sorry, forgot to respond earlier. Which V1 label are you using? You might try thresholding it to remove the low-probability vertices that make it larger than it should be
cheers Bruce On Mon, 11 Jul 2016, Halbertsma, HN (ohk) wrote:
I’m having issues with the conversion of labels drawn in fsaverage to subject’s space (using mri_label2label). I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left and right hemisphere that I want to convert to a subjects brain. I’ve successfully managed to do this for the left hemisphere of all the subjects, where the V1-bins converted from the fsaverage fall perfectly within subject specific V1. However, for the right hemisphere, the bins seem slightly misaligned for all the subjects (they’re usually a bit bigger than they should be). Any idea what could have caused this?!
Attached the image that shows the fine conversion for the lh (on the left) and the misaligned conversion for the rh (on the right)
[IMAGE]
I used the following commands:
left hemisphere, first bin: mri_label2label --srcsubject fsaverage --srclabel ./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel ./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface
right hemisphere mri_label2label --srcsubject fsaverage --srclabel ./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel ./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface
The output is as follows: left hemisphere, first bin: srclabel = ./fsaverage/label/lh.v1_nbin1.label srcsubject = fsaverage trgsubject = HHcon_8 trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage regmethod = surface
srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Found 102 points in source label. Starting surface-based mapping Reading source registration /Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Applications/freesurfer/subjects/HHcon_8/surf/lh.white Reading target registration /Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 102 nlabel points Performing mapping from target back to the source label 118606 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132 mri_label2label: Done
right hemisphere, first bin: srclabel = ./fsaverage/label/rh.v1_nbin1.label srcsubject = fsaverage trgsubject = con21_oxford trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage regmethod = surface
srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Found 209 points in source label. Starting surface-based mapping Reading source registration /Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Applications/freesurfer/subjects/con21_oxford/surf/rh.white Reading target registration /Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 209 nlabel points Performing mapping from target back to the source label 145838 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294 mri_label2label: Done
So for some reason the conversion for the right hemisphere works but is not perfect, which is also reflected in the fact that extracting the label statistics (using mris_anatomical_stats) will sometimes give different values after re-running the conversion.
Hinke N. Halbertsma, MSc
PhD Student University Medical Center Groningen (UMCG) Department of Ophthalmology NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124 T. (+31) 050 363 4431 E. h.n.halbertsma@umcg.nl
On 01 Jul 2016, at 16:11, Halbertsma, HN (ohk) <h.n.halbertsma@umcg.nl> wrote:Hi Bruce,
Attached the image that show the fine conversion for the lh (on the left) and the misaligned conversion for the rh (on the right)
<mri_label2label_leftright.jpg>
I used the following commands:
left hemisphere, first bin: mri_label2label --srcsubject fsaverage --srclabel ./fsaverage/label/lh.v1_nbin1.label --trgsubject $SUBJECT --trglabel ./$SUBJECT/label/lh.v1_nbin1_from_fsaverage --hemi lh --regmethod surface
right hemisphere mri_label2label --srcsubject fsaverage --srclabel ./fsaverage/label/rh.v1_nbin1.label --trgsubject $SUBJECT --trglabel ./$SUBJECT/label/rh.v1_nbin1_from_fsaverage --hemi rh --regmethod surface
The output is as follows: left hemisphere, first bin: srclabel = ./fsaverage/label/lh.v1_nbin1.label srcsubject = fsaverage trgsubject = HHcon_8 trglabel = ./HHcon_8/label/lh.v1_nbin1_from_fsaverage regmethod = surface
srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Found 102 points in source label. Starting surface-based mapping Reading source registration /Applications/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Applications/freesurfer/subjects/HHcon_8/surf/lh.white Reading target registration /Applications/freesurfer/subjects/HHcon_8/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 102 nlabel points Performing mapping from target back to the source label 118606 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./HHcon_8/label/lh.v1_nbin1_from_fsaverage 132 mri_label2label: Done
right hemisphere, first bin: srclabel = ./fsaverage/label/rh.v1_nbin1.label srcsubject = fsaverage trgsubject = con21_oxford trglabel = ./con21_oxford/label/rh.v1_nbin1_from_fsaverage regmethod = surface
srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0
SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Loading source label. Found 209 points in source label. Starting surface-based mapping Reading source registration /Applications/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /Applications/freesurfer/subjects/con21_oxford/surf/rh.white Reading target registration /Applications/freesurfer/subjects/con21_oxford/surf/rh.sphere.reg Rescaling ... original radius = 99.9999 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 209 nlabel points Performing mapping from target back to the source label 145838 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./con21_oxford/label/rh.v1_nbin1_from_fsaverage 294 mri_label2label: Done
So for some reason the conversion for the right hemisphere works but is not perfect, which is also reflected in the fact that extracting the label statistics (using mris_anatomical_stats) will sometimes give different values after re-running the conversion.
Hope this helps.
Hinke N. Halbertsma, MSc
PhD Student University Medical Center Groningen (UMCG) Department of Ophthalmology NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124 T. (+31) 050 363 4431 E. h.n.halbertsma@umcg.nl
On 01 Jul 2016, at 15:40, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Hinke
we need more details if you want us to help you. Images, exact command lines and outputs, etc....
cheers Bruce On Fri, 1 Jul 2016, Halbertsma, HN (ohk) wrote:
I’m having issues with the conversion of labels drawn in fsaverage to subject’s space (using mri_label2label). I’ve manually drawn labels (V1-bins) in the fsaverage brain in both the left and right hemisphere that I want to convert to a subjects brain. I’ve successfully managed to do this for the left hemisphere of all the subjects, where the V1-bins converted from the fsaverage fall perfectly within subject specific V1. However, for the right hemisphere, the bins seem slightly misaligned for all the subjects (they’re usually a bit bigger than they should be). Any idea what could have caused this?! Many thanks. Hinke Hinke N. Halbertsma, MSc PhD Student University Medical Center Groningen (UMCG) Department of Ophthalmology NeuroImaging Center (Antonius Deusinglaan 2, 9713 AW Groningen), room 124 T. (+31) 050 363 4431 E. h.n.halbertsma@umcg.nl
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The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.