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Thank you!

When I run:

stem2fname /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/f.even

I obtain this output:

/Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/f.even.nii.gz

Anyway when I test also for other files, I found f.nii.gz ok, but an error that occurs on fmcpr.nii.gz, which is present in the folder after visual check.

stem2fname /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.nii.gz ERROR: could not determine file for /Users/stefano/Desktop/XXX/rs-fMRI/003_S_6014/rest/001/fmcpr.nii.gz

Kind regards

Stefano

Il giorno 14 feb 2024, alle ore 21:28, Huang, Yujing YHUANG43@mgh.harvard.edu ha scritto:

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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/10UYWaHnqx4BENWI9xbmA4UTtoBV8-qeSvbi4Ygpl66AsqD... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/19R-KHUg-mJTpyNchJK6kESVPGdGZ65kDU18vi0_YzFb4VN... https://secure-web.cisco.com/19R-KHUg-mJTpyNchJK6kESVPGdGZ65kDU18vi0_YzFb4VNoMYqOU7qKpo4ChvJ7cJs2XXxMoSPzaoa2AKf_fqKXXaRWpCCnLInvVo-M4ybuv98pyMJfrFh7aHIEpNpNV4lV9RlTpFhS9QNGx97xiLzYjSl-zmHTF-uOGMLdzh7v_HVIpccjkbgCadGbh-TsO5NmsyCck9oO3IAnrxQP6t3eUB9xembmyJd9E8PP8FH7ZPMyen_c74UJCy-DmV6SnlHp-fZ1KT4O6MlRiOl0cQCgFbadwc_8J_ezXzrjumUrYiKjNyFdVt7H6bKf0ZLFoh1iPCOPe3jfgqgcj94UrcQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline .