are you sure the config file is right? it should be defining the intrareg variable
On 7/25/2022 2:11 PM, kingwai.chu@gmail.com wrote:
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Hi Douglas,
Thank you for looking into this.
It gives the following error.
trac-preproc.sh -c config.file
intrareg: Undefined variable.
Thanks,
King-Wai
*From:*freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Douglas N. Greve *Sent:* Monday, July 25, 2022 1:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3
Can you copy the attached trac-preproc into $FREESURFER/bin and try again (after removing the link)?
On 7/22/2022 8:36 AM, kingwai.chu@gmail.com wrote:
* External Email - Use Caution * Hi Anastasia, Just downloaded FreeSurfer version 7.3 and trying out TRACULA. Ran recon-all, segmentThalamicNuclei.sh, and trac-all in v7.3 However trac-all -prep is looking for ThalamicNuclei.v12.T1.FSvoxelSpace.mgz from segmentThalamicNuclei.sh which doesn’t exist. Because in v7.3, segmentThalamicNuclei.sh output a new version v13 (ThalamicNuclei.v13.T1.FSvoxelSpace.mgz). I worked around this problem by linking ThalamicNuclei.v12.T1.FSvoxelSpace.mgz to ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ln -s ThalamicNuclei.v13.T1.FSvoxelSpace.mgz ThalamicNuclei.v12.T1.FSvoxelSpace.mgz trac-all finished w/o problem. trac-all -version trac-all 7.3.0 I seems trac-all in v7.3 forgets to update the fact that segmentThalamicNuclei.sh output v13 of the file. Or it is looking for v12 for a reason? Is my fix correct? Thanks, King-Wai _______________________________________________ Freesurfer mailing list 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/freesurfer <https://secure-web.cisco.com/1mfowdBcxH4LnEHqsQ4eF-CAYl64n3ckGL8BGt4nPbtL4OeGumkxM8MllrxFKmlByW-LDM0iMEYy94ixKM1KG3D-kKHOVUO8yLsvCtRWCmCwq0XtztyJyTf4VVuC9j4oGmFvWyMZHOnLCIisJpgKeApdTCX-4yI8tH5YJehBsANpbd_YTkwiTtKJMmy3b2t9gJoR0e19abaQXY_1HDz5kr8IlMEUasxk6j9EZY4il5LllVP2dIL6ENMUR3_yH1DE_Jx0srZwfJk-1YClbUR44-7qjZtjJNof8WulEr0kzdYcSPacrNREGNjxFBBnDIBqlC0sAF6ORBWT3SuDX5McR9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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