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!
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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: [image: Inline image 1]
It looks more like this (though more like a 70degree shift than 90): [image: 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.eduwrote:
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 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
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.
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Paul Beach