Sorry, just recognized it. The option to pass label file is ‘-l’. It looks like you have ‘-1’ instead.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Kavanaugh, Brian
Sent: Wednesday, March 6, 2024 8:55 AM
To: 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