External Email - Use Caution

I forgot to mention: to check whether it worked out in your shell, after the export/setenv command and before running bbregister, you can type:

echo $SUBJECTS_DIR

This should work for all shells.

Best,

Tim

> On 11/15/2021 1:17 PM Tim Schäfer <ts+ml@rcmd.org> wrote:
>
>
> External Email - Use Caution
>
> I think what you want to do is reset the environment variable SUBJECTS_DIR to the location of your subject before running the command.
>
> How to do that depends on your shell. For bash-like shells, this should do it:
>
> export SUBJECTS_DIR=/path/to/your/data
>
> for csh-like shells it would be:
>
> setenv SUBJECTS_DIR /path/to/your/data
>
> Best,
>
> Tim
>
> Just to be sure: this only lasts for the current shell session.
>
> > On 11/15/2021 12:37 PM m-maiworm@web.de wrote:
> >
> >
> > External Email - Use Caution
> >
> > Dear List,
> >
> > when I try to use bbregister it gives out an ERROR saying it can't find the subject.
> >
> > I use freesurfer on a server where it is installed for everybody to use, but i'm not allowed to write in the subject_dir in this home-directory (e.g. "apps/freesurfer/subjects". Therefor I want to tell via command line where to find the subject and where to put the output data.
> >
> > bbregister --s $SUBJ_DIR --mov $TEMP_DIR --reg registration.reg --init-rr --t1 --o $OUT_DIR
> >
> > when I try it like this, freesurfer seems to look for the path given in $SUBJ_DIR in the homedirectory "apps/freesurfer/subjects", which doesn't make sense at all...
> >
> > Can anybody help me with this problem?
> >
> > Thanks a lot! M_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://secure-web.cisco.com/1Gb2RE4cQhf99F8py43LFQdGB24tR2xTZt5x33licyLpK7USP5w9Po6ScKefAWMNmodYuDLHFrNWcEbLkMN_4IhA3BRXXj0oETOCzYLptIlrCmHtBX3_zz5ppBqgse4cAOKXA7DK0q9fPK0MpAufW5T8HG21EKX4dKJV0X81WnaBdQSAnDVrdo6zdVRAV_40wtuOvpXtNOvm7SXVUEa3sgLooz10w3-WPvHevnd1tu7vDE2oO9elepkZjZ1wkn7X2JTYLviVC6_j-HSHqFsx2ZAb0H5sVkEL1PXr7sl0N8JvH2y5-04osq4j14xIne2sFUVyFMHKZMC9EiVzLz3WsEw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1gkxY7omH4gT7shLswU79sxuqQ-i3YaTeRV8ut0cOS0ZO78LButZvqIo8hcb2XILOYobS4KO4_nj2mXZUZQNeWuDjFRGkjIIdUM-HkjBmi3vlhd_H-m2yK3zLv68xv9WGlIebEdNql4szF3EE9D-_JvyMF3ZmOg2IBU4lyTuELGSZKCQeQtmhGM9CNwpj37-nVbNW4Xx6v_0OsW8BLAvpzNygtmYxXVToILH-7NTWsQ5Nt1kwj6v6Plwguyp1rpwW_bkYg5jwwn-WjvktIt02nwoast4kgp8zhzro0HxTuSSuVWEV2JZrlq9fhtkKP44d/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

_______________________________________________
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