EXAMPLE 1
APPLYING TRANSFORMS (INCLUDING TALAIRACH)
The volume can be resampled into another space by supplying a
transform using the --apply_transform flag. This reads the transform
file and applies the transform (when --apply_inverse_transform is
used, the transform is inverted and then applied). An example of a
transform file is talairach.xfm as found in subjectid/mri/transforms.
To convert a subject's orig volume to talairach space, execute the
following lines:
* cd subjectid/mri mkdir talairach mri_convert --apply_transform
transforms/talariach.xfm --devolvexfm subjectid --ic 0 0 0 orig
talairach
This properly accounts for the case where the input volume does not
have it's coordinate center at 0.To evaluate the result, run:
* tkmedit -f $SUBJECTS_DIR/talairach/mri/orig -aux talairach
The main and aux volumes should overlap very closely. If they do not,
use tkregister2 to fix it (run tkregister --help for docs).
EXAMPLE 2
From the subject directory: mri_convert -at mri/transforms/talairach_
one.m3z mri/norm.mgz mri/norm_transformed_by_gca_one.mgz
BUGS
None
REPORTING
Report bugs to <freesurfer@nmr.mgh.harvard.edu>
SEE ALSO
mris_convert
Jasmins-MacBook-Pro:subjects jasminalves$
What happens if you try to run mri_convert ?
On 01/14/2016 05:10 PM, Jasmin Alves wrote:
>
> Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
> $FREESURFER_HOME/bin/tksurfer
>
> -rwxr-xr-x 1 root wheel 103 May 14 2013
> /Applications/freesurfer/bin/tksurfer
>
>
> Jasmins-MacBook-Pro:freesurfer jasminalves$ $> freeview -v
> $SUBJECTS_DIR/bert/mri/brainmask.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
>
> -bash: freeview: Permission denied
>
>
> On Thu, Jan 14, 2016 at 2:04 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> Jasmin, can you just cut and paste it into the email?
>
> On 01/14/2016 04:59 PM, Jasmin Alves wrote:
> > Here is the output to the ls command
> >
> > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves <jalves@usc.edu
> <mailto:jalves@usc.edu>
> > <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>> wrote:
> >
> > Hi Dr. Greve,
> >
> > I am still receiving the same message that I am denied access to
> > freeview. Is there anything I can do?
> >
> > Thanks,
> > Jasmin
> >
> > On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > Hi Jasmin, do you have permission to execute FS
> commands? What
> > is the
> > result of
> > ls -l $FREESURFER_HOME/bin/tksurfer
> >
> >
> >
> > On 01/14/2016 04:16 PM, Jasmin Alves wrote:
> > > Hello,
> > >
> > > I recently downloaded freesurfer on my mac with a Yosemite
> > operating
> > > system. The application itself appears to work,
> however I am
> > not able
> > > to use the command line to do any of the testing free
> surfer
> > commands,
> > > as I keep getting a access denied. I have attached a
> > screenshot. Your
> > > help would be very useful.
> > >
> > > Thank you,
> > > Jasmin
> > >
> > > --
> > > Jasmin Alves
> > > Predoctoral Student
> > > Medical Biology Graduate Program
> > > University of Southern California
> > > jalves@usc.edu <mailto:jalves@usc.edu>
> <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>
> > <mailto:jalves@usc.edu <mailto:jalves@usc.edu>
> <mailto:jalves@usc.edu <mailto:jalves@usc.edu>>>
> > >
> > >
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > > 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.
> >
> >
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu
> <mailto:jalves@usc.edu>>
> >
> >
> >
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jalves@usc.edu <mailto:jalves@usc.edu> <mailto:jalves@usc.edu
> <mailto:jalves@usc.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
>
>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jalves@usc.edu <mailto:jalves@usc.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/
_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu
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