Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve <dgreve@mgh.harvard.edu> ha scritto:

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

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

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>

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

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:

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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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<preproc-sess.txt><rawfunc2surf-sess.txt><rawfunc2tal-sess.txt>