What is your fcseed-config command line? If the input is not fmcpr, then
you have to set the input when you config, eg, -funcstem f.even
On 3/19/2024 11:37 AM, Stefano Delli Pizzi wrote:
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Thank you Doug.
The preproc-sess command line runs fine.
An error occurs on:
fcseed-sess -s ID -cfg wm.config -overwrite
ERROR: could not determine file for rs-fMRI_AROMA/ID/rest/001/fmcpr
Best regards
Stefano
Il giorno 19 mar 2024, alle ore 15:54, Douglas N. Greve
<dgr...@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
<sdellipi...@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
<sdellipi...@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
<dgr...@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
<dgr...@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
<dgr...@mgh.harvard.edu> ha scritto:
entire terminal output
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