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
