Is this in tkmedit?
On 09/30/2013 06:59 PM, Paul Beach wrote:
Hi Doug,
Sorry, I should have been more specific. I meant for when one looks at the resulting transformation in a sagittal view.
More specifically... Instead of this: Inline image 1
It looks more like this (though more like a 70degree shift than 90): Inline image 2 The other views are obviously affected as well. Performing a dataset "nudge" using afni generally "corrects" this problem, but I'd like to prevent it from happening in the first place.
I'm suspicious that this is occurring because I'm using '/mni305.cor.mgz/' instead of '/mni305.2mm.nii.gz/' for the 'mov' command. However, I don't have the latter file anywhere in my Freesurfer directory. The former file is the closest thing I could find.
Thoughts? Paul
On Mon, Sep 30, 2013 at 5:52 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what do you mean the frontal lobe is pointing straight up? On 09/30/2013 02:32 PM, Paul Beach wrote: > Freesurfer experts, > > I'm attempting to utilize an archived e-mail's contents to resample > data in MNI152 to 305. > > The script I'm using is as follows: > /mri_vol2vol \/ > /--mov > /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz > \/ > /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz \/ > /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ > /--inv --o FSL_MNI305_2mm.nii.gz/ > / > / > / > / > This series of commands is based on the following suggestion from Doug > in a previously archived e-mail exchange from someone attempting to do > something similar: > />> To go from mni152 to the MNI305 2mm space, use/ > />>/ > />> mri_vol2vol --mov mni305.2mm.nii.gz \/ > />> --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \/ > />> --reg > $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat \/ > />> --inv --o output.mni305.2mm.nii.gz/ > />>/ > />> This will resample MNI152_T1_2mm.nii.gz (or anything in that > space) to the/ > />> mni305 2mm space./ > > > However, this changing the orientation of my data - essentially all > images are being rotated 90degrees so the frontal lobe is pointed > straight up. > > Are there any suggestions to ameliorate this problem? > > Thanks! > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > > > _______________________________________________ > 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 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
- Bozoki Lab: Neurology/Radiology