The immediate problem is with permissions. The bigger problem is what you are trying to do. To transfer the label, use mri_label2vol and $FREESURFER_HOME/mni152.register.dat to map aparc+aseg.mgz to mni152 space. But this is not going to work very well because the label is small. Mixing volume-based and surface-based analysis in this way is strongly discouraged.

doug

On 05/12/2014 01:45 PM, Paul Beach wrote:

Nathan,

I've run into problems like these before when the fsaverage directory is read only. This may be behind your "permission denied" error. Perhaps try to deconstruct the annotation file into your subjects_dir and do the bbregister command on your label of interest from there - or just copy the annotation to your subjects_dir...

Cheers

On Mon, May 12, 2014 at 1:34 PM, Nathan Hutcheson <nhutche@gmail.com mailto:nhutche@gmail.com> wrote:

Hello,

I am trying to use bbrestier to take an .annot file of a
particular structure and register it to MNI space. I want to be
able to use one of the FreeSurfer parcellations of the ACC
(lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction
in FSL in MNI space. Below is the command I used and the error
message I am getting. Please let me know if what I am doing makes
any sense or if I am way off base.


Input

    bbregister --s fsaverage --mov
    /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label
    --t1 --init-fsl --reg register.dat


 Output

    mkdir: cannot create directory `./tmp.bbregister.6489':
    Permission denied

    Log file is register.dat.log

    register.dat.log: Permission denied.






Take care,
Dr. Nathan Hutcheson
Postdoctoral Researcher
University of California Los Angeles
Semel Institute
760 Westwood Plaza C8-202
Los Angeles, CA 90024
T: 770.841.1694 <tel:770.841.1694>
nathanhutcheson.com <http://nathanhutcheson.com>
<http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46>

_______________________________________________
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.

-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer