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.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> <mailto: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> <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> <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> <mailto: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 -- 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/-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
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.eduwrote:
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
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer 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<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>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<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
-- 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/
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
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<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>Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting><http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html><http://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/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
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Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz * * * and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
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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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<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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<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
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Paul,
Just to clarify,
1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your other software?
2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does it look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.com wrote:
Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz
and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
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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-- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<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
-- 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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
Thomas,
1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Paul,
Just to clarify,
- If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your
other software?
- If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does it
look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.com wrote:
Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz
and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
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.**edugreve@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 > <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>>>
> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 tel:617-724-2358 <tel:617-724-2358 tel:617-724-2358> Fax: 617-726-7422 tel:617-726-7422 <tel:617-726-7422
<tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** BugReporting http://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 <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>>>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contactthe 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://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 <http://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
-- 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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.com wrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks fine
- strangely FSLview of this is mis-oriented, but Freeview and AFNI look
fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Paul,
Just to clarify,
- If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your
other software?
- If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does it
look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.com wrote:
Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz
and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
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.**edugreve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.**edugreve@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 > > > <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu > >> > > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > freesurferhttps://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 greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu > > <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu > >> > Phone Number: 617-724-2358 tel:617-724-2358 > <tel:617-724-2358 tel:617-724-2358> > Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 > tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > http://surfer.nmr.mgh.**harvard.edu/fswiki/** BugReporting http://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 > http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > http://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/ > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu > > > <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu > >> > > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** > freesurferhttps://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/**compliancelinehttp://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 > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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 > <http://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 >
-- 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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
The mri_convert command did not work... * * *[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz* *mri_convert mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from mni305.cor.mgz...* *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.com wrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks fine
- strangely FSLview of this is mis-oriented, but Freeview and AFNI look
fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Just to clarify,
- If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your
other software?
- If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does
it look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.com wrote:
Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz
and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
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.**edugreve@nmr.mgh.harvard.edu >> >> <mailto:greve@nmr.mgh.harvard.**edugreve@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 >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >> >> >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/* >> *freesurferhttps://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 greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >> >> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >> >> >> Phone Number: 617-724-2358 tel:617-724-2358 >> <tel:617-724-2358 tel:617-724-2358> >> Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 > >> tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> http://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 >> http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.* > *html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> > >> http://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/ >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurferhttps://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/**compliancelinehttp://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 >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://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 >> http://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/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 >> > > -- > 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
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.
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
Hi Paul,
You have to give it the full path:
*mri_convert **/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz* * * *--Thomas*
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabeach1@gmail.com wrote:
The mri_convert command did not work...
*[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz* *mri_convert mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from mni305.cor.mgz...* *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.com wrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks fine
- strangely FSLview of this is mis-oriented, but Freeview and AFNI look
fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Just to clarify,
- If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in
your other software?
- If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does
it look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.com wrote:
Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz
and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
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.comwrote:
> 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.**edugreve@nmr.mgh.harvard.edu >>> >>> <mailto:greve@nmr.mgh.harvard.**edugreve@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 >>> > >>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>> >>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>> >> >>> >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/ >>> **freesurferhttps://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 greve@nmr.mgh.harvard.edu> >>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>> >>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>> >> >>> Phone Number: 617-724-2358 tel:617-724-2358 >>> <tel:617-724-2358 tel:617-724-2358> >>> Fax: 617-726-7422 tel:617-726-7422 tel:617-726-7422 >> >>> tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > >>> http://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 >>> http://www.nmr.mgh.harvard.**edu/facility/filedrop/index. >> **htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> > >>> http://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/ >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>> > >>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>> >>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>> >> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>> freesurferhttps://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/**compliancelinehttp://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 >>> >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> <http://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 >>> http://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/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 >>> >> >> -- >> 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 > > _______________________________________________ > 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. > >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
I'm getting the same error, despite doing just that. :-/
*[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz* *mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz... * *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Paul,
You have to give it the full path:
*mri_convert **/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz*
*--Thomas*
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabeach1@gmail.com wrote:
The mri_convert command did not work...
*[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz* *mri_convert mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from mni305.cor.mgz...* *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.com wrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks
fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Just to clarify,
- If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in
your other software?
- If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does
it look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.comwrote:
Hi Thomas,
Thank you for the advice.
I ran: *tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz
and tkmedit opened the transformed subject.
This is what I see: [image: Inline image 1]
So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic.
On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
> 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.comwrote: > >> 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.**edugreve@nmr.mgh.harvard.edu >>>> >>>> <mailto:greve@nmr.mgh.harvard.**edugreve@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 >>>> > >>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>> >>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>> >> >>>> >>>> > https://mail.nmr.mgh.harvard.** >>>> edu/mailman/listinfo/**freesurferhttps://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 greve@nmr.mgh.harvard.edu> >>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>> >>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>> >> >>>> Phone Number: 617-724-2358 tel:617-724-2358 >>>> <tel:617-724-2358 tel:617-724-2358> >>>> Fax: 617-726-7422 tel:617-726-7422 tel: >>> 617-726-7422 >>>> >>>> tel:617-726-7422> >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/** >>>> fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> > >>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> > >>>> FileDrop: https://gate.nmr.mgh.harvard.** >>>> edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> http://www.nmr.mgh.harvard.** >>> edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> > >>>> http://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/ >>>> >>>> ______________________________**_________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>> > >>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>> >>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>> >> >>>> >>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>>> freesurferhttps://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/**compliancelinehttp://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 >>>> >>>> >>>> -- Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> <http://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 >>>> http://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 >>>> >>> >>> -- >>> 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 >> >> _______________________________________________ >> 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. >> >> >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
Oh I see. You probably don't have write access to the current directory (which I assume to be * /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)*, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory.
--Thomas
On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach pabeach1@gmail.com wrote:
I'm getting the same error, despite doing just that. :-/
*[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz* *mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz...
*TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Paul,
You have to give it the full path:
*mri_convert **/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz*
*--Thomas*
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabeach1@gmail.com wrote:
The mri_convert command did not work...
*[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz* *mri_convert mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from mni305.cor.mgz...* *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.com wrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks
fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Just to clarify,
- If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in
your other software?
- If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY,
does it look mis-oriented in your other software?
--Thomas
On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.comwrote:
> Hi Thomas, > > Thank you for the advice. > > I ran: > *tkmedit FSL_MNI305_2mm.nii.gz \ > /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz > * > * > * > and tkmedit opened the transformed subject. > > This is what I see: > [image: Inline image 1] > > So in tkmedit it is oriented properly. However, I utilize AFNI just > as much as Freesurfer in viewing results (my functional data is not ran > through fsfast). So, not having things oriented properly in other viewers > is problematic. > > > On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote: > >> 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.comwrote: >> >>> 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.**edugreve@nmr.mgh.harvard.edu >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@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 >>>>> > >>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>> >>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>> >> >>>>> >>>>> > https://mail.nmr.mgh.harvard.** >>>>> edu/mailman/listinfo/**freesurferhttps://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 greve@nmr.mgh.harvard.edu> >>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>> >>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>> >> >>>>> Phone Number: 617-724-2358 tel:617-724-2358 >>>>> <tel:617-724-2358 tel:617-724-2358> >>>>> Fax: 617-726-7422 tel:617-726-7422 tel: >>>> 617-726-7422 >>>>> >>>>> tel:617-726-7422> >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/** >>>>> fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> > >>>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> > >>>>> FileDrop: https://gate.nmr.mgh.harvard.** >>>>> edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> http://www.nmr.mgh.harvard.** >>>> edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> > >>>>> http://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/ >>>>> >>>>> ______________________________**_________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>> > >>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>> >>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>> >> >>>>> >>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>>>> freesurferhttps://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/**compliancelinehttp://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 >>>>> >>>>> >>>>> -- Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.** >>>> edu 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> <http://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 >>>>> http://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 >>>>> >>>> >>>> -- >>>> 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 >>> >>> _______________________________________________ >>> 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. >>> >>> >> > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
Ah! Yes. I changed directories to my subjects_dir and the command worked.
I then re-tried my original mri_vol2vol script. * * *mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz * *--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz * *--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat * *--inv --o FSL_MNI305_2mm.nii.gz* * * Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview.
On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo ythomas@csail.mit.edu wrote:
Oh I see. You probably don't have write access to the current directory (which I assume to be * /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)*, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory.
--Thomas
On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach pabeach1@gmail.com wrote:
I'm getting the same error, despite doing just that. :-/
*[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz* *mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz...
*TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
You have to give it the full path:
*mri_convert **/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz*
*--Thomas*
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach pabeach1@gmail.com wrote:
The mri_convert command did not work...
*[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz* *mri_convert mni305.cor.mgz mni305.nii.gz * *$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $* *reading from mni305.cor.mgz...* *TR=0.00, TE=0.00, TI=0.00, flip angle=0.00* *i_ras = (-1, 0, 0)* *j_ras = (0, 0, -1)* *k_ras = (0, 1, 0)* *writing to mni305.nii.gz...* *niiWrite(): error opening file mni305.nii.gz* *ERROR: failure writing mni305.nii.gz*
On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
Hi Paul,
Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview?
--Thomas
On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach pabeach1@gmail.comwrote:
Thomas,
- this cannot be loaded into AFNI or fslview - in freeview it looks
fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine
I'm not sure if that clarifies anything, though.
On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo ythomas@csail.mit.eduwrote:
> Hi Paul, > > Just to clarify, > > 1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in > your other software? > > 2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, > does it look mis-oriented in your other software? > > --Thomas > > > On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach pabeach1@gmail.comwrote: > >> Hi Thomas, >> >> Thank you for the advice. >> >> I ran: >> *tkmedit FSL_MNI305_2mm.nii.gz \ >> /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz >> * >> * >> * >> and tkmedit opened the transformed subject. >> >> This is what I see: >> [image: Inline image 1] >> >> So in tkmedit it is oriented properly. However, I utilize AFNI just >> as much as Freesurfer in viewing results (my functional data is not ran >> through fsfast). So, not having things oriented properly in other viewers >> is problematic. >> >> >> On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo ythomas@csail.mit.eduwrote: >> >>> 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.comwrote: >>> >>>> 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.**edugreve@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@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 >>>>>> > >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >> >>>>>> >>>>>> > https://mail.nmr.mgh.harvard.** >>>>>> edu/mailman/listinfo/**freesurferhttps://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 greve@nmr.mgh.harvard.edu> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu >>>>>> >> >>>>>> Phone Number: 617-724-2358 tel:617-724-2358 >>>>>> <tel:617-724-2358 tel:617-724-2358> >>>>>> Fax: 617-726-7422 tel:617-726-7422 tel: >>>>> 617-726-7422 >>>>>> >>>>>> tel:617-726-7422> >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/** >>>>>> fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> > >>>>>> http://surfer.nmr.mgh.**harvard.edu/fswiki/** >>>>> BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> > >>>>>> FileDrop: https://gate.nmr.mgh.harvard.** >>>>>> edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> http://www.nmr.mgh.harvard.** >>>>> edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> > >>>>>> http://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/ >>>>>> >>>>>> ______________________________**_________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> > >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >>>>>> <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu >>>>>> >> >>>>>> >>>>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >>>>>> freesurferhttps://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/**compliancelinehttp://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 >>>>>> >>>>>> >>>>>> -- Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.** >>>>> edu 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> <http://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 >>>>>> http://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 >>>>>> >>>>> >>>>> -- >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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. >>>> >>>> >>> >> >> >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program >> - Bozoki Lab: Neurology/Radiology >> > >
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
-- Paul Beach DO/PhD candidate - Year VI Michigan State University
- College of Osteopathic Medicine
- Neuroscience Program
- Bozoki Lab: Neurology/Radiology
Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and tkmedit do). I know that fslview will not reorient but puts little letters on the side of the image to tell you what the orientation is. I think they also have tools to reorient so that it is displayed more reasonably. Have you looked into that? doug
ps. You can try using the reorder feature in mri_convert, but it will be trial and error.
On 10/01/2013 11:55 AM, Paul Beach wrote:
Ah! Yes. I changed directories to my subjects_dir and the command worked.
I then re-tried my original mri_vol2vol script. / / /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz / /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz / /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat / /--inv --o FSL_MNI305_2mm.nii.gz/ / / Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview.
On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo <ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu> wrote:
Oh I see. You probably don't have write access to the current directory (which I assume to be //extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory. --Thomas On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: I'm getting the same error, despite doing just that. :-/ /[beachpau@gauss mri.2mm]$ mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ /mri_convert /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from /extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, You have to give it the full path: /mri_convert ///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ / / /--Thomas/ On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: The mri_convert command did not work... / / /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz/ /mri_convert mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview? --Thomas On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: Thomas, 1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine I'm not sure if that clarifies anything, though. On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, Just to clarify, 1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your other software? 2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz" ONLY, does it look mis-oriented in your other software? --Thomas On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: Hi Thomas, Thank you for the advice. I ran: /tkmedit FSL_MNI305_2mm.nii.gz \ /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz/ / / and tkmedit opened the transformed subject. This is what I see: Inline image 1 So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic. On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto: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 <mailto: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 Inline image 1 Freeview 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 <mailto: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.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto: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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://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> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: 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 -- 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/ -- 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 The information in this e-mail is intended only for the person to whom it is addressed. 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- Bozoki Lab: Neurology/Radiology
Hi Doug,
except Paul was saying the mni305.cor.mgz does not show up correctly in freeview as well. Doesn't freeview handle header orientation information properly?
--Thomas
On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and tkmedit do). I know that fslview will not reorient but puts little letters on the side of the image to tell you what the orientation is. I think they also have tools to reorient so that it is displayed more reasonably. Have you looked into that? doug
ps. You can try using the reorder feature in mri_convert, but it will be trial and error.
On 10/01/2013 11:55 AM, Paul Beach wrote:
Ah! Yes. I changed directories to my subjects_dir and the command worked.
I then re-tried my original mri_vol2vol script. / / /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz / /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz / /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat / /--inv --o FSL_MNI305_2mm.nii.gz/ / / Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview.
On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo <ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu> wrote:
Oh I see. You probably don't have write access to the current directory (which I assume to be//extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory.
--Thomas On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: I'm getting the same error, despite doing just that. :-/ /[beachpau@gauss mri.2mm]$ mri_convert/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ /mri_convert
/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from
/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/
On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, You have to give it the full path: /mri_convert///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ / / /--Thomas/
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: The mri_convert command did not work... / / /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz/ /mri_convert mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview? --Thomas On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: Thomas, 1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine I'm not sure if that clarifies anything, though. On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, Just to clarify, 1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your other software? 2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz"ONLY, does it look mis-oriented in your other software?
--Thomas On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: Hi Thomas, Thank you for the advice. I ran: /tkmedit FSL_MNI305_2mm.nii.gz \/extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz/ / / and tkmedit opened the transformed subject.
This is what I see: Inline image 1 So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic. On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto: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 >> freeviewFSL_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 <mailto: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 Inline image 1 Freeview 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.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu
mailto:greve@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
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<mailto: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 > > >
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Hi Thomas, it loads properly for me. doug
On 10/01/2013 08:21 PM, Thomas Yeo wrote:
Hi Doug,
except Paul was saying the mni305.cor.mgz does not show up correctly in freeview as well. Doesn't freeview handle header orientation information properly?
--Thomas
On Wed, Oct 2, 2013 at 1:05 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Hi Paul, IMHO this is not a problem with the FreeSurfer output it is a problem with the visualization tools you are using. Have you contacted the developers? I think the data are fine and the information in the header is sufficient for a visualization tool to orient it properly (as freeview and tkmedit do). I know that fslview will not reorient but puts little letters on the side of the image to tell you what the orientation is. I think they also have tools to reorient so that it is displayed more reasonably. Have you looked into that? doug
ps. You can try using the reorder feature in mri_convert, but it will be trial and error.
On 10/01/2013 11:55 AM, Paul Beach wrote:
Ah! Yes. I changed directories to my subjects_dir and the command worked.
I then re-tried my original mri_vol2vol script. / / /mri_vol2vol --mov $SUBJECTS_DIR/mni305.nii.gz / /--targ FSL_MNI152_FreeSurferConformed_1mm.nii.gz / /--reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat / /--inv --o FSL_MNI305_2mm.nii.gz/ / / Unfortunately I'm getting the same mis-orientation result in AFNI, freeview, and fslview.
On Tue, Oct 1, 2013 at 11:47 AM, Thomas Yeo <ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu> wrote:
Oh I see. You probably don't have write access to the current directory (which I assume to be//extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/)/, so it can't write out mni305.nii.gz. Write out mni305.nii.gz to another directory.
--Thomas On Tue, Oct 1, 2013 at 11:41 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: I'm getting the same error, despite doing just that. :-/ /[beachpau@gauss mri.2mm]$ mri_convert/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ /mri_convert
/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from
/extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/
On Tue, Oct 1, 2013 at 11:38 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, You have to give it the full path: /mri_convert///extern/research/tools/freesurfer-5.3.0/subjects/fsaverage/mri.2mm/mni305.cor.mgz mni305.nii.gz/ / / /--Thomas/
On Tue, Oct 1, 2013 at 11:28 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: The mri_convert command did not work... / / /[beachpau@gauss mri.2mm]$ mri_convert mni305.cor.mgz mni305.nii.gz/ /mri_convert mni305.cor.mgz mni305.nii.gz / /$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $/ /reading from mni305.cor.mgz.../ /TR=0.00, TE=0.00, TI=0.00, flip angle=0.00/ /i_ras = (-1, 0, 0)/ /j_ras = (0, 0, -1)/ /k_ras = (0, 1, 0)/ /writing to mni305.nii.gz.../ /niiWrite(): error opening file mni305.nii.gz/ /ERROR: failure writing mni305.nii.gz/ On Tue, Oct 1, 2013 at 11:23 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, Ok. Do a "mri_convert mni305.cor.mgz mni305.nii.gz". How does mni305.cor.nii.gz look in AFNI and fslview? --Thomas On Tue, Oct 1, 2013 at 11:20 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: Thomas, 1) this cannot be loaded into AFNI or fslview - in freeview it looks fine 2) strangely FSLview of this is mis-oriented, but Freeview and AFNI look fine I'm not sure if that clarifies anything, though. On Tue, Oct 1, 2013 at 11:13 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto:ythomas@csail.mit.edu>> wrote: Hi Paul, Just to clarify, 1) If you load "mni305.cor.mgz" ONLY, does it look mis-oriented in your other software? 2) If you load "FSL_MNI152_FreeSurferConformed_1mm.nii.gz"ONLY, does it look mis-oriented in your other software?
--Thomas On Tue, Oct 1, 2013 at 10:38 PM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote: Hi Thomas, Thank you for the advice. I ran: /tkmedit FSL_MNI305_2mm.nii.gz \/extern/research/PI/training/beachpau/Beach_FreeSurfer_data/fsaverage/mri.2mm/mni305.cor.mgz/ / / and tkmedit opened the transformed subject.
This is what I see: Inline image 1 So in tkmedit it is oriented properly. However, I utilize AFNI just as much as Freesurfer in viewing results (my functional data is not ran through fsfast). So, not having things oriented properly in other viewers is problematic. On Tue, Oct 1, 2013 at 10:28 AM, Thomas Yeo <ythomas@csail.mit.edu <mailto: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 >> freeviewFSL_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 <mailto: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 Inline image 1 Freeview 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.edumailto: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.edumailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu
mailto:greve@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
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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 > > >
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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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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<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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<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> <http://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/<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
-- 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
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.
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Paul Beach -
Thomas Yeo