Sending on behalf of Brian who was having trouble sending a reply:
Dear Yujing, Thank you! Haha yes, a silly error there with the -1/-l. When I correctly put -l, I now get the following error: "segmentation fault core dumped". Might this error make any sense to you? Brian From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 11:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory Sorry, just recognized it. The option to pass label file is ‘-l’. It looks like you have ‘-1’ instead. From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Wednesday, March 6, 2024 10:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory I’m not sure which version of Freesurfer you are using. But it seems the command line options are not in the right order. Here is the wiki help - https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Kavanaugh, Brian Sent: Wednesday, March 6, 2024 8:55 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] ascii: bad interpreter: No such file or directory External Email - Use Caution Hello everyone, I am new to freesurfer so I apologize if this is a simple answer. i'm running mris_ca_label to get the BN atlas parcellation: mris_ca_label -1 /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label 001 lh /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/surf/lh.sphere.reg /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/lh.BN_Atlas.gcs /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.BN_Atlas.annot But it seems freesurfer is having an issue reading my lh.cortex.label file: /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/sub-004/label/lh.cortex.label: ascii: bad interpreter: No such file or directory Might anyone have thoughts on how to resolve? I've seen adjacent errors before, but none related to ascii specifically. thank you! brian Brian Kavanaugh, PsyD, ABPP Board Certified Pediatric Neuropsychologist, E. P. Bradley Hospital Assistant Professor, Warren Alpert Medical School of Brown University
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