As suggested, I have modified the .csh file (since the last version does not
have a .cshrc file).I have edited according with my current directories, but
when I try
source $FREESURFER_HOME/SetUpFreeSurfer.csh
I get the following:
-------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------Setting
up environment for FreeSurfer/FS-FAST (and FSL)WARNING:
/Application/freesurfer//Applications/freesurfer/subjects does not
existFREESURFER_HOME /Applications/freesurfer/FSFAST_HOME
/Applications/freesurfer//fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR
/Application/freesurfer//Applications/freesurfer/subjectsMNI_DIR
/Applications/freesurfer//mni
The editing I made to the .csh file are the following:
setenv FREESURFER_HOME /usr/local/freesurfer/stable5-pub CHANGED TO:setenv
FREESURFER_HOME /Applications/freesurfer/endif
setenv SUBJECTS_DIR $FREESURFER_HOME/subjectsendifCHANGED TO:setenv
SUBJECTS_DIR $FREESURFER_HOME/subjectsendif
Many thanks,Pablo
> Date: Thu, 6 Jun 2013 14:22:07 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Enquire about running FreeSurfer {Disarmed}
>
>
> 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: gr...@nmr.mgh.harvard.edu
> > > To: pablon...@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: gr...@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
> > > > > >
> > > >
> > <https://connect.yale.edu/owa/14.3.123.3/scripts/premium/redir.aspx?C=Alh1YjfYCUe8ElP16xL_q_5yptViNtAIG4dh8kuWzHm46SgPyyH76vPaU4_Khh3GCekIs1EN4G4.&URL=https%3a%2f%2fsurfer.nmr.mgh.harvard.edu%2ffswiki%2fTestingFreeSurfer>),
> >
> >
> > > >
> > > > > > I always get "command not found". I was wondering if you would be
> > > > able
> > > > > > to help me.
> > > > > > Thanks,
> > > > > > Pablo
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > 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
> > > > > gr...@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
> > > > >
> > > > >
> > > > > 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.
> > > > >
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@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
> >
> >
> > _______________________________________________
> > 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
> gr...@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
_______________________________________________
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.
