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/1Gb2RE4cQhf99F8py43LFQdGB24tR2xTZt5x33licyLpK7U...
-- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
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/datafor csh-like shells it would be:
setenv SUBJECTS_DIR /path/to/your/dataBest,
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/1Gb2RE4cQhf99F8py43LFQdGB24tR2xTZt5x33licyLpK7U...
-- 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-i3YaTeRV8ut0cOS0ZO78...
-- 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@nmr.mgh.harvard.edu
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m-maiworm＠web.de -
Michelle Maiworm
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Tim Schäfer