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)"

I think before you asked which free surfer version, which is here:

On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:

It is hard to tell without the data. Is there any output before the core dump?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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>
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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@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-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 - 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

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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.