Sure, no problem.

Run from within the folder $SUBJECTS/fsaverage/mri :-

mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov aseg.mgz 
--reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz

mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --mov 
aparc+aseg.mgz --reg transforms/reg.mni152.1mm.dat --o aparc_aseg_mni152.nii.gz

-roddy
________________________________________
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, November 05, 2013 5:21 PM
To: Roderick McColl; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into 
$FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem

Can you send your command lines for both aparc+aseg and aseg?
doug

ps. Please remember to post to the list and not to me personally. Thanks!



On 11/05/2013 12:45 PM, Roderick McColl wrote:
> Actually does not display properly at least not in freeview.
> Slices are also upside down.
> Also the output dims are 256x256x256 and I was expecting 182x218x182 which 
> are the dims
> For $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz.
> But I agree that I should get in contact which the FSL people also.
> Thanks
> -roddy
>
> -----Original Message-----
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, November 04, 2013 5:22 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into 
> $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
>
>
> Hi Roddy, aparc+aseg.mgz and aseg.mgz are in the exact same space and the 
> same command line should generate the same result. Does it display properly 
> in tkmedit? If so and if you're having problems visualizing with fslview, 
> contact the FSL crew.
> doug
>
>
>
>
> On 11/04/2013 05:52 PM, Roderick McColl wrote:
>> Hmmm,
>>
>> Actually using aseg.mgz works just fine (just tried this now),
>> displays correctly on fslview.
>> What I was really trying to do was convert aparc+aseg.mgz which does
>> not provide the expected orientation in fslview.
>> Does this mean aparc+aseg.mgz and aseg.mgz are in different spaces somehow?
>>
>> For the aparc_aseg_mni152.nii.gz output,
>> 1) the coronal image in fslview (top left)
>>      has the S/I labels upside down compared to the coronal slice,
>>      (or the coronal slice upside down compared to the S/I labels)
>> 2) the sagittal image (top right) has the same S/I issue
>> 3) the axial image (bottom left) has the A/P labels the
>>      opposite of the image slice.
>>
>> Thanks for any advice
>>
>> -roddy
>>
>> ________________________________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Roderick McColl
>> [roderick.mcc...@utsouthwestern.edu]
>> Sent: Monday, November 04, 2013 3:37 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into
>> $FSLDIR Nifti with MNI152_T1_1mm target
>>
>> I am obviously using mri_vol2vol incorrectly but I'm stumped.
>>
>> Goal is to get the $SUBJECTS/fsaverage/mri/aseg.mgz file into the FSL MNI152 
>> space to do some fslmaths.
>>
>> >From looking around it seemed the command to accomplish this is
>>> (inside $SUBJECTS/fsaverage/mri)
>> mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz  \
>>       --mov aseg.mgz --reg transforms/reg.mni152.1mm.dat --o
>> asegmni152.nii.gz
>>
>> which does execute but if I load asegmni152.nii.gz into fslview all of the 
>> orthogonal views are upside down.
>>
>> There is something missing regarding the co-ordinate system but I'm not sure 
>> what.
>>
>> Can anyone point me in the right direction?
>>
>> Thanks
>>
>> -roddy
>>
>> ________________________________
>>
>> UT Southwestern Medical Center
>> The future of medicine, today.
>>
>>
>> _______________________________________________
>> 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 mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Reply via email to