[Freesurfer] FW: convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
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
[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.
Re: [Freesurfer] convert (resample) fsaverage/mri/aseg.mgz into $FSLDIR Nifti with MNI152_T1_1mm target - aparc+aseg.mgz problem
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
[Freesurfer] Convert aseg.mgz to .nii and into MNI space with FSL dimensions
Hello all, I have a need to generate LH and RH WM masks for analysis. I can convert aseg.mgz to aseg.nii but the dims are 256x256x256 and I need to use the FSL MNI format which is 182x218x182. Is there a recipe for cropping / translating etc to match the aseg.mgz atlas with the FSL atlases? 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.
Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons?
Would this new tool also be able to provide a better delineation of both pial surface and inner table of the skull (assuming T2 and not FLAIR i.e. hyperintense CSF)) and thus provide the possibility of computing extra-ventricular CSF and thus cerebral atrophy? Some of us would like that I'm sure :-) -roddy -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 20, 2012 2:02 PM To: Winter, Warren Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tool for incorporating T2-SPACE data in pial surface recons? Hi Warren yes, it will be part of the upcoming 5.2 release, hopefully in Dec. It will use either a FLAIR or T2 (ideally T2-SPACE for either one) cheers Bruce On Tue, 20 Nov 2012, Winter, Warren wrote: Hi all, Back in January and October Bruce mentioned that he had under development some scripts designed to utilize T2-SPACE images for better pial surface reconstruction in the presence of dura -- I was just wondering if any of that is ready for trial? Thanks! Warren -- Warren Winter Research Coordinator Boston Children's Hospital Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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. 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
Re: [Freesurfer] mri_watershed for inner_skull_surface question
Hi Bruce, Thanks for responding. We do have T2, but not PD. Of course the resolution of the T2 is much lower (5mm slices). -roddy -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Wednesday, September 21, 2011 7:54 AM To: Roderick McColl; Matti Hamalainen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_watershed for inner_skull_surface question Matti Hamalainen (ccd) might have some thoughts. Do you have T2 or PD images? cheers Bruce On Tue, 20 Sep 2011, Roderick McColl wrote: Hi all, Trying to get mri_watershed to give me a good inner_skull_surface, which I want to combine with the pial surface to estimate sulcal CSF, as I don't see any other way. Unfortunately the data I have tested on all generate unreliable inner_skull surfaces. Can anyone provide a tip for optimizing the result? Thanks -roddy __ __ ___ UT Southwestern Medical Center The future of medicine, today. 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
[Freesurfer] mri_watershed for inner_skull_surface question
Hi all, Trying to get mri_watershed to give me a good inner_skull_surface, which I want to combine with the pial surface to estimate sulcal CSF, as I don't see any other way. Unfortunately the data I have tested on all generate unreliable inner_skull surfaces. Can anyone provide a tip for optimizing the result? 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.
