External Email - Use Caution
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Hi Safi,
you definitely need the inverse tkr_vox2ras transform, that is correct. Also your approach in general seems fine, I tried it in R, and I get the expected results:
(My subject is called 'subject1', and I put the created midbrain label into 'label/mdb.label' in its directory.)
---------------
library("fsbrain")
library("freesurferformats")
# load label and apply ras2vox to the coords to get voxel indices
lbl = read.fs.label("~/data/subject1_only/subject1/label/mdb.label", full=TRUE)
coords = cbind(lbl$vertexdata$coord1, lbl$vertexdata$coord2, lbl$vertexdata$coord3)
mbc = apply.transform(coords, ras2vox_tkr())
# load the brain volume and mark the midbrain voxels
brain = read.fs.mgh("~/data/subject1_only/subject1/mri/brain.mgz", drop=TRUE)
brain[mbc] = 255L; # mark the midbrain region in white (full intensity)
volvis.lightbox(vol.boundary.box(brain,apply = T)/255)
# see attached image, the white part is the label
---------------
I would check first whether the values in 'mdb_label_inv' and 'mdb_label' make sense. E.g., are the former all positive integers, and is the length of both matrices equal to the number of voxels in your midbrain label.
Best,
Tim
--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> On April 20, 2020 at 11:37 AM "Safi Ullah ." <safi.ullah@uog.edu.pk> wrote:
>
>
> External Email - Use Caution
>
> Hello Programmers and Freesurfer Experts,
> Can any body please help me? Specially programmers are requested. I want to
> copy the voxels values from a volume (which is read in a matlab struct)
> using the coordinates given in the label file. which transformation do i
> need to correctly map the coordinates from label file over to mri.vol
> matrix?
>
> Warm Regards,
>
> Safi
>
>
> On Mon, Apr 20, 2020 at 12:12 AM Safi Ullah . <safi.ullah@uog.edu.pk> wrote:
>
> > Thank you Doug,
> > I tried all the transformation matrices (although as per case 1 of the
> > referred link, i need only inv(tkrvox2ras) which is present in the MRI
> > struct). but no one is able to map to the desired label location.
> > Let me explain my scenario little more, may be i am missing something.
> > *My Task:* I want to find out the coordinates of a certain tissue, let
> > say midbrain, which can be used in matlab to read/process the tissue voxel
> > values.
> > *My Pipeline:*
> > *Step 1*> recon-all -all -i
> > $SUBJECTS_DIR/PPMI_3817_MR_T1-anatomical_Br_20140129144055847_S184115_I410987.nii
> > -s test -brainstem-structures %
> > PPMI_3817_MR_T1-anatomical_Br_20140129144055847_S184115_I410987.nii is the
> > volume, downloaded from PPMI. As I am interested in midbrain only, so using
> > the -brainstem-substructure flag.
> > *Step 2*> recon-all -s test -brainstem-structures
> > *Step 3*> mri_vol2label --c
> > $SUBJECTS_DIR/test/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz --id 173 --l
> > mdb.label
> > Now at matlab command line
> > *Step 4*> mri_segtd =
> > MRIread('path/to/test/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz'); %
> > mri_segtd is a matlab struct containing transformation matrices and
> > volumetric data e.t.c.
> > *Step 5*> mdb_label = read_label(path/to/mdb.label);
> > *Step 6*> mdb_label(:,4) = 1 ; % to make the label file ready for
> > transformation (following the instructions of the referred link)
> >
> > Now if I want to copy the voxels data from
> > brainstemSsLabels.v10.FSvoxelSpace.mgz into a test matrix as per the
> > coordinates given in label matrix mdb_label
> > *Step 7*> test_vol = mri_segtd.vol*0 ; %to create a blank matrix of same
> > size of MRI volume
> > *Step 8*> Now transforming mdb_label using tkrvox2ras transformation
> > matrix
> > > mdb_label_inv = int8(inv(mri_segtd.tkrvox2ras)*mdb_label');
> > *Step 9*> Now copying the voxel data from mri_segtd to test_vol
> > > for i = 1:length( mdb_label )
> > > k = mdb_label_inv(i,:,:,:);
> > > test_vol(k(1),k(2),k(3)) = mri_segtd(k(1),k(2),k(3));
> > > end
> >
> > Now when I view the resultant test_vol and the original segmented vol mri_segtd
> > using imshow or imshow3d (
> > https://www.mathworks.com/matlabcentral/fileexchange/47463-imshow3dfull)
> > both are not same, which meant the coordinates in the mdb_label_inv are
> > incorrect.
> > even when I tried test_vol(k(1),k(2),k(3)) = 1; to check whether the mdb_label_inv
> > matrix carry the midbrain shape or not, that was even not correct. please
> > look at the attached images.
> > I also tried other transformation matrices given in the struct. but no
> > success.
> >
> > [image: image.png]
> > Any help shall be highly appreciated.
> >
> > Warm Regards,
> >
> > Safi
> >
> > On Thu, Apr 16, 2020 at 1:04 AM Douglas N. Greve <dgreve@mgh.harvard.edu>
> > wrote:
> >
> >>
> >>
> >> On 4/15/2020 11:17 AM, Safi Ullah . wrote:
> >>
> >> External Email - Use Caution
> >> Dear Freesurfers,
> >>
> >> I recently started working on an brain sMRI related project. I have a
> >> minor (may be a major) issue.
> >> when I generate label files for a tissue e.g midbrain by using the
> >> command
> >> mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id
> >> 173
> >> --l midbrain.label
> >> or in voxel space
> >> mri_vol2label --c
> >> $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz --id 173 --l
> >> midbrain1.label
> >> 👉Now I want to lad the label file and the MRI volume,
> >> brainstemSsLabels.v10 , in Matlab (I can do this by using MRIread
> >> function given in FSmatlab directory. the function read mri in a matlab
> >> struct, which along with other info also contain a 'vol' 3D data matrix)
> >>
> >> read_label.m will read in the label
> >> MRIread.m will load the volume
> >>
> >> 👉 Using the coordinates given in label file, how to extract a specific
> >> slice, row, column from a matlab matrix? as the label file need some
> >> transformation, I dont know this part.
> >>
> >> See this page for converting between coordinates
> >> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
> >>
> >>
> >> Any help shall be highly appreciated.
> >>
> >> Regards,
> >>
> >> Safi
> >>
> >>
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