Just to follow-up, the sd command is an alias for setting the SUBJECTS_DIR environmental variable to the present working directory.

Mihaela was able to get rid of the "Bad fd number" error by running the following commands on her ubuntu workstation. It seems like this error is not freesurfer-specific, and relates to recent versions of ubuntu. See links for details.

sudo mv /bin/sh /bin/sh.bkp sudo ln -s /bin/bash /bin/sh

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg08333.html https://wiki.ubuntu.com/DashAsBinSh

-Louis

On Tue, 4 Mar 2014, Mihaela Stefan wrote:

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
  >> >>
  >> >
  >> >
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