That command seems to work; Here is the output. However in order to prevent the message "access denied" though, should I re-download freesurfer and make a new license text file?
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 $SUBJECTS_DIR/talairach/mri/orig -aux talairach
The main and aux volumes should overlap very closely. If they do not,
use tkregister2 to fix it (run tkregister --help for docs).
EXAMPLE 2
From the subject directory: mri_convert -at mri/transforms/talairach_
one.m3z mri/norm.mgz mri/norm_transformed_by_gca_one.mgz
BUGS
None
REPORTING
Report bugs to freesurfer@nmr.mgh.harvard.edu
SEE ALSO
mris_convert
Jasmins-MacBook-Pro:subjects jasminalves$
On Fri, Jan 15, 2016 at 9:09 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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 accessto
> 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: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 aYosemite
> 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 <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 contactthe
> 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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer