External Email - Use Caution Hi Anastasia,
I have posted a solution to the thread "TRACULA -bedp parallel processing" Maybe you can include it in a future release. Thanks, King-Wai On Mon, Aug 1, 2022 at 12:57 AM Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote: > Good to hear, thanks for testing it. We'll implement a permanent solution > so you won't have to replace anything in the future. > ------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai....@gmail.com > <kingwai....@gmail.com> > *Sent:* Monday, August 1, 2022 12:44 AM > *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 > > > External Email - Use Caution > > Hi Anastasia, > > > > I thought he wants me to run trac-preproc.sh he sent to run it directly. > > I wasn’t told to replace it with the one in the original 7.3. > > > > After replacing the original one with the modified one Doug sent, trac-all > -prep -c config.file runs w/o problem. > > > > Thanks, > > > > King-Wai > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia > *Sent:* Monday, August 1, 2022 12:15 AM > *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 > > > > Indeed. Doug sent you a modified version of trac-preproc, which is a > script that's called by trac-all. The idea was for you to overwrite > $FREESURFER_HOME/bin/trac-preproc with the version that Doug sent, then run > trac-all like before. Did you try that? > ------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai....@gmail.com > <kingwai....@gmail.com> > *Sent:* Monday, August 1, 2022 12:10 AM > *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 > > > > * External Email - Use Caution * > > Hi Anastasia, > > > > The problem is in 7.3, trac-all -prep -c config.file 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). > > > > Thanks, > > > > King-Wai > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Yendiki, Anastasia > *Sent:* Monday, August 1, 2022 12:03 AM > *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 > > > > Hi King-Wai - You are not supposed to run trac-preproc directly. Run > trac-all -c configfile, like before. > > > > Anastasia. > > > ------------------------------ > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of kingwai....@gmail.com > <kingwai....@gmail.com> > *Sent:* Monday, July 25, 2022 2:11 PM > *To:* 'Freesurfer support list' <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] TRACULA in FreeSurfer version 7.3 > > > > * External Email - Use Caution * > > 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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@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....@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://secure-web.cisco.com/1eRQUDfx8dovMIVSd5Ci-Vh8QXzCD8sqsMqAE6RBovIp_Ywq-ghf8KE2awRd8WbBOrvjw2OFnkvyu5YcAWeM6CWtpDyNHygv6s1DveI7djN4iO_jT0kR9iE-Xb_ugt-8LoTXToIZVKlMA6tbwWdTwxmCO32LmLIukYMVp1PT-i49jKWPQxIL521z4Q3PrL1Ht7JPeZHkDkbBpi1A6DV4b6QVadl6Y2NB4ObP0uKuKD6YDXN9Zjx1roOhGYl6MAll22kvB68-AKv8EhYbK8LtadSKkbEnfDzajB5ee8v01bqzp3IECpWchoe13pZ9wnZTz0OR48r3dr48D3sf8ANN5CA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <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> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1eRQUDfx8dovMIVSd5Ci-Vh8QXzCD8sqsMqAE6RBovIp_Ywq-ghf8KE2awRd8WbBOrvjw2OFnkvyu5YcAWeM6CWtpDyNHygv6s1DveI7djN4iO_jT0kR9iE-Xb_ugt-8LoTXToIZVKlMA6tbwWdTwxmCO32LmLIukYMVp1PT-i49jKWPQxIL521z4Q3PrL1Ht7JPeZHkDkbBpi1A6DV4b6QVadl6Y2NB4ObP0uKuKD6YDXN9Zjx1roOhGYl6MAll22kvB68-AKv8EhYbK8LtadSKkbEnfDzajB5ee8v01bqzp3IECpWchoe13pZ9wnZTz0OR48r3dr48D3sf8ANN5CA/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/1WsVlijlmEIyYQfyg72ys4BBEuYJZFav7e9xZaoM93vyCLbmdNyo2ARMZciTNNLm4hqhnFDEVE4HXEwH2nqMSupMjkbsFAW-RKm0wvIIDsiIxWhoAV-trbLifyMg8lvPQe2kZQHEJL58EuX8dKNRvJIcl9mGWmvhQMCrATvb5jrWDdO4W4I1ovh8yv5OFBfsTBDqMizrV-juTaCD9bQDHQ5tjjl7t5vHh2Qx_SOW0b5DSTsSQhlNMIAv9RJNwGdaEZanorvNvbDo3h60iD2ZmDSsGwI1XGfm_vM4bV61-S0FoRwKO5BKZzWketDhTuM2U1Y-ynYTkCx6dSQurKVseOA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1WsVlijlmEIyYQfyg72ys4BBEuYJZFav7e9xZaoM93vyCLbmdNyo2ARMZciTNNLm4hqhnFDEVE4HXEwH2nqMSupMjkbsFAW-RKm0wvIIDsiIxWhoAV-trbLifyMg8lvPQe2kZQHEJL58EuX8dKNRvJIcl9mGWmvhQMCrATvb5jrWDdO4W4I1ovh8yv5OFBfsTBDqMizrV-juTaCD9bQDHQ5tjjl7t5vHh2Qx_SOW0b5DSTsSQhlNMIAv9RJNwGdaEZanorvNvbDo3h60iD2ZmDSsGwI1XGfm_vM4bV61-S0FoRwKO5BKZzWketDhTuM2U1Y-ynYTkCx6dSQurKVseOA/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. > -- King-Wai Chu, Ph.D. Program Analyst Mental Illness Research, Education and Clinical Center (MIRECC, VISN3) James J. Peters Dept. of Veterans Administration Medical Center (OOMH) 130 W. Kingsbridge Road Bronx, NY 10468
_______________________________________________ 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.
