Anastasia,

Thanks for your help on this!

I looked through the subjects for which the corticospinal tract failed, and the scans didn’t seem truncated compared to the ones that ran successfully. But since we are not particularly concerned with the cst, I thought I’d try to run all other pathways. Based on info for setting up the config file, I thought adding this line to the config file would work:

set pathlist = ( acomm cc.bodyc cc.bodypf cc.bodypm cc.bodyp cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af lh.ar lh.atr lh.cbd lh.cbv lh.emc lh.fat lh.fx lh.ilf lh.mlf lf.or lh.slf1 lh.sl2 lh.slf3 lh.uf rh.af rh.ar rh.atr rh.cbd rh.cbv rh.emc rh.fat rh.fx rh.ilf rh.mlf rh.or rh.slf1 rh.slf2 rh.slf3 rh.uf )

But I got this error message:

ERROR: length of pathway list (acomm cc.bodyc cc.bodypf cc.bodypm cc.bodyp cc.bodyt cc.genu cc.rostrum cc.splenium mcp lh.af lh.ar lh.atr lh.cbd lh.cbv lh.emc lh.fat lh.fx lh.ilf lh.mlf lf.or lh.slf1 lh.sl2 lh.slf3 lh.uf rh.af rh.ar rh.atr rh.cbd rh.cbv rh.emc rh.fat rh.fx rh.ilf rh.mlf rh.or rh.slf1 rh.slf2 rh.slf3 rh.uf) and endpoint label ID list

ERROR: (0 0 0 0 0 0 0 0 0 0 0 10 10 0 0 0 0 28 0 0 0 0 0 0 49 49 0 0 0 0 60 0 0 49 0 0 0 0) do not match

Looks like I need to change the endpoint label ID list? How would I do that?

Bryna Goeckner (she/her)

Graduate Student

Medical College of Wisconsin

Neuroscience Doctoral Program

Date: Thu, 17 Mar 2022 18:18:26 +0000
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Subject: Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes
        with    errors
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <MN2PR04MB681631333C83A03772141E4B8A129@MN2PR04MB6816.namprd04.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

Hi Bryna - I see that the error occurs in the corticospinal tract. Any change the top or bottom of the brain is truncated in this subject's scan?

Anastasia.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Goeckner, Bryna <bgoeckner@mcw.edu>
Sent: Thursday, March 17, 2022 11:53 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Reposting TRACULA trac-all -prep finishes with errors

        External Email - Use Caution

Attaching config file & link to trac-all.log (trac-all/log is kind of big ? so freesurfer listserv blocked email). Hopefully you are able to access them this way.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://urldefense.com/v3/__https://mcw.box.com/s/fol3dnv5wjbicyfop0rvhl0sampczfm1__;!!H8mHWRdzp34!rgNFqBAcXDJHpyrgh9A57PXSD63Gyirur-56bz2aRp7JXEtZcKuZwC2GMhHn9JUB$ <https://urldefense.com/v3/__https://secure-web.cisco.com/12mEXYhuUBlTXDgjHzPTswpMwBUz25h_vFGE_6-rakbDLzhA78zhVmjjzpHRJ41t3cPhXy3LS4CvSydc4N12DdWNDs4XI5knriU8kSYNeogIj_l7HEliRL9VvZKr-a6RmP6noUihIHhn-80-4O8qhtMEsDDIFVDk6hgmTiHvv6KCDpFEJ2-TX4xK-d6HCcj8YZISTdZWBjoFVQ2ACwNC4DBSN5TcG_t29f_vw7T9pPc_19KAZPKHIwpH0CWGWO6tT-_tvPlOhygDQ6nwEDEcxkncQPXTJO3V9I8nUliLJZ_-yBKE4vhPhkEUQa4HeDgURWEEfrwcUinateQIKKBYVEA/https*3A*2F*2Fmcw.box.com*2Fs*2Ffol3dnv5wjbicyfop0rvhl0sampczfm1__;JSUlJSU!!H8mHWRdzp34!rgNFqBAcXDJHpyrgh9A57PXSD63Gyirur-56bz2aRp7JXEtZcKuZwC2GMkUBdjzn$ >

From: Goeckner, Bryna <bgoeckner@mcw.edu>
Date: Monday, February 14, 2022 at 4:42 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: TRACULA trac-all -prep finishes with errors

Hi FreeSurfer Developers,

I am attempting to run data for several subjects through TRACULA using trac-all -prep, but some of them have finished with errors. I have checked registration for all of them and it looks ok.

I am including a link to my confi