You can loop through all the subjects, run mris_ca_label for each subject.
1. export SUBJECTS_DIR=/users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/ 2. cd $SUBJECTS_DIR 3. for subj in subj1, subj2, … do echo “mris_ca_label -l $SUBJECTS_DIR/$subj/label/lh.cortex.label -seed 1234 $subj lh $SUBJECTS_DIR/$subj/surf/lh.sphere.reg $SUBJECTS_DIR/lh.BN_Atlas.gcs $SUBJECTS_DIR/$subj/label/lh.BN_Atlas.annot” mris_ca_label -l $SUBJECTS_DIR/$subj/label/lh.cortex.label -seed 1234 $subj lh $SUBJECTS_DIR/$subj/surf/lh.sphere.reg $SUBJECTS_DIR/lh.BN_Atlas.gcs $SUBJECTS_DIR/$subj/label/lh.BN_Atlas.annot done
List the subjects you would like to run in the ‘for’ statement.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Kavanaugh, Brian Sent: Thursday, March 7, 2024 1:34 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 IT WORKED! Thank you Yujing!
Can you quickly explain how I can run this through all participants instead of just 004?
On Thu, Mar 7, 2024 at 12:26 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: It complains ‘lh.smoothwm’ could not be opened. If you do ‘ls -lt <full-path-to-lh.smoothwm>’, does it complain ‘file not found’?
If you have the files copied over to your local ‘/freesurfer/sub-004'. I believe you pass ‘– sdir /users/bkavanau/data/bkavanau/temp/derivatives/fmriprep/sourcedata/freesurfer/’ to mris_ca_label.
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Kavanaugh, Brian Sent: Thursday, March 7, 2024 12:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
External Email - Use Caution sorry, i'm confused, could you explain that in a slightly different way?
On Thu, Mar 7, 2024 at 12:14 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> wrote: 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
External Email - Use Caution Yes! Novice error. my fault. but tremendous progress, I made it all on the same line, and now it is getting close. [cid:image001.png@01DA7098.DCA9DAF0]
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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ascii: bad interpreter: No such file or directory
External Email - Use Caution 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: [cid:image002.png@01DA7098.DCA9DAF0] 3. it looks like the '-seed 1234' option doesn't change anything? [cid:image003.png@01DA7098.DCA9DAF0] 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.edumailto: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/LabelsClutsAnnotationFileshttps://secure-web.cisco.com/1D9Syh3NYN7I28QF5jG1xR5xRF4e9KITLihEKambbot8Pi9h9hjXSsrMQm6TZAPeTq7XktttMSA3Vep-VWqo9rVDGPnYOJ3LrWFQCwEVxLVTd-xSp6QnhAXur8w1Z8Z_AqZmIeYOpn3HOPDd-2wifpbDpYIKm802ffZEGbB3T3KdbbHybri4sqAE5elpFZTLTFVFblMSSlJP10mz6gFcaX7fY8H3McsjY-_TBYN_nIm0TL5PNk0Dmq5hm--Q0BP_48H46Mu6J-QP_7U0m1bInwCIFptU4chR9a_17qZOPhf3maA8nffbAtG7EsaKKMJGoG-jUbUMXue7Wp4X-ItduVA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLabelsClutsAnnotationFiles 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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:image004.png@01DA7098.DCA9DAF0]
I think before you asked which free surfer version, which is here:
[cid:image005.png@01DA7098.DCA9DAF0]
On Wed, Mar 6, 2024 at 4:51 PM Huang, Yujing <YHUANG43@mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> Date: Wednesday, March 6, 2024 at 11:05 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto: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_labelhttps://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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Kavanaugh, Brian Sent: Wednesday, March 6, 2024 8:55 AM To: freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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/freesurferhttps://secure-web.cisco.com/11FXAvokWdGG1GR5U7xeYh1rMOdGS-c0BK9U5p6XtRuBhoFwOJqR6jL_7Yl7ZF28V67YFPkKqv7ju7XVylbEMudspKBCUItBWsXKTtmVfP-ESRtpWUd5Isvm4gKRKmTNSRSos0HzO9iLgH9tNiY8B_hcMyyXQOniMU41M8ozD1hr0icjyGhfxP7JhglOahz0l_uolZNA5ghSWQl84TqflvmLh0BTrrjF8IrWlm3yelCyIezql6Hk44ag-fWxQzD5K0Uey-_wUu388rOE-TWpNvpN6_nlmiBrIBq-ea8jhmiWigwJeWW3fqjcywqZeNoH62og6SpGHQTPEdW0L84TakA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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