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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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,
- 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)
- the sagittal image (top right) has the same S/I issue
- the axial image (bottom left) has the A/P labels the opposite of the image slice.
Thanks for any advice
-roddy
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Roderick McColl [Roderick.McColl@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 [greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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,
- 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)
- the sagittal image (top right) has the same S/I issue
- the axial image (bottom left) has the A/P labels the opposite of the image slice.
Thanks for any advice
-roddy
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Roderick McColl [Roderick.McColl@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
OK, try this cmd
mri_vol2vol --mov $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz --targ aseg.mgz --reg transforms/reg.mni152.1mm.dat --o aseg_mni152.nii.gz --inv --interp nearest
On 11/05/2013 06:49 PM, Roderick McColl wrote:
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 [greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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,
- 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)
- the sagittal image (top right) has the same S/I issue
- the axial image (bottom left) has the A/P labels the opposite of the image slice.
Thanks for any advice
-roddy
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Roderick McColl [Roderick.McColl@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Roderick McColl