Hi Stefano,

I looked at the log files that you sent in a separate email. I see 2 problems here:

1. when running preproc-sess with -nomc option,  rawfunc2surf-sess couldn’t find file fmcpr.up or fmcpr.even in the directory

2. I think the ‘if: Expression Syntax‘ error is from stem2fname

To confirm #2, can you try ‘stem2fname /home/dylan/Documents/TRACULA/INPUTS/BIDS/derivatives/freesurfer/sub-01/mri/brainmask’ from your command line?

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Stefano Delli Pizzi
Sent: Tuesday, February 13, 2024 4:32 AM
To: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] if: Expression Syntax - preproc-sess with -nomc option

        External Email - Use Caution        

Thank you.

Stefano

Binarizing based on threshold

min        1e-09

max        +infinity

binval        1

binvalnot     0

fstart = 0, fend = 0, nframes = 1

Found 149926 values in range

Counting number of voxels in first frame

Found 149925 voxels in final mask

Writing output to /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/masks/brain.fsaverage.rh.pr.nii.gz

Count: 149925 149925.000000 163842 91.505841

mri_binarize done

  1/1 003_S_6014 001 lh ---------

    Mar 13 Feb 2024 10:28:12 CET

ERROR: could not determine file for /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.even

if ( $status ) exit 1 ;

if ( 1 ) exit 1

exit 1