I’m not familiar with your environment setup. But can you do ‘ls -l’ of the file it is complaining?
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Kavanaugh, Brian
Sent: Thursday, March 7, 2024 12:02 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
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Yes! Novice error. my fault. but tremendous progress, I made it all on the same line, and now it is getting close.
It now appears to be an error related to the directory? my inputs aren't in the subject_dir, but it is trying to pull from the directory? Is there a way I could have it pull from my current files in '/freesurfer/sub-004'? Maybe relates
back to freesurfer is part of the ood/virtual environment?
thank you again!
On Thu, Mar 7, 2024 at 11:47 AM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
It looks like your command line is split into multiple lines. Put ‘\’ at the end of each line before hitting ‘enter’. For example, ‘mris_ca_label -l \’
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Kavanaugh, Brian
Sent: Thursday, March 7, 2024 11:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
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Hi Yujing,
Thanks again.
1. I think the lh.cortex.label should be correct, it looks good in freeview and works when uploaded to brainstorm. But certainly I could be missing something.
2. SUBJECTS_DIR:
3. it looks like the '-seed 1234' option doesn't change anything?
4. Yes, that was my error, I was trying a few participants in case the issue was with one person.
One bigger contextual variable is that i'm running freesurfer in a virtual environment within our university OOD/virtual desktop. So I didn't download freesurfer, and the files I'm pulling from are not part of the 'SUBJECTS_DIR'.
Maybe this isn't important, but I notice the "segmentation fault (core dumped) error occurs before the lh.cortex.label, so it is in response to the primary mris_ca_label command, so maybe it is related to my access of free surfer?
brian
On Thu, Mar 7, 2024 at 10:18 AM Huang, Yujing <YHUANG43@mgh.harvard.edu> wrote:
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 - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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
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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
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