Re: [Freesurfer] convert FS volume in scanner space
1.v10.mgz >>>> FS_outfile.nii >>>> (identical dimensions, voxel spacing, origin and orientation) however, >>>> segmentation have wholes that renders shape analysis impossible. Running >>>> >>>> mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ orig/001.mgz >>>> --regheader --o FS_outfile.nii --no-save-reg (or —targ rawavg) >>>> >>>> resulted in perfect segmentations, but the coordinates had (identical >>>> dimensions and voxel spacing) but different origin and orientation >>>> (dicom: AIL; FS_outfile: ASR) when I open both files in ITK Snap. >>>> Also, FS seems to involve more/ other steps in mri_vol2vol as compared >>>> to mri_convert. So I figured I would either need other commands for >>>> mri_vol2vol or an additional step to have my (perfect) segmention in >>>> dicom-coordinates. I tried >>>> >>>> mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS >>>> --out_orientation LPS >>>> >>>> but the output was completely wrong oriented. >>>> >>>> So that’s were I am stuck. Back to your question - I guess I need the >>>> voxel-to-RAS matrix to have FS-output in the original real world >>>> coordinates to enable direct comparisons and then guidance on how to >>>> calculate the image translations with FS (on a larger data set). >>>> >>>> >>>> >>>>> Am 09.07.2015 um 19:00 schrieb Douglas N Greve >>>>> mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu>>: >>>>> >>>>> There are a lot of details here that can easily get confused. The pixel >>>>> data are not in any particular space. The order of the pixel data are >>>>> not changed when converted to mgz. The direction cosines that indicate >>>>> how to convert a col-row-slice to a real world coordinate dictate how >>>>> the pixels are displayed or interpreted spatially. The direction >>>>> cosines >>>>> in the dicom file will be LPS. The direction cosines in RAS space are >>>>> computed and saved in the mgz file. The coordinate center will not >>>>> change. Thus if you use the voxel-to-RAS matrix to compute the location >>>>> in the scanner of a given col-row-slice, it will do so accurately. >>>>> >>>>> Given that, can you explain more about what you actually need? >>>>> >>>>> >>>>> >>>>> On 07/08/2015 10:51 AM, von Polier, Georg wrote: >>>>>> Sorry for the confusion: According to the presentation >>>>>> fswiki/CoordinateSystems (below) I meant, the data are in native >>>>>> space/ RAS, with coordinate center not at magnet center, which is >>>>>> what I need. >>>>>> >>>>>> Scanner Space - coordinate center at magnet isocenter, bore axis is >>>>>> Z, X to the left, Y to the ceiling. Direction cosines and P0 defined >>>>>> in DICOM file (note: this is an LPS, not RAS coordinate system) >>>>>> Native - basically the same as scanner, but RAS. >>>>>> >>>>>> -Ursprüngliche Nachricht- >>>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von >>>>>> Douglas Greve >>>>>> Gesendet: Mittwoch, 8. Juli 2015 16:37 >>>>>> An: freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>> Betreff: Re: [Freesurfer] convert FS volume in scanner space >>>>>> >>>>>> what do you mean the coords are still in RAS? >>>>>> >>>>>> On 7/8/15 8:25 AM, von Polier, Georg wrote: >>>>>>> My command line was >>>>>>> >>>>>>> cd $SUBJECTS_DIR//mri >>>>>>> mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o >>>>>>> brain-in-rawavg.mgz --no-save-reg >>>>>>> >>>>>>> according to fswiki/FsAnat-to-NativeAnat. >>>>>>> >>>&
Re: [Freesurfer] convert FS volume in scanner space
gt;> mri_vol2vol or an additional step to have my (perfect) segmention in >>> dicom-coordinates. I tried >>> >>> mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS >>> --out_orientation LPS >>> >>> but the output was completely wrong oriented. >>> >>> So that’s were I am stuck. Back to your question - I guess I need the >>> voxel-to-RAS matrix to have FS-output in the original real world >>> coordinates to enable direct comparisons and then guidance on how to >>> calculate the image translations with FS (on a larger data set). >>> >>> >>> >>>> Am 09.07.2015 um 19:00 schrieb Douglas N Greve >>>> mailto:gr...@nmr.mgh.harvard.edu> >>>> <mailto:gr...@nmr.mgh.harvard.edu>>: >>>> >>>> There are a lot of details here that can easily get confused. The pixel >>>> data are not in any particular space. The order of the pixel data are >>>> not changed when converted to mgz. The direction cosines that indicate >>>> how to convert a col-row-slice to a real world coordinate dictate how >>>> the pixels are displayed or interpreted spatially. The direction >>>> cosines >>>> in the dicom file will be LPS. The direction cosines in RAS space are >>>> computed and saved in the mgz file. The coordinate center will not >>>> change. Thus if you use the voxel-to-RAS matrix to compute the location >>>> in the scanner of a given col-row-slice, it will do so accurately. >>>> >>>> Given that, can you explain more about what you actually need? >>>> >>>> >>>> >>>> On 07/08/2015 10:51 AM, von Polier, Georg wrote: >>>>> Sorry for the confusion: According to the presentation >>>>> fswiki/CoordinateSystems (below) I meant, the data are in native >>>>> space/ RAS, with coordinate center not at magnet center, which is >>>>> what I need. >>>>> >>>>> Scanner Space - coordinate center at magnet isocenter, bore axis is >>>>> Z, X to the left, Y to the ceiling. Direction cosines and P0 defined >>>>> in DICOM file (note: this is an LPS, not RAS coordinate system) >>>>> Native - basically the same as scanner, but RAS. >>>>> >>>>> -Ursprüngliche Nachricht- >>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von >>>>> Douglas Greve >>>>> Gesendet: Mittwoch, 8. Juli 2015 16:37 >>>>> An: freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>> Betreff: Re: [Freesurfer] convert FS volume in scanner space >>>>> >>>>> what do you mean the coords are still in RAS? >>>>> >>>>> On 7/8/15 8:25 AM, von Polier, Georg wrote: >>>>>> My command line was >>>>>> >>>>>> cd $SUBJECTS_DIR//mri >>>>>> mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o >>>>>> brain-in-rawavg.mgz --no-save-reg >>>>>> >>>>>> according to fswiki/FsAnat-to-NativeAnat. >>>>>> >>>>>> As I mentioned, I am happy with the results but the coordinates are >>>>>> still RAS (from my understanding) and different from the original >>>>>> dicom-coordinates (that my manual segmentations are in). When I use >>>>>> mri_convert, the coordinates are in dicom-space (0 in center of >>>>>> image/ coil; offset and z-axis identical with original dicoms), but >>>>>> the segmentation seems different/ more prone to artifacts, also >>>>>> when I use rt- nearest. >>>>>> >>>>>> Georg >>>>>> >>>>>> -Ursprüngliche Nachricht- >>>>>> Von: freesurfer-boun...@nmr.mgh.harvard.edu >>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>>>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von >>>>>> Douglas >>>>>> Greve >>>>>> Ges
Re: [Freesurfer] convert FS volume in scanner space
get confused. The pixel data are not in any particular space. The order of the pixel data are not changed when converted to mgz. The direction cosines that indicate how to convert a col-row-slice to a real world coordinate dictate how the pixels are displayed or interpreted spatially. The direction cosines in the dicom file will be LPS. The direction cosines in RAS space are computed and saved in the mgz file. The coordinate center will not change. Thus if you use the voxel-to-RAS matrix to compute the location in the scanner of a given col-row-slice, it will do so accurately. Given that, can you explain more about what you actually need? On 07/08/2015 10:51 AM, von Polier, Georg wrote: Sorry for the confusion: According to the presentation fswiki/CoordinateSystems (below) I meant, the data are in native space/ RAS, with coordinate center not at magnet center, which is what I need. Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to the left, Y to the ceiling. Direction cosines and P0 defined in DICOM file (note: this is an LPS, not RAS coordinate system) Native - basically the same as scanner, but RAS. -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 16:37 An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] convert FS volume in scanner space what do you mean the coords are still in RAS? On 7/8/15 8:25 AM, von Polier, Georg wrote: My command line was cd $SUBJECTS_DIR//mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg according to fswiki/FsAnat-to-NativeAnat. As I mentioned, I am happy with the results but the coordinates are still RAS (from my understanding) and different from the original dicom-coordinates (that my manual segmentations are in). When I use mri_convert, the coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis identical with original dicoms), but the segmentation seems different/ more prone to artifacts, also when I use rt- nearest. Georg -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 04:20 An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] convert FS volume in scanner space what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On Wed, 8 Jul 2015, von Polier, Georg wrote: Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however, the results were partially prone to artifacts and different from those I get with mir_vol2vol (but in dicom space). Is there a way using mir_vol2vol with results in dicom space, or a second step that gives a vox2vox from conformed/anatomical space to dicom space? I use the .mgz-output of hippo_subfields (FS_dev). Thanks again, Georg Am 07.07.2015 um 02:34 schrieb Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu> <mailto:fis...@nmr.mgh.harvard.edu>>: Hi Georg if you have a volume (like the 001.mgz) that is in scanner coordinates you can use the "reslice like" and "resample type" flags in mri_convert: mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz cheers Bruce On Mon, 6 Jul 2015, von Polier, Georg wrote: Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu&
Re: [Freesurfer] convert FS volume in scanner space
vol2vol is the right way to go on this. When you run mri_info on rawavg.mgz and FS_outfile.nii, do they have the same geometry? What if you convert rawavg.mgz to nii and open it and outfile.nii in ITK Snap, so they look the same? On 07/09/2015 02:44 PM, von Polier, Georg wrote: > Thanks for getting back. What I need is hippoSflabels in the original > coordinates/space of the dicom-files (to compare with manual > segmentation). Basically I had success with > mri_convert -rl rawavg.mgz -rt nearest lh.hippoSfLabels-T1.v10.mgz > FS_outfile.nii > (identical dimensions, voxel spacing, origin and orientation) however, > segmentation have wholes that renders shape analysis impossible. Running > > mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ orig/001.mgz > --regheader --o FS_outfile.nii --no-save-reg (or —targ rawavg) > > resulted in perfect segmentations, but the coordinates had (identical > dimensions and voxel spacing) but different origin and orientation > (dicom: AIL; FS_outfile: ASR) when I open both files in ITK Snap. > Also, FS seems to involve more/ other steps in mri_vol2vol as compared > to mri_convert. So I figured I would either need other commands for > mri_vol2vol or an additional step to have my (perfect) segmention in > dicom-coordinates. I tried > > mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS > --out_orientation LPS > > but the output was completely wrong oriented. > > So that’s were I am stuck. Back to your question - I guess I need the > voxel-to-RAS matrix to have FS-output in the original real world > coordinates to enable direct comparisons and then guidance on how to > calculate the image translations with FS (on a larger data set). > > > >> Am 09.07.2015 um 19:00 schrieb Douglas N Greve >> mailto:gr...@nmr.mgh.harvard.edu>>: >> >> There are a lot of details here that can easily get confused. The pixel >> data are not in any particular space. The order of the pixel data are >> not changed when converted to mgz. The direction cosines that indicate >> how to convert a col-row-slice to a real world coordinate dictate how >> the pixels are displayed or interpreted spatially. The direction cosines >> in the dicom file will be LPS. The direction cosines in RAS space are >> computed and saved in the mgz file. The coordinate center will not >> change. Thus if you use the voxel-to-RAS matrix to compute the location >> in the scanner of a given col-row-slice, it will do so accurately. >> >> Given that, can you explain more about what you actually need? >> >> >> >> On 07/08/2015 10:51 AM, von Polier, Georg wrote: >>> Sorry for the confusion: According to the presentation >>> fswiki/CoordinateSystems (below) I meant, the data are in native >>> space/ RAS, with coordinate center not at magnet center, which is >>> what I need. >>> >>> Scanner Space - coordinate center at magnet isocenter, bore axis is >>> Z, X to the left, Y to the ceiling. Direction cosines and P0 defined >>> in DICOM file (note: this is an LPS, not RAS coordinate system) >>> Native - basically the same as scanner, but RAS. >>> >>> -Ursprüngliche Nachricht- >>> Von: freesurfer-boun...@nmr.mgh.harvard.edu >>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von >>> Douglas Greve >>> Gesendet: Mittwoch, 8. Juli 2015 16:37 >>> An: freesurfer@nmr.mgh.harvard.edu >>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>> Betreff: Re: [Freesurfer] convert FS volume in scanner space >>> >>> what do you mean the coords are still in RAS? >>> >>> On 7/8/15 8:25 AM, von Polier, Georg wrote: >>>> My command line was >>>> >>>> cd $SUBJECTS_DIR//mri >>>> mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o >>>> brain-in-rawavg.mgz --no-save-reg >>>> >>>> according to fswiki/FsAnat-to-NativeAnat. >>>> >>>> As I mentioned, I am happy with the results but the coordinates are >>>> still RAS (from my understanding) and different from the original >>>> dicom-coordinates (that my manual segmentations are in). When I use >>>> mri_convert, the coordinates are in dicom-space (0 in center of >>>> image/ coil; offset and z-axis identical with original dicoms), but >>>> the segmentation seems different/ more prone to artifacts, also >>>> when I use rt- nearest. >>>> >>>> Georg >>>> >>&
Re: [Freesurfer] convert FS volume in scanner space
Thanks for getting back. What I need is hippoSflabels in the original coordinates/space of the dicom-files (to compare with manual segmentation). Basically I had success with mri_convert -rl rawavg.mgz -rt nearest lh.hippoSfLabels-T1.v10.mgz FS_outfile.nii (identical dimensions, voxel spacing, origin and orientation) however, segmentation have wholes that renders shape analysis impossible. Running mri_vol2vol --mov lh.hippoSfLabels-T1.v10.mgz --targ orig/001.mgz --regheader --o FS_outfile.nii --no-save-reg (or —targ rawavg) resulted in perfect segmentations, but the coordinates had (identical dimensions and voxel spacing) but different origin and orientation (dicom: AIL; FS_outfile: ASR) when I open both files in ITK Snap. Also, FS seems to involve more/ other steps in mri_vol2vol as compared to mri_convert. So I figured I would either need other commands for mri_vol2vol or an additional step to have my (perfect) segmention in dicom-coordinates. I tried mri_convert FS_outfile.nii FS_outfile_LPS.nii --in_orientation RAS --out_orientation LPS but the output was completely wrong oriented. So that’s were I am stuck. Back to your question - I guess I need the voxel-to-RAS matrix to have FS-output in the original real world coordinates to enable direct comparisons and then guidance on how to calculate the image translations with FS (on a larger data set). Am 09.07.2015 um 19:00 schrieb Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>>: There are a lot of details here that can easily get confused. The pixel data are not in any particular space. The order of the pixel data are not changed when converted to mgz. The direction cosines that indicate how to convert a col-row-slice to a real world coordinate dictate how the pixels are displayed or interpreted spatially. The direction cosines in the dicom file will be LPS. The direction cosines in RAS space are computed and saved in the mgz file. The coordinate center will not change. Thus if you use the voxel-to-RAS matrix to compute the location in the scanner of a given col-row-slice, it will do so accurately. Given that, can you explain more about what you actually need? On 07/08/2015 10:51 AM, von Polier, Georg wrote: Sorry for the confusion: According to the presentation fswiki/CoordinateSystems (below) I meant, the data are in native space/ RAS, with coordinate center not at magnet center, which is what I need. Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to the left, Y to the ceiling. Direction cosines and P0 defined in DICOM file (note: this is an LPS, not RAS coordinate system) Native - basically the same as scanner, but RAS. -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 16:37 An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] convert FS volume in scanner space what do you mean the coords are still in RAS? On 7/8/15 8:25 AM, von Polier, Georg wrote: My command line was cd $SUBJECTS_DIR//mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg according to fswiki/FsAnat-to-NativeAnat. As I mentioned, I am happy with the results but the coordinates are still RAS (from my understanding) and different from the original dicom-coordinates (that my manual segmentations are in). When I use mri_convert, the coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis identical with original dicoms), but the segmentation seems different/ more prone to artifacts, also when I use rt- nearest. Georg -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 04:20 An: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] convert FS volume in scanner space what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On Wed, 8 Jul 2015, von Polier, Georg wrote: Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however, the results were partially prone to artifacts and different from those I get with mir_vol2vol (but in dicom space). Is there a way using mir_vol2vol with results in dicom space, or a second step that gives a vox2vox from conformed/anatomical space to dicom space? I use the .mgz-output of hippo_subfields (FS_dev). Thanks again, Georg Am 07.07.2015
Re: [Freesurfer] convert FS volume in scanner space
There are a lot of details here that can easily get confused. The pixel data are not in any particular space. The order of the pixel data are not changed when converted to mgz. The direction cosines that indicate how to convert a col-row-slice to a real world coordinate dictate how the pixels are displayed or interpreted spatially. The direction cosines in the dicom file will be LPS. The direction cosines in RAS space are computed and saved in the mgz file. The coordinate center will not change. Thus if you use the voxel-to-RAS matrix to compute the location in the scanner of a given col-row-slice, it will do so accurately. Given that, can you explain more about what you actually need? On 07/08/2015 10:51 AM, von Polier, Georg wrote: > Sorry for the confusion: According to the presentation > fswiki/CoordinateSystems (below) I meant, the data are in native space/ RAS, > with coordinate center not at magnet center, which is what I need. > > Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to > the left, Y to the ceiling. Direction cosines and P0 defined in DICOM file > (note: this is an LPS, not RAS coordinate system) Native - basically the > same as scanner, but RAS. > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve > Gesendet: Mittwoch, 8. Juli 2015 16:37 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] convert FS volume in scanner space > > what do you mean the coords are still in RAS? > > On 7/8/15 8:25 AM, von Polier, Georg wrote: >> My command line was >> >> cd $SUBJECTS_DIR//mri >> mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o >> brain-in-rawavg.mgz --no-save-reg >> >> according to fswiki/FsAnat-to-NativeAnat. >> >> As I mentioned, I am happy with the results but the coordinates are still >> RAS (from my understanding) and different from the original >> dicom-coordinates (that my manual segmentations are in). When I use >> mri_convert, the coordinates are in dicom-space (0 in center of image/ coil; >> offset and z-axis identical with original dicoms), but the segmentation >> seems different/ more prone to artifacts, also when I use rt- nearest. >> >> Georg >> >> -Ursprüngliche Nachricht- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas >> Greve >> Gesendet: Mittwoch, 8. Juli 2015 04:20 >> An: freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] convert FS volume in scanner space >> >> what was your vol2vol command line? What wiki page were you referencing? >> What was the problem with the coordinates? >> >> On 7/7/15 8:11 PM, Bruce Fischl wrote: >>> I think you meant you want nearest neighbor interpolation, not >>> trilinear, since you are mapping labels. Try using -rt nearest insted >>> On Wed, 8 Jul 2015, von Polier, Georg wrote: >>> >>>> Thanks for your reply. I tried mri_convert with -rt interpolate (resulting >>>> in trilinear interpolation), however, the results were partially prone to >>>> artifacts and different from those I get with mir_vol2vol (but in dicom >>>> space). >>>> >>>> Is there a way using mir_vol2vol with results in dicom space, or a second >>>> step that gives a vox2vox from conformed/anatomical space to dicom space? >>>> >>>> I use the .mgz-output of hippo_subfields (FS_dev). >>>> >>>> Thanks again, >>>> Georg >>>> >>>> >>>> >>>>> Am 07.07.2015 um 02:34 schrieb Bruce Fischl : >>>>> >>>>> Hi Georg >>>>> >>>>> if you have a volume (like the 001.mgz) that is in scanner >>>>> coordinates you can use the "reslice like" and "resample type" flags in >>>>> mri_convert: >>>>> >>>>> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz >>>>> >>>>> cheers >>>>> Bruce >>>>> >>>>> On Mon, 6 Jul 2015, von >>>>> Polier, Georg wrote: >>>>> >>>>>> Dear FreeSurfers, >>>>>> >>>>>> I need to convert an FS-volume back in scanner space (to calculate >>>>>> overlap with manual segmentation). >>>>>> I went through the wiki-entry and converted to native space with >>>>>> mir_vol2vol, however the coordinates are st
Re: [Freesurfer] convert FS volume in scanner space
Sorry for the confusion: According to the presentation fswiki/CoordinateSystems (below) I meant, the data are in native space/ RAS, with coordinate center not at magnet center, which is what I need. Scanner Space - coordinate center at magnet isocenter, bore axis is Z, X to the left, Y to the ceiling. Direction cosines and P0 defined in DICOM file (note: this is an LPS, not RAS coordinate system) Native - basically the same as scanner, but RAS. -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 16:37 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] convert FS volume in scanner space what do you mean the coords are still in RAS? On 7/8/15 8:25 AM, von Polier, Georg wrote: > My command line was > > cd $SUBJECTS_DIR//mri > mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o > brain-in-rawavg.mgz --no-save-reg > > according to fswiki/FsAnat-to-NativeAnat. > > As I mentioned, I am happy with the results but the coordinates are still RAS > (from my understanding) and different from the original dicom-coordinates > (that my manual segmentations are in). When I use mri_convert, the > coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis > identical with original dicoms), but the segmentation seems different/ more > prone to artifacts, also when I use rt- nearest. > > Georg > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas > Greve > Gesendet: Mittwoch, 8. Juli 2015 04:20 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] convert FS volume in scanner space > > what was your vol2vol command line? What wiki page were you referencing? > What was the problem with the coordinates? > > On 7/7/15 8:11 PM, Bruce Fischl wrote: >> I think you meant you want nearest neighbor interpolation, not >> trilinear, since you are mapping labels. Try using -rt nearest insted >> On Wed, 8 Jul 2015, von Polier, Georg wrote: >> >>> Thanks for your reply. I tried mri_convert with -rt interpolate (resulting >>> in trilinear interpolation), however, the results were partially prone to >>> artifacts and different from those I get with mir_vol2vol (but in dicom >>> space). >>> >>> Is there a way using mir_vol2vol with results in dicom space, or a second >>> step that gives a vox2vox from conformed/anatomical space to dicom space? >>> >>> I use the .mgz-output of hippo_subfields (FS_dev). >>> >>> Thanks again, >>> Georg >>> >>> >>> >>>> Am 07.07.2015 um 02:34 schrieb Bruce Fischl : >>>> >>>> Hi Georg >>>> >>>> if you have a volume (like the 001.mgz) that is in scanner >>>> coordinates you can use the "reslice like" and "resample type" flags in >>>> mri_convert: >>>> >>>> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz >>>> >>>> cheers >>>> Bruce >>>> >>>> On Mon, 6 Jul 2015, von >>>> Polier, Georg wrote: >>>> >>>>> Dear FreeSurfers, >>>>> >>>>> I need to convert an FS-volume back in scanner space (to calculate >>>>> overlap with manual segmentation). >>>>> I went through the wiki-entry and converted to native space with >>>>> mir_vol2vol, however the coordinates are still RAS and not identical with >>>>> the original Scanner-coordinates. I tried mri_convert, however, the >>>>> results were not as good as mri_vol2vol (apparently need trilinear >>>>> interpolation, not available in mri_convert). >>>>> >>>>> Any help would be greatly appreciated, >>>>> >>>>> Cheers, Georg >>>>> ___ >>>>> 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
Re: [Freesurfer] convert FS volume in scanner space
what do you mean the coords are still in RAS? On 7/8/15 8:25 AM, von Polier, Georg wrote: > My command line was > > cd $SUBJECTS_DIR//mri > mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o > brain-in-rawavg.mgz --no-save-reg > > according to fswiki/FsAnat-to-NativeAnat. > > As I mentioned, I am happy with the results but the coordinates are still RAS > (from my understanding) and different from the original dicom-coordinates > (that my manual segmentations are in). When I use mri_convert, the > coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis > identical with original dicoms), but the segmentation seems different/ more > prone to artifacts, also when I use rt- nearest. > > Georg > > -Ursprüngliche Nachricht- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve > Gesendet: Mittwoch, 8. Juli 2015 04:20 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] convert FS volume in scanner space > > what was your vol2vol command line? What wiki page were you referencing? > What was the problem with the coordinates? > > On 7/7/15 8:11 PM, Bruce Fischl wrote: >> I think you meant you want nearest neighbor interpolation, not >> trilinear, since you are mapping labels. Try using -rt nearest insted >> On Wed, 8 Jul 2015, von Polier, Georg wrote: >> >>> Thanks for your reply. I tried mri_convert with -rt interpolate (resulting >>> in trilinear interpolation), however, the results were partially prone to >>> artifacts and different from those I get with mir_vol2vol (but in dicom >>> space). >>> >>> Is there a way using mir_vol2vol with results in dicom space, or a second >>> step that gives a vox2vox from conformed/anatomical space to dicom space? >>> >>> I use the .mgz-output of hippo_subfields (FS_dev). >>> >>> Thanks again, >>> Georg >>> >>> >>> >>>> Am 07.07.2015 um 02:34 schrieb Bruce Fischl : >>>> >>>> Hi Georg >>>> >>>> if you have a volume (like the 001.mgz) that is in scanner >>>> coordinates you can use the "reslice like" and "resample type" flags in >>>> mri_convert: >>>> >>>> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz >>>> >>>> cheers >>>> Bruce >>>> >>>> On Mon, 6 Jul 2015, von >>>> Polier, Georg wrote: >>>> >>>>> Dear FreeSurfers, >>>>> >>>>> I need to convert an FS-volume back in scanner space (to calculate >>>>> overlap with manual segmentation). >>>>> I went through the wiki-entry and converted to native space with >>>>> mir_vol2vol, however the coordinates are still RAS and not identical with >>>>> the original Scanner-coordinates. I tried mri_convert, however, the >>>>> results were not as good as mri_vol2vol (apparently need trilinear >>>>> interpolation, not available in mri_convert). >>>>> >>>>> Any help would be greatly appreciated, >>>>> >>>>> Cheers, Georg >>>>> ___ >>>>> 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. >>>> >>> ___ >>> 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 >> >> > ___ > 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] convert FS volume in scanner space
My command line was cd $SUBJECTS_DIR//mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz --no-save-reg according to fswiki/FsAnat-to-NativeAnat. As I mentioned, I am happy with the results but the coordinates are still RAS (from my understanding) and different from the original dicom-coordinates (that my manual segmentations are in). When I use mri_convert, the coordinates are in dicom-space (0 in center of image/ coil; offset and z-axis identical with original dicoms), but the segmentation seems different/ more prone to artifacts, also when I use rt- nearest. Georg -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve Gesendet: Mittwoch, 8. Juli 2015 04:20 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] convert FS volume in scanner space what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: > I think you meant you want nearest neighbor interpolation, not > trilinear, since you are mapping labels. Try using -rt nearest insted > On Wed, 8 Jul 2015, von Polier, Georg wrote: > >> Thanks for your reply. I tried mri_convert with -rt interpolate (resulting >> in trilinear interpolation), however, the results were partially prone to >> artifacts and different from those I get with mir_vol2vol (but in dicom >> space). >> >> Is there a way using mir_vol2vol with results in dicom space, or a second >> step that gives a vox2vox from conformed/anatomical space to dicom space? >> >> I use the .mgz-output of hippo_subfields (FS_dev). >> >> Thanks again, >> Georg >> >> >> >>> Am 07.07.2015 um 02:34 schrieb Bruce Fischl : >>> >>> Hi Georg >>> >>> if you have a volume (like the 001.mgz) that is in scanner >>> coordinates you can use the "reslice like" and "resample type" flags in >>> mri_convert: >>> >>> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz >>> >>> cheers >>> Bruce >>> >>> On Mon, 6 Jul 2015, von >>> Polier, Georg wrote: >>> >>>> Dear FreeSurfers, >>>> >>>> I need to convert an FS-volume back in scanner space (to calculate overlap >>>> with manual segmentation). >>>> I went through the wiki-entry and converted to native space with >>>> mir_vol2vol, however the coordinates are still RAS and not identical with >>>> the original Scanner-coordinates. I tried mri_convert, however, the >>>> results were not as good as mri_vol2vol (apparently need trilinear >>>> interpolation, not available in mri_convert). >>>> >>>> Any help would be greatly appreciated, >>>> >>>> Cheers, Georg >>>> ___ >>>> 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. >>> >> >> ___ >> 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 > > ___ 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
Re: [Freesurfer] convert FS volume in scanner space
what was your vol2vol command line? What wiki page were you referencing? What was the problem with the coordinates? On 7/7/15 8:11 PM, Bruce Fischl wrote: > I think you meant you want nearest neighbor interpolation, not trilinear, > since you are mapping labels. Try using -rt nearest insted > On Wed, 8 Jul > 2015, von Polier, Georg wrote: > >> Thanks for your reply. I tried mri_convert with -rt interpolate (resulting >> in trilinear interpolation), however, the results were partially prone to >> artifacts and different from those I get with mir_vol2vol (but in dicom >> space). >> >> Is there a way using mir_vol2vol with results in dicom space, or a second >> step that gives a vox2vox from conformed/anatomical space to dicom space? >> >> I use the .mgz-output of hippo_subfields (FS_dev). >> >> Thanks again, >> Georg >> >> >> >>> Am 07.07.2015 um 02:34 schrieb Bruce Fischl : >>> >>> Hi Georg >>> >>> if you have a volume (like the 001.mgz) that is in scanner coordinates >>> you can use the "reslice like" and "resample type" flags in mri_convert: >>> >>> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz >>> >>> cheers >>> Bruce >>> >>> On Mon, 6 Jul 2015, von >>> Polier, Georg wrote: >>> Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ 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. >>> >> >> ___ >> 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 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] convert FS volume in scanner space
I think you meant you want nearest neighbor interpolation, not trilinear, since you are mapping labels. Try using -rt nearest insted On Wed, 8 Jul 2015, von Polier, Georg wrote: > Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in > trilinear interpolation), however, the results were partially prone to > artifacts and different from those I get with mir_vol2vol (but in dicom > space). > > Is there a way using mir_vol2vol with results in dicom space, or a second > step that gives a vox2vox from conformed/anatomical space to dicom space? > > I use the .mgz-output of hippo_subfields (FS_dev). > > Thanks again, > Georg > > > >> Am 07.07.2015 um 02:34 schrieb Bruce Fischl : >> >> Hi Georg >> >> if you have a volume (like the 001.mgz) that is in scanner coordinates >> you can use the "reslice like" and "resample type" flags in mri_convert: >> >> mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz >> >> cheers >> Bruce >> >> On Mon, 6 Jul 2015, von >> Polier, Georg wrote: >> >>> Dear FreeSurfers, >>> >>> I need to convert an FS-volume back in scanner space (to calculate overlap >>> with manual segmentation). >>> I went through the wiki-entry and converted to native space with >>> mir_vol2vol, however the coordinates are still RAS and not identical with >>> the original Scanner-coordinates. I tried mri_convert, however, the results >>> were not as good as mri_vol2vol (apparently need trilinear interpolation, >>> not available in mri_convert). >>> >>> Any help would be greatly appreciated, >>> >>> Cheers, Georg >>> ___ >>> 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. >> > > > ___ > 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
Re: [Freesurfer] convert FS volume in scanner space
Thanks for your reply. I tried mri_convert with -rt interpolate (resulting in trilinear interpolation), however, the results were partially prone to artifacts and different from those I get with mir_vol2vol (but in dicom space). Is there a way using mir_vol2vol with results in dicom space, or a second step that gives a vox2vox from conformed/anatomical space to dicom space? I use the .mgz-output of hippo_subfields (FS_dev). Thanks again, Georg > Am 07.07.2015 um 02:34 schrieb Bruce Fischl : > > Hi Georg > > if you have a volume (like the 001.mgz) that is in scanner coordinates > you can use the "reslice like" and "resample type" flags in mri_convert: > > mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz > > cheers > Bruce > > On Mon, 6 Jul 2015, von > Polier, Georg wrote: > >> Dear FreeSurfers, >> >> I need to convert an FS-volume back in scanner space (to calculate overlap >> with manual segmentation). >> I went through the wiki-entry and converted to native space with >> mir_vol2vol, however the coordinates are still RAS and not identical with >> the original Scanner-coordinates. I tried mri_convert, however, the results >> were not as good as mri_vol2vol (apparently need trilinear interpolation, >> not available in mri_convert). >> >> Any help would be greatly appreciated, >> >> Cheers, Georg >> ___ >> 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. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] convert FS volume in scanner space
Hi Georg if you have a volume (like the 001.mgz) that is in scanner coordinates you can use the "reslice like" and "resample type" flags in mri_convert: mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz cheers Bruce On Mon, 6 Jul 2015, von Polier, Georg wrote: > Dear FreeSurfers, > > I need to convert an FS-volume back in scanner space (to calculate overlap > with manual segmentation). > I went through the wiki-entry and converted to native space with mir_vol2vol, > however the coordinates are still RAS and not identical with the original > Scanner-coordinates. I tried mri_convert, however, the results were not as > good as mri_vol2vol (apparently need trilinear interpolation, not available > in mri_convert). > > Any help would be greatly appreciated, > > Cheers, Georg > ___ > 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.
[Freesurfer] convert FS volume in scanner space
Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ 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.
