Sorry..
We had Louis Vinke come here to train our lab last year. He helped us set the environment for FS He taught us to cd to the working directory and then use the command sd to set the directory. I thought that was enough to use freesurfer tools.
On Tue, Mar 4, 2014 at 2:09 PM, dgw dgwakeman@gmail.com wrote:
Please be sure to 'reply all' so everyone may participate.
Yes, You need to set the SUBJECTS_DIR before using freesurfer tools.
HTH D
On Tue, Mar 4, 2014 at 2:02 PM, Mihaela Stefan mikaelastephan@gmail.com wrote:
It says "No such file or directory" The environment for SUBJECTS_DIR was set as
/usr/local/freesurfer/subjects
but I have my working folder in a different location. Could that be the problem?
On Tue, Mar 4, 2014 at 1:34 PM, dgw dgwakeman@gmail.com wrote:
Are those subjects in your SUBJECTS_DIR?
What is the output of ls $SUBJECTS_DIR ?
On Tue, Mar 4, 2014 at 1:10 PM, Mihaela Stefan <
mikaelastephan@gmail.com>
wrote:
Hello, I am re-posting this since I haven't got an answer yet.
Thanks! Mihaela
On Fri, Feb 21, 2014 at 3:55 PM, Mihaela Stefan mikaelastephan@gmail.com wrote:
Hi freesurfers,
I get this error when I load qdec.table.dat. Is it something wrong or should I ignore it? Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6027' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6209' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '6243' in SUBJECTS_DIR . . . ERROR: QdecProject::VerifySubjects: Couldn't find subject '6052' in SUBJECTS_DIR Too many subjects not found!
Someone else complained about the same problem but there was no
reply:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08288.html
My qdec.table looks like this: fsid diagnosis Cage 6027 ABN -1.39 6209 ABN 2.61 . .
Thanks! Mihaela
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to
you
in error but does not contain patient information, please contact the sender
and
properly dispose of the e-mail.