Thanks for all your advice, Thomas and Doug.
I'm going to try running $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz through recon-all myself to get the norm.mgz and talairach.m3z files. I have some mri_convert commands that should be able to warp this to talairach.m3z space which, as Doug mentioned in a previous e-mail to me, is essentially MNI305.
Hopefully that will work the way I want it to!
Cheers, Paul
On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
That's strange. FSL_MNI152_FreeSurferConformed_1mm.nii.gz should correspond exactly to norm.mgz obtained from running $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz through recon-all (FS4.5).
So Doug's command should work as well. Just to confirm, can you run
freeview FSL_MNI152_FreeSurferConformed_1mm.nii.gz
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
The two templates should be exactly overlapping.
--Thomas
On Tue, Oct 1, 2013 at 9:40 PM, Paul Beach pabeach1@gmail.com wrote:
Doug,
Unfortunately I cannot load this volume into tkmedit as this is not a subject that has been ran through Freesurfer - it's the downloadable FSL-based T1 volume from the "Yeo_JNeurophysiol11_MNI152" package available on the Freesurfer website. I'm trying to convert this and subsequent functional networks to MNI305 for connectivity analysis.
However, I did open up the results in FSLview and Freeview. I have attached screen shots of each, respectively. FSLview [image: Inline image 1] Freeview [image: Inline image 2]
Again, these images are resultant from the following script: *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*
Thanks, Paul
On Mon, Sep 30, 2013 at 7:46 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
View it in tkmedit to see if it is really a problem with your vol2vol command. doug
On 09/30/2013 07:33 PM, Paul Beach wrote:
No. That was just a general example of how the image looks - from a stock google image of an FSL brain (I'm not in the lab and so cannot put up actual images). I've been using AFNI to view them.
On Mon, Sep 30, 2013 at 7:23 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
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<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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.eduFreesurfer@nmr.mgh.harvard.edu
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- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
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