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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 > <yhuan...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Stefano Delli Pizzi > Sent: Tuesday, February 13, 2024 4:32 AM > To: Greve, Douglas N.,Ph.D. <dgr...@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-qeSvbi4Ygpl66AsqDp5jQhfgYnt8nhdklQlgisL8SMyMDGItqm1nm6aj4HLQ5A2cS2ruIkz77VKfqHTuzVKihDCJfTw_VvZM7RrLvHW4EpNNFCq8MJu7m0cSGKWwePlXzfQaQ555gFD2zSc4ic4CXGltAOQ0XZo9-tF9aF1MoM1CtniYpeabnzR4LXnk6_s3WC83t2f1EIVg-Z6LzzkgD6KBMY-j8AnAiDwp44K5lWJaPdOZ3pWCUxN6lYAtuSKHw5TYVjUtcjbQPK8ikT1owDwPD2ns6u7Rp2caDw9TI4rygEeFdExhrDRDQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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_YzFb4VNoMYqOU7qKpo4ChvJ7cJs2XXxMoSPzaoa2AKf_fqKXXaRWpCCnLInvVo-M4ybuv98pyMJfrFh7aHIEpNpNV4lV9RlTpFhS9QNGx97xiLzYjSl-zmHTF-uOGMLdzh7v_HVIpccjkbgCadGbh-TsO5NmsyCck9oO3IAnrxQP6t3eUB9xembmyJd9E8PP8FH7ZPMyen_c74UJCy-DmV6SnlHp-fZ1KT4O6MlRiOl0cQCgFbadwc_8J_ezXzrjumUrYiKjNyFdVt7H6bKf0ZLFoh1iPCOPe3jfgqgcj94UrcQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <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> > .
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