Hi Brian, Since there is no output, I’m wondering if it passed reading lh.cortex.label.
Some questions: 1. how did you generate lh.cortex.label? It needs to have the format described here - https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles 2. what is your SUBJECTS_DIR? ‘echo $SUBJECTS_DIR’ will show it. 3. can you try adding ‘-seed 1234’ option to your command line? Make sure to add it after ‘-l <lh.cortext.label>’. I just wanted to confirm if mris_ca_label read your lh.cortex.label correctly. It should print ‘setting seed for random number generator to 1234’ if lh.cortex.label is read fine. 4. I noticed that you have ‘sub-004’ in the path to lh.cortex.label, but the subject id passed to mris_ca_label is ‘001’. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Kavanaugh, Brian Sent: Wednesday, March 6, 2024 5:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory External Email - Use Caution Thanks again Yujing. There is not, here is a screen shot of the command (I removed the other inputs for clarity) followed by the output, which is just "segmentation fault (core dumped)" [cid:image001.png@01DA7077.5F9EC230] I think before you asked which free surfer version, which is here: [cid:image002.png@01DA7077.5F9EC230] On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> wrote: It is hard to tell without the data. Is there any output before the core dump? 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 Sennott, Liam Ricker Sent: Wednesday, March 6, 2024 4:28 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory 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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Huang, Yujing <yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>> Date: Wednesday, March 6, 2024 at 11:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto: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<mailto: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 - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_label<https://secure-web.cisco.com/1mpplmqgALrQMWIYrLdz3-T81mClV9RLqIm7McPPGsKuRnj2GZ84HFV-m2wmxmkJ5F593L8IKHZ6sZ0aXD-oWhfy15Bp_Xd7OwdkVBmvVpSKi8WWDeqld0BFIAoDNKizWPhuE2G5HuZftvudh-oEvUhJcnqegcfT3_TP3ZKvuoIidvkW5WDXhEmzC8X_Qo_Hs3sR3msa2y9vowhXlfwNWiuswFZpnOye-0L2s3kPrbLeG9zsuTUy_ti2vaoEgrbTLEZfbCmM4pyT0SpKTovARJbhi48KwmGxudsIgYOh6QRGNps6NRKE4ji8J2aOK0SQ_Pgx40qIepWK3rUepCcTJ6g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_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. 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