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 <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 < > 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> > *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 < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing < > yhuan...@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-boun...@nmr.mgh.harvard.edu < > 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> > *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-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 < > 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 > *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-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. 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-G81gbFSb9zQA8WKLnmkiWu8DsqYFUWRLzIt5qpOrIJsjr5tDtfLLMVYSwnNIR_4Uj8goIJKIDWM3GkrPm-D31YY6zl9czfIFhbrfzZcxNyQIC6EKW9rPJo57kGSnboooeNk9RLiYXKML44NWAp1kWS5tfPx55A46caX601ks6vrsLKzKGyJUYgNXn9hQhvkEFkU4k9yCWr_JatqxuYuXnpwdNCsEjiMEzT1fxGmhf0y5FPPptq4Y3hFRBj_8DfQKXN974F-W-DGQSAlNQDAaXgMd2opS4Uly7TwrjVh6Yuz7Mu1QEYcKN5HAyfX3eig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1Gm9xMJP1-95CeB9NnSY61u-G81gbFSb9zQA8WKLnmkiWu8DsqYFUWRLzIt5qpOrIJsjr5tDtfLLMVYSwnNIR_4Uj8goIJKIDWM3GkrPm-D31YY6zl9czfIFhbrfzZcxNyQIC6EKW9rPJo57kGSnboooeNk9RLiYXKML44NWAp1kWS5tfPx55A46caX601ks6vrsLKzKGyJUYgNXn9hQhvkEFkU4k9yCWr_JatqxuYuXnpwdNCsEjiMEzT1fxGmhf0y5FPPptq4Y3hFRBj_8DfQKXN974F-W-DGQSAlNQDAaXgMd2opS4Uly7TwrjVh6Yuz7Mu1QEYcKN5HAyfX3eig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > 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. >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 https://www.massgeneralbrigham.org/complianceline <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.
