, goktekin.duru...@boun.edu.tr wrote:
>>>   External Email - Use Caution
>>>
>>> Hi,
>>>
>>> I am using freesurfer 5.3.0. I would like to ask whether it is
>>> possible or not to have different results for destrieux atlas
>>> parcellation for the same data. (aparc.a2009s+aseg.mgz file). It seems
>>> there is a little difference in terms of parcellation locations and
>>> their volumes.
>>>
>>> Thank you,
>>>
>>> Goktekin Durusoy
>>>
>>> ___
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>>
>
>
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Re: [Freesurfer] Resting state fMRI - volume analysis

[Wenzhen Zhao]

External Email - Use Caution

Hi,

I find it weird that it does not show full brain after smoothing (-fwhm 5).
Is this normal?

Also, even with -no-subcort-mask, volume analysis does not do full brain
analysis.

Best,
Wenzhen

On Wed, Oct 7, 2020 at 10:16 AM Douglas N. Greve 
wrote:

> What is wrong?
>
>
> On 10/6/2020 12:28 PM, Wenzhen Zhao wrote:
>
> External Email - Use Caution
> Thank you for your help.
>
> The smoothing issue occurs only on volume. It works okay with surface.
> When I smooth the volume by 5, the results look like below. The command I
> used was $preproc-sess -s sess01 -fsd rest -stc siemens -noreg  -mni305
> -vol-fwhm 5 -no-subcort-mask -per-run -update
>
>
> Thanks,
> Wenzhen
>
> On Oct 6, 2020, at 11:53 AM, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>
> Correct, we analyze the cortical surface using surface-based analysis. If
> you want to have full volume analysis, you can add -no-subcort-mask to
> preproc-sess. Not sure what the problem is with smoothing.
>
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wenzhen Zhao <
> wenzhen.z...@yale.edu>
> *Sent:* Monday, October 5, 2020 3:22 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Resting state fMRI - volume analysis
>
> External Email - Use Caution
> Dear Freesurfer Developers,
>
> I have a question regarding volume analysis of fMRI data. I wanted to
> perform volume analysis in MNI305 space, and I used following command after
> creating a seed;
>
> $mkanalysis-sess -analysis lh.pcc.mni305.vol -mni305 2 -stc siemens -fwhm
> 0 -notask -taskreg lh.pcc.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5
> -mcextreg -polyfit 5 -nskip 10 -fsd rest -hpf 0.01 -TR 3 -per-run
>
> $selxavg3-sess -s sess01 -a lh.pcc.mni305.vol -no-preproc -overwrite
>
> The resulting analysis seems only showing subcortical regions, not the
> whole brain. (Shown in the attachment) I read on the page that volume
> analysis is only for subcortical regions, is this the reason that I only
> see subcortical regions?
>
> Another problem is that in the preprocessing step, I could not smooth the
> volume. If I do, it seems to distort the image and only gives something
> similar to the picture shown. Could this be the reason for the distorted
> analysis?
>
> Thanks for your help.
>
> Best,
> Wenzhen
>
> 
> ___
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>
>
>
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Re: [Freesurfer] Recon-all Results for fMRI

[goktekin . durusoy]

External Email - Use Caution

Hi Douglas,

I am trying to understand the reproducibility of  
"aparc.a2009s+aseg.mgz" file. The main question is :

If I use the same data as an input (T1, T2 images), should I get the  
"exactly" same result of   "aparc.a2009s+aseg.mgz" file for freesurfer  
version 5.3.0?

Thanks

Goktekin

> not sure what you mean. can you elaborate?
>
> On 10/7/2020 2:59 AM, goktekin.duru...@boun.edu.tr wrote:
>>  External Email - Use Caution
>>
>> Hi,
>>
>> I am using freesurfer 5.3.0. I would like to ask whether it is
>> possible or not to have different results for destrieux atlas
>> parcellation for the same data. (aparc.a2009s+aseg.mgz file). It seems
>> there is a little difference in terms of parcellation locations and
>> their volumes.
>>
>> Thank you,
>>
>> Goktekin Durusoy
>>
>> ___
>> Freesurfer mailing list
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>
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>



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[Freesurfer] qdec problems not receiving keyboard input

[Agurne Sampedro Calvete]

External Email - Use Caution

Dear Freesurfer Experts,

Although I haven't had any problems with the qdec until now, this week the
qdec is having some errors when receiving inputs from the keyboard. For
example, I can't write in the design name box, nor can I change the minimum
or maximum threshold in the display page. I've seen that other people have
had a similar problem too. How can I solve it?

Thanks in advance.

Kind regards,
Agurne Sampedro
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Re: [Freesurfer] recon-all -s -autorecon2-cp -autorecon3 error

[Douglas N. Greve]

I've never seen that one before. Can you post pictures of where you put 
the control points? Are you sure you put them in voxels that are clearly WM?


On 10/6/2020 4:33 PM, Kazuki Sakakura wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute recon-all after putting control point, but 
for some of my subjects I get the attached error when I run the 
recon-all -s  -autorecon2-cp -autorecon3 command.




I've searched the list and no similar errors have been reported. Does 
anyone have any thoughts on how to trouble-shoot this one? Also, Ive 
attached the recon-all.log in case it's of any use.


1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2) Platform: Ubuuntu 14.04

3) recon-all.log: see attached


Best Regards,

Kazuki Sakakura



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Re: [Freesurfer] extracting beta coefficients and p-values

[Douglas N. Greve]

On 10/6/2020 4:26 PM, Batool Rizvi wrote:


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Hi,

I had a couple additional questions related to this topic.

1. The beta-coefficients I derived from using the mri_segstats command 
with the input beta.mgh, are these values unstandardized?

Yes, that have not been standarized


2. Just wondering, is there a possible way to also derive 95% 
confidence intervals for my covariates that were included in the 
mri_glmfit analyses?
You can standardize them yourself. rvar.mgh is the residual variance and 
Xg is the design matrix. Between those and the beta values, you can 
standarize the betas


Thanks so much for your help!
Batool


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Re: [Freesurfer] Recon-all Results for fMRI

[Douglas N. Greve]

not sure what you mean. can you elaborate?

On 10/7/2020 2:59 AM, goktekin.duru...@boun.edu.tr wrote:
>  External Email - Use Caution
>
> Hi,
>
> I am using freesurfer 5.3.0. I would like to ask whether it is
> possible or not to have different results for destrieux atlas
> parcellation for the same data. (aparc.a2009s+aseg.mgz file). It seems
> there is a little difference in terms of parcellation locations and
> their volumes.
>
> Thank you,
>
> Goktekin Durusoy
>
> ___
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Re: [Freesurfer] create .nv or .pial file with atlas based values

[Douglas N. Greve]

Sounds like you need to contact the people at BrainNetViewer

On 10/6/2020 8:00 PM, Xin Niu wrote:


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Dear freesurfer experts,

We have some files containing the values for regions based on the 
Deskian/Killiany atlas like :

ROI, value
'lh_bankssts', .9
'lh_caudalanteriorcingulate', .1
'lh_caudalmiddlefrontal', .5
'lh_cuneus', .2
'lh_entorhinal', .5
'lh_fusiform', .9
'lh_inferiorparietal', .7

And we have the information on the labels in Matlab data format:
image.png
I wish to create a surface file (.nv or .pial) based on the atlas and 
values which can be visualized directly in software like BrainNetViewer.
We are also considering to visualized the brain images with SurfStat 
which needs a .obj file and .txt file:

s100 = SurfStatReadSurf( {...
 'c:/keith/fMRI/ICBM/surfaces/mni_icbm_00100_mid_surface_left_81920.obj',... 

 'c:/keith/fMRI/ICBM/surfaces/mni_icbm_00100_mid_surface_right_81920.obj'} 
);


t100 = SurfStatReadData( {... 
'c:/keith/fMRI/ICBM/thickness/mni_icbm_00100_native_rms_rsl_tlink_20mm_left.txt',...
 'c:/keith/fMRI/ICBM/thickness/mni_icbm_00100_native_rms_rsl_tlink_20mm_right.txt'} 
);


SurfStatView( t100, s100, 'Cort Thick (mm), Subj 00100' );

But I have no idea how the .obj file is created and how the .txt file 
should be organized.


Is there any way to make it?

Thanks in advance!

Best,
Xin




Xin Niu
Drexel University, Department of Psychology
Stratton Hall 314
3201 Chestnut Street
Philadelphia, PA 19104


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Re: [Freesurfer] qdec problems not receiving keyboard input

[Douglas N. Greve]

Sorry, qdec has been mothballed and we are not supporting it anymore

On 10/7/2020 7:12 AM, Agurne Sampedro Calvete wrote:


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Dear Freesurfer Experts,

Although I haven't had any problems with the qdec until now, this week 
the qdec is having some errors when receiving inputs from the 
keyboard. For example, I can't write in the design name box, nor can I 
change the minimum or maximum threshold in the display page. I've seen 
that other people have had a similar problem too. How can I solve it?


Thanks in advance.

Kind regards,
Agurne Sampedro



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Re: [Freesurfer] Resting state fMRI - volume analysis

[Douglas N. Greve]

What is wrong?

On 10/6/2020 12:28 PM, Wenzhen Zhao wrote:


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Thank you for your help.

The smoothing issue occurs only on volume. It works okay with surface. 
When I smooth the volume by 5, the results look like below. The 
command I used was $preproc-sess -s sess01 -fsd rest -stc siemens 
-noreg  -mni305 -vol-fwhm 5 -no-subcort-mask -per-run -update



Thanks,
Wenzhen

On Oct 6, 2020, at 11:53 AM, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:


Correct, we analyze the cortical surface using surface-based 
analysis. If you want to have full volume analysis, you can add 
-no-subcort-mask to preproc-sess. Not sure what the problem is with 
smoothing.






*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> on behalf of Wenzhen 
Zhao mailto:wenzhen.z...@yale.edu>>

*Sent:*Monday, October 5, 2020 3:22 PM
*To:*Freesurfer support list >

*Subject:*[Freesurfer] Resting state fMRI - volume analysis
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Dear Freesurfer Developers,

I have a question regarding volume analysis of fMRI data. I wanted to 
perform volume analysis in MNI305 space, and I used following command 
after creating a seed;


$mkanalysis-sess -analysis lh.pcc.mni305.vol -mni305 2 -stc siemens 
-fwhm 0 -notask -taskreg lh.pcc.dat 1 -nuisreg vcsf.dat 5 -nuisreg 
wm.dat 5 -mcextreg -polyfit 5 -nskip 10 -fsd rest -hpf 0.01 -TR 3 
-per-run


$selxavg3-sess -s sess01 -a lh.pcc.mni305.vol -no-preproc -overwrite

The resulting analysis seems only showing subcortical regions, not 
the whole brain. (Shown in the attachment) I read on the page that 
volume analysis is only for subcortical regions, is this the reason 
that I only see subcortical regions?


Another problem is that in the preprocessing step, I could not smooth 
the volume. If I do, it seems to distort the image and only gives 
something similar to the picture shown. Could this be the reason for 
the distorted analysis?


Thanks for your help.

Best,
Wenzhen


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[Freesurfer] lta files longitudinal pipeline

[Marisa Johanna Nordt]

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Hi,

I have a question about the lta files from the longitudinal pipeline (using the 
–affine flag). Instead of just one .lta file from each timepoint to the 
template 3 different .lta files are saved
-tp1_to_templ_norm.lta,
-tp1_to_templ_affine.lta,
-tp1_to_templ.lta

Is the one created last (tp1_to_templ.lta) the final lta-file that I can use to 
align additional files from tp 1 to the template?

Thanks a lot!
Marisa

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[Freesurfer] Recon-all Results for fMRI

[goktekin . durusoy]

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Hi,

I am using freesurfer 5.3.0. I would like to ask whether it is  
possible or not to have different results for destrieux atlas  
parcellation for the same data. (aparc.a2009s+aseg.mgz file). It seems  
there is a little difference in terms of parcellation locations and  
their volumes.

Thank you,

Goktekin Durusoy

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