does it exist in the same folder that you are running the command from?

On 03/25/2014 05:15 PM, Carl Anderson wrote:
> Oh yes,
>
> /Applications/freesurfer/subjects/bert/label/aparc.annot.ctab
>
>
> On Tue, Mar 25, 2014 at 11:35 AM, Douglas N Greve

> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     does that file exist?
>     On 03/25/2014 10:04 AM, Carl Anderson wrote:
>     > Dear list,
>     > I tried runing the example in mris_label2annot's help:
>     >
>     > mris_label2annot --s bert --h lh --ctab aparc.annot.ctab --a myaparc
>     > --l lh.unknown.label --l lh.bankssts.label --l
>     > lh.caudalanteriorcingulate.label --nhits nhits.mgh
>     >
>     > got the following result:
>     >
>     > ERROR: cannot find or read aparc.annot.ctab
>     >
>     > aparc.annot.ctab is in bert and here is my setup:
>     >
>     > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>     --------
>     > Setting up environment for FreeSurfer/FS-FAST (and FSL)
>     > FREESURFER_HOME /Applications/freesurfer
>     > FSFAST_HOME /Applications/freesurfer/fsfast
>     > FSF_OUTPUT_FORMAT nii.gz
>     > SUBJECTS_DIR /Applications/freesurfer/subjects
>     > MNI_DIR /Applications/freesurfer/mni
>     > FSL_DIR /usr/local/fsl
>     >
>     > could this be a bash vs tcsh problem as I am using bash?
>     >
>     > --
>     > <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
>     > Carl M. Anderson, Ph.D. (mail stop 204)
>     > Assistant Professor of Psychiatry,
>     > Harvard Medical School &
>     > The Neuroimaging Center,
>     > McLean Hospital 115 Mill St. Belmont, MA 02478
>     > Ph: 617-855-2972; Fax: 617-855-2770
>     > e-mail: remfract@gmail.com <mailto:remfract@gmail.com>

>     <mailto:remfract@gmail.com <mailto:remfract@gmail.com>>;
>     > carl_anderson@hms.harvard.edu
>     <mailto:carl_anderson@hms.harvard.edu>
>     <mailto:carl_anderson@hms.harvard.edu

>     <mailto:carl_anderson@hms.harvard.edu>>
>     > <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu

>     <mailto:Freesurfer@nmr.mgh.harvard.edu>

>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>     --
>     Douglas N. Greve, Ph.D.
>     MGH-NMR Center

>     greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
>     Phone Number: 617-724-2358 <tel:617-724-2358>
>     Fax: 617-726-7422 <tel:617-726-7422>
>
>     Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>     <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
>     FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>     www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>     <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

>     Outgoing:
>     ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>     _______________________________________________
>     Freesurfer mailing list

>     Freesurfer@nmr.mgh.harvard.edu <mailto: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.
>
>
>
>
> --
> <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
> Carl M. Anderson, Ph.D. (mail stop 204)
> Assistant Professor of Psychiatry,
> Harvard Medical School &
> The Neuroimaging Center,
> McLean Hospital 115 Mill St. Belmont, MA 02478
> Ph: 617-855-2972; Fax: 617-855-2770
> e-mail: remfract@gmail.com <mailto:remfract@gmail.com>;
> carl_anderson@hms.harvard.edu <mailto:carl_anderson@hms.harvard.edu>
> <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer