You will need to put the FreeSurfer environment variables into your .cshrc file to have it be in effect every time you open a new shell. doug
On 06/06/2013 02:14 PM, pablo najt wrote:
Hello My previous problem seemed to be fixed by reinstalling xquartz. However, the strange thing that I get it that I can perfectly run the following and display the images. This is what I have done. (commands in yellow)
- setenv FREESURFER_HOME /Applications/freesurfer/*
*source $FREESURFER_HOME/SetUpFreeSurfer.csh*
-------- 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 [Pablo-Najts-MacBook-Pro:/Applications/freesurfer] pablonajt%
- setenv SUBJECTS_DIR /Applications/freesurfer/subjects/*
(After this I am able to run)
*freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red*
2013-06-06 14:07:11.155 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.160 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.183 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.186 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.209 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.212 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.235 Freeview[624:903] invalid drawable 2013-06-06 14:07:11.237 Freeview[624:903] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
*However, eerytime I want to open the display I have to repeat all the commands (setenv FRESURFER... ; source ...; setenv SUBJECTS_DIR)
The other problem is that commands such asqdec, tkmedit bert orig.mgz, give "me command not found".
Please let me know if I need to provide you with further information. Many thanks, Pablo
Date: Thu, 6 Jun 2013 13:45:42 -0400 From: greve@nmr.mgh.harvard.edu To: pablonajt@hotmail.com; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
Hi Pablo, please respond to the list and not to us directly. Please
just
cut and paste the text of the error into the email. thanks doug
On 06/06/2013 12:30 PM, pablo najt wrote:
Thank you for your quick response. I have re run the installation but I get the following erros with _tkmedit bert orig.mgz_ and _tksurfer bert rh pial_ commands. Please see attach for the detailed errors. Best, Pablo
Date: Thu, 6 Jun 2013 12:01:22 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Enquire about running FreeSurfer
{Disarmed}
what command is not found? On 06/06/2013 11:58 AM, pablo najt wrote:
Hello I have a question regarding the installation/running
FreeSurfer.
I have just completed the installation and got the
confirmation that
Free surfer was installed. Please see snapshot. However when I follow the steps for testing (*MailScanner has
detected
a possible fraud attempt from "connect.yale.edu" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer
I always get "command not found". I was wondering if you would be
able
to help me. Thanks, Pablo
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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:
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whom it is
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the e-mail
contains patient information, please contact the Partners
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HelpLine at
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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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