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)"
[image: image.png]
I think before you asked which free surfer version, which is here:
[image: image.png]
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 - https://secure-web.cisco.com/1mpplmqgALrQMWIYrLdz3-T81mClV9RLqIm7McPPGsKuRnj...
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 https://secure-web.cisco.com/11FXAvokWdGG1GR5U7xeYh1rMOdGS-c0BK9U5p6XtRuBhoF... 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/1Gm9xMJP1-95CeB9NnSY61u-G81gbFSb9zQA8WKLnmkiWu8... < https://secure-web.cisco.com/1Gm9xMJP1-95CeB9NnSY61u-G81gbFSb9zQA8WKLnmkiWu8... . 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.
