Hi,
I have recently started to look at the HCP single subject rfMRI data and I
have a couple of beginner questions:
1) What is the difference between the various files (I downloaded just the
FIX-compact version) in 100307/MNINonLinear/Results/rfMRI_REST1_LR?
Is the one with MSMAll the most relevant one? What is the
use/interpretation of the other ones?
2) I gather that the files describing the cortex surfaces corresponding to
the rfMRI results are the *.surf.gii in
100307/MNINonLinear/fsaverage_LR32k. These files are identical for all
other subjects?
In the literature sometimes one has seed locations given in MNI
coordinates. In order to find the closest vertex I understand that one has
to use the command
wb_command -surface-closest-vertex
.../100307/MNINonLinear/fsaverage_LR32k/100307.R.midthickness_MSMAll.32k_fs_LR.surf.gii
seeds.txt out.txt
In connection with that I have the following questions:
- which surface file one should use in this context: pial, midthickness..?
- the coordinates of the points in the surf.gii files in this directory are
in MNI space?
- the answer is vertex number (one of the 32492 surface vertices?). So in
order to map it to a point in the rfMRI *.dtseries.nii file I have to
translate it `by hand' backwards through the VertexIndices structure in the
.dtseries.nii file? Is there a shortcut or better way to do it?
3) In order to check whether I understand the CIFTI2 *.dtseries.nii file I
wanted to reproduce the examples from the paper Minimal Preprocessing
Pipelines for the Human Connectome Project:
"...For example, inside the HCP’s 2mm standard grayordinates space, row
1000 of the matrix would correspond to vertex 2152 of the left hemisphere
surface (not
vertex 1000, because vertices in the medial wall are excluded) and row
91000 would
correspond to voxel (3.9,−1.4, 10.6) of the right thalamus..."
I could reproduce vertex 2152 through the VertexIndices structure but I
cannot reproduce the exact answer for row 91000 (assume row numbers start
from 0).
First I get IJK voxel indices (bms[20] is the BrainModel of right thalamus):
IJK=bms[20].voxel_indices_ijk[91000-bms[20].index_offset]
IJK is [43, 62, 41]
Then I get the transformation matrix from
map1.volume.transformation_matrix_voxel_indices_ijk_to_xyz.matrix
which is
array([[ -2., 0., 0., 90.],
[ 0., 2., 0., -126.],
[ 0., 0., 2., -72.],
[ 0., 0., 0., 1.]])
Applying this transformation to IJK I get [4, -2, 10] which is close to
(3.9,−1.4, 10.6) but different.
Does one have to do some other transformation still or am I doing something
wrong? (or is it just rounding tolerance of the voxel positions which can
just be ignored?)
These coordinates are in the same standard MNI system as the surface ones?
Sorry for these elementary questions but the structure of the file formats
and the sheer number of files is overwhelming for an outsider...
Many thanks,
Romuald
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