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 nathanhutcheson.com http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46
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 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 nathanhutcheson.com http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46
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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*)
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