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?
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; carl_anderson@hms.harvard.edu mailto:carl_anderson@hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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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
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; carl_anderson@hms.harvard.edu mailto:carl_anderson@hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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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
No...I will try running it from lables
On Tue, Mar 25, 2014 at 6:04 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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 --amyaparc
> --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 <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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-- 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/
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or just give it the full path to the file
On 03/25/2014 06:12 PM, Carl Anderson wrote:
No...I will try running it from lables
On Tue, Mar 25, 2014 at 6:04 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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> <mailto: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>> > <mailto: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>> > <mailto: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> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> > <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> <mailto: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 <tel:617-855-2972>; Fax: 617-855-2770 <tel: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-- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> 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 <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>
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freesurfer@nmr.mgh.harvard.edu
-
Carl Anderson -
Douglas N Greve