New subject: if: Expression Syntax - preproc-sess

19 Mar 2024

      Hi Stefano, I think I found and fixed the problem. Can you try these?
On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote:
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Hi Doug,
The raw functional file is firstly passed with motion correction 
(i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering.
Next, I have renamed the ICA filtered file as f.nii.gz.
Then, I run:
preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 
-fsd rest -per-run -sliceorder even -force
There are issues with labels since excluding motion correction doesn't 
produce key files necessary for concatenating the files.
The preprocessing script is searching for the fmcpr.nii.gz file, which 
cannot be found because it is not created using the -nomc option.
When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and 
rerun preproc, the operation is done and the 
fmcpr.odd.sm0.fsaverage.lh is created.
However, when I run the next steps (fcseed-sess -s ID -cfg wm.config 
-overwrite), a second error occurs (reported below) because the script 
searches for fmcpr, which cannot be produced since I used -mc.
ERROR: could not determine file for 
/Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr 
This error seems to be related to the script searching for the fmcpr 
file, which isn't available due to the use of -mc.
Thank you.
Best regards,
Stefano
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Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi 
sdellipizzi@gmail.com ha scritto:
Hi Doug have you any news
Thank you very much!
Stefano
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Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi 
sdellipizzi@gmail.com ha scritto:
Thank you.
I’m attaching the file.
Stefano
<preproc-sess>
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Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve 
dgreve@mgh.harvard.edu ha scritto:
can you send me this file 
/Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess
On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote:
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It seems to me that I've done what you suggest. Attached is a new 
outputs.
Thanks
Stefano
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Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve 
dgreve@mgh.harvard.edu ha scritto:
Are you sure that you are using the new version that I gave you? 
It looks like the previous version. Also, it does not look like 
the entire terminal output.
On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:
>
>         External Email - Use Caution
>
> The entire terminal output is attached.
> Thanks!
>
>> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
>> dgreve@mgh.harvard.edu ha scritto:
>>
>> entire terminal output
>

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Re: [Freesurfer] if: Expression Syntax - preproc-sess