Re: [Freesurfer] TRACULA -bedp parallel processing

2022-06-07 Thread Yendiki, Anastasia 
What if you create the directory (that shows up in the "not a directory" error)?

From: Salar Dini, Elaheh 
Sent: Tuesday, June 7, 2022 11:46 AM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing


External Email - Use Caution

Hi Anastasia,


FSL version is 6.0.5.1


Thanks,

Ela





From: Yendiki, 
Anastasia

Sent: Mon, 06 Jun 2022 20:17:47 
-0700

To: Salar Dini, Elaheh ; Freesurfer support list 


Subject: Re: TRACULA -bedp parallel processin

Hi Ela - Which version of FSL are you using?

Anastasia.



From: Salar Dini, Elaheh 
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

Thanks for the reply. I'm not sure if you are looking for this: we use a small 
cluster with 40 nodes, 512 CPU cores. We are still using PBS.


Thanks,
Ela

From: Yendiki, Anastasia 
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


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Thank you for the guidance.


When it tries to run pre.ParallelI , I'll get this:

Copying files to bedpost directory

cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is 
not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected
Done


This happens for all subjects.


After this, when I check the subject 57 folder in subjects_dir, there is a file 
named "dmri.bedpostX.nii.gz".


However, when it tries to run Parallel lines, these errors coming up:

/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log: No 
such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No 
such file or directory

...


If I run trac-all -bedp -c  , and not try to process parallelly, 
it runs without any errors to the end.


Do you have any thoughts what goes wrong?


Thanks again,

Ela




From:Yendiki, 
Anastasia

Fri, 03 Jun 2022 12:24:56 
-0700

Re: [Freesurfer] vertex ID in the contralateral hemisphere

2022-06-07 Thread Wighton, Paul 
Hi Marina,

I believe mris_left_right_register can do this.

-Paul

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Marina Fern?ndez 

Sent: Tuesday, June 7, 2022 4:16 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] vertex ID in the contralateral hemisphere


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Dear experts,

I would like to know the corresponding vertex in the contralateral hemisphere 
of a given vertex. Do you have a function that allows me to know it?

Thank you very much in advance.

Best regards,
Marina
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Re: [Freesurfer] Custom LUT

2022-06-07 Thread Douglas N. Greve 

yes, send the LUT file

On 6/3/2022 3:03 PM, Benjamin Deck wrote:


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Hi there,

I created the file via a linux computer by hand. I also checked that 
there weren't any hidden characters and made sure that the file had 
spaces instead of tabs like the default LUT file.


again here are my files when I list them:

Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz 
 Net_19_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz
Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz 
 Net_2_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz
Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz 
 Net_2_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz


And here is my LUT:

0 unknown  5   5   5   0
1 Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol   25  5  25  0
2 Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol   25  100 40  0
3 Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol   70  130 180 0
4 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol  100 100 0   0
5 Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol   196 58  250 0
6 Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol  100 25  0   0
7 Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol  120 70  50  0


Could I possibly send you my LUT file? I am really at a loss for what 
the problem is.

Ben

On Fri, Jun 3, 2022 at 1:29 PM Douglas N. Greve 
 wrote:


No, there is a problem with your LUT (for the default, there might
not be entries for all of your segs which is why you are not
seeing them). I don't know what the problem is. Try making it a
different way or doing it by hand in linux.

On 6/3/2022 1:20 PM, Benjamin Deck wrote:


External Email - Use Caution

Responding re: Douglas Greve

How exactly did you create the LUT? Eg, in windows using notepad?
I'm thinking that there might be some hidden characters in there
as the color is wrong. I did notice that  your first entry had a
value of 5 in the last column; usually this is 0 (not sure what
it is for). What happens if you switch the LUT to the default? Do
you get reasonable colors (even if the names are wrong)?


Reply:

I used a custom python script that creates a LUT for each
subject. Then I ran dos2unix to ensure the line endings were
appropriate.

If I load the default FS LUT only 2 ROIs are being labeled.

Does this mean that I have an issue with my mri_concat call?

Which is:

mri_concat --sum --f vols.txt --o sub_vols.mgz

Thanks,
Ben

-- 
*Benjamin L. Deck*

/Doctoral Student/
/Applied Cognitive and Brain Sciences/
/Department of Psychological and Brain Sciences/
/Drexel University/



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Re: [Freesurfer] aseg and surface edit corrections - grey matter surface fails editing

2022-06-07 Thread Douglas N. Greve 
The problem here is that the white surface is not extending far enough 
because the white matter is underlabeled. I know it seems intuitive to 
edit the aseg to influence the the surface placement, it actually will 
have very little effect. In this case, you should edit the wm.mgz to 
fill in the WM in that area then run recon-all -s subject -autorecon2-wm 
-autorecon3



On 5/21/2022 7:25 AM, Helena Pereira wrote:


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Hello FreeSurfer Developers,

I'm attempting to get the new surface pial from the grey-matter. I 
note that the grey-matter from the temporal areas is not correctly 
segmented (a few slices are not identified as grey-matter nor with any 
label) in the aseg file, which influences the surface pial of the grey 
matter. To correct this, I manually corrected the aseg file expecting 
to get the correct surface pials. Nevertheless, after running 
recon-all make -all, the surface remains the same.


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, I've attached an example of my problem, after recon-all make -all.

1) FreeSurfer version: 7.1.1
2) Operating system info: AlmaLinux 8.5, rhel centos fedora 8.5

Thanks in advance,
Best regards,
Helena Pereira


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Re: [Freesurfer] mris_preproc read error

2022-06-07 Thread Joanna L Eckhardt 
External Email - Use Caution

Dear FS team,

I am emailing to check in on the status of this issue. Any insights on how to 
move forward with this error? I can try rerunning this subject in the meantime 
to see if that fixes the problem.

Thank you very much your assistance!

Best wishes,
Joanna


--

Joanna Eckhardt

Neurosciences Graduate Program

University of California, San Diego


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Joanna L Eckhardt 

Sent: Friday, June 3, 2022 10:37 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_preproc read error


External Email - Use Caution

Dear FreeSurfer team,

I reran -qcache for sub-101 (also, I had specified -qcache processing for all 
subjects during initial recon-all so it should have already occurred), and it 
exited with errors. Below is the output from the -qcache rerun, with the error 
being:

ERROR: reading 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Read 0 bytes, expected 1
error: No such file or directory
error: mri_surf2surf: could not read surface 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf/lh.sphere.reg
Command exited with non-zero status 1

Let me know if you have any insights, or if I need to rerun the recon-all for 
this subject.

Thank you for your assistance!
Joanna


developer@developer-VirtualBox:~/FreeSurfer/osg-outputs/cannabis-BL$ recon-all 
-s sub-101 -qcache
INFO: FreeSurfer build stamps do not match
Subject Stamp:
Current Stamp: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
INFO: SUBJECTS_DIR is /home/developer/FreeSurfer/osg-outputs/cannabis-BL
Actual FREESURFER_HOME /usr/local/freesurfer/7.2.0
-rw-rw-r-- 1 developer developer 35431 Jun  3 13:28 
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/scripts/recon-all.log
Linux developer-VirtualBox 5.4.0-113-generic #127~18.04.1-Ubuntu SMP Wed May 18 
15:40:23 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri/transforms 
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
~/FreeSurfer/osg-outputs/cannabis-BL/sub-101
#@# white curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv
   Update not needed
#@# white area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.white ../surf/lh.area
   Update not needed
#@# pial curv lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial
   Update not needed
#@# pial area lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial
   Update not needed
#@# thickness lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# area and vertex vol lh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 
../surf/lh.thickness
   Update not needed
#@# white curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv
   Update not needed
#@# white area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.white ../surf/rh.area
   Update not needed
#@# pial curv rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial
   Update not needed
#@# pial area rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial
   Update not needed
#@# thickness rh Fri Jun  3 13:29:47 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness
   Update not needed
#@# area and vertex vol rh Fri Jun  3 13:29:48 EDT 2022
cd /home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/mri
mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 
../surf/rh.thickness
   Update not needed
#
#@# Qdec Cache preproc lh thickness fsaverage Fri Jun  3 13:29:48 EDT 2022
/home/developer/FreeSurfer/osg-outputs/cannabis-BL/sub-101/surf

 mris_preproc --s sub-101 --hemi lh --meas thickness --target fsaverage --out 
lh.thickness.fsaverage.mgh

nsubjects = 1
tmpdir is

Re: [Freesurfer] TRACULA -bedp parallel processing

2022-06-07 Thread Salar Dini, Elaheh 
External Email - Use Caution

Hi Anastasia,


FSL version is 6.0.5.1


Thanks,

Ela





From: Yendiki, 
Anastasia

Sent: Mon, 06 Jun 2022 20:17:47 
-0700

To: Salar Dini, Elaheh ; Freesurfer support list 


Subject: Re: TRACULA -bedp parallel processin

Hi Ela - Which version of FSL are you using?

Anastasia.



From: Salar Dini, Elaheh 
Sent: Monday, June 6, 2022 5:26 PM
To: Yendiki, Anastasia ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

Thanks for the reply. I'm not sure if you are looking for this: we use a small 
cluster with 40 nodes, 512 CPU cores. We are still using PBS.


Thanks,
Ela

From: Yendiki, Anastasia 
Sent: Saturday, June 4, 2022 1:05 AM
To: Salar Dini, Elaheh ; Freesurfer support list 

Subject: Re: TRACULA -bedp parallel processing

What kind of cluster are you running the parallel processes on?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Friday, June 3, 2022 7:44 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] TRACULA -bedp parallel processing


External Email - Use Caution

Thank you for the guidance.


When it tries to run pre.ParallelI , I'll get this:

Copying files to bedpost directory

cp: target '/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX' is 
not a directory
/home1/es2263/fsl//bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator 
expected
Done


This happens for all subjects.


After this, when I check the subject 57 folder in subjects_dir, there is a file 
named "dmri.bedpostX.nii.gz".


However, when it tries to run Parallel lines, these errors coming up:

/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log: No 
such file or directory
/home1/es2263/fsl//bin/bedpostx_single_slice.sh: line 77: 
/home2/am2359/fs6_data/TRACULA/subjects_dir/57/dmri.bedpostX/logs/log0001: No 
such file or directory

...


If I run trac-all -bedp -c  , and not try to process parallelly, 
it runs without any errors to the end.


Do you have any thoughts what goes wrong?


Thanks again,

Ela




From:Yendiki, 
Anastasia

Fri, 03 Jun 2022 12:24:56 
-0700

[Freesurfer] surface based analysis using Infant FS

2022-06-07 Thread Steger Celine 
External Email - Use Caution

Dear FS experts,

We are currently exploring the Infant Freesurfer pipeline for surface based 
analysis in our cohort. The generated surfaces seem reasonable, but now we are 
wondering, how to proceed. To our understanding, by looking at the recon-all 
for adult data, the next step would be to register each subject to standard 
space (using the -qcache flag this happens directly to fsaverage). Since the 
-qcache flag is not available in infant_recon_all we would like to clarify if 
this is not advised to do so with subjects processed via infant_recon_all or if 
we could just proceed with recon_all from here. Is there is any alternative 
procedure that should be followed in order to map all subjects into one space, 
e.g. creating a cohort specific average?

Kind regards,

Céline
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[Freesurfer] VM password

2022-06-07 Thread fabianhuth1 
External Email - Use CautionDear FS experts,

I am using the Oracle Virtual Box to install FS 7.2 on Windows. Could you send to me the passcode for the 7z archieve?

 

Thanks!



bw
Fabian
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[Freesurfer] vertex ID in the contralateral hemisphere

2022-06-07 Thread Marina Fernández 
External Email - Use Caution

Dear experts,

I would like to know the corresponding vertex in the contralateral
hemisphere of a given vertex. Do you have a function that allows me to know
it?

Thank you very much in advance.

Best regards,
Marina
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Re: [Freesurfer] HRF with derivatives: results

2022-06-07 Thread Laura Doll 
External Email - Use Caution

Yes, I think so. That would mean, that the additional frames correspond to the 
weights of the derivatives, right?

But as I mentioned in the previous mail, they do have the same dimensions (in 
matlab, checking the beta.vol).  
Do you have any idea, what could have gone wrong?
I double checked for Copy/Paste errors or stuff like that, but didn't find any.

These are the exact terminal entries from last week:

mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 -notask 
-spmhrf 1 -TR 2 -polyfit 2 -analysis TestPupAvg.lh -per-run -taskreg PupAvg 1
selxavg3-sess -s S05 -analysis TestPupAvg.lh
mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 -notask 
-spmhrf 0 -TR 2 -polyfit 2 -analysis Test0PupAvg.lh -per-run -taskreg PupAvg 1
selxavg3-sess -s S05 -analysis Test0PupAvg.lh

And I loaded the results in Matlab with
beta1 = load_nifti('./S05/bold/TestPupAvg.lh/beta.nii.gz')
beta0 = load_nifti('./S05/bold/Test0PupAvg.lh/beta.nii.gz')

Which results in equal beta1 and beta0.


Best,
Laura

Am Freitag, 03. Juni 2022 19:04 CEST, "Douglas N. Greve" 
 schrieb: 
 
> The -spmhrf 1 and 2 should have had additional frame in the beta.nii.gz. 
> Is that what you are looking at?
> 
> On 6/3/2022 4:51 AM, Laura Doll wrote:
> >  External Email - Use Caution
> >
> > Okay, thanks.
> > But how can I find out the influence of the derivatives used?
> > I also tried to check the beta.nii.gz files for three different versions of 
> > the analysis (-spmhrf 0 1 and 2), assuming that the weights for the 
> > derivatives might be saved as additional dimensions, but the dimensions 
> > were the same for all (163842x1x1x10).
> >
> > I feel like I am missing something here, or maybe there is some mistake in 
> > my analysis?
> > This is what I used:
> >
> > mkanalysis-sess -fsd bold -stc siemens  -surface fsaverage lh -fwhm 5 
> > -notask -spmhrf 0 -TR 2 -polyfit 2 -analysis Test0.lh -per-run -taskreg 
> > PupAvg 1
> >
> > selxavg3-sess -s S05 -analysis Test0.lh
> >
> > And Test1/2 with -spmhrf 1/2, respectively.
> >
> > Thanks in Advance!
> >
> > Laura
> >
> >   
> > Am Mittwoch, 01. Juni 2022 16:50 CEST, "Douglas N. Greve" 
> >  schrieb:
> >   
> >> It uses the default parameters:
> >>     tau1 = 1;
> >>     tau2 = 1;
> >>     ttp1 = 5*tau1;  % 6 %
> >>     ttp2 = 15*tau1; % 16 %
> >>     c  = 1/6;
> >>
> >>
> >>
> >> On 6/1/2022 4:27 AM, Laura Doll wrote:
> >>>   External Email - Use Caution
> >>>
> >>> Hi Doug,
> >>>
> >>> Thanks for your hint where to find the actual function.
> >>> But how can I find which values were used in my analysis? I.e. the input 
> >>> to this function?
> >>>
> >>> Best,
> >>> Laura
> >>>
> >>> Am Dienstag, 31. Mai 2022 17:19 CEST, "Douglas N. Greve" 
> >>>  schrieb:
> >>>
>  Look here $FREESURFER/fsfast/toolbox/fast_spmhrf.m
> 
>  On 5/25/2022 9:19 AM, Laura Doll wrote:
> >External Email - Use Caution
> >
> > Hi everyone,
> >
> > I need some help regarding the SPM-HRF with two derivatives:
> > Where can I find the actual function that was used for the analysis? I 
> > am mostly interested in the peak latency, but would also appreciate if 
> > I can check the other parameters of the function somewhere.
> >
> > Best,
> > Laura
> >
> >
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