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
