Dear Anastasia,
I followed your suggestion:
I calculated the FA maps in freesurfer using the script below (see last
message): I did it with both the rotated and the not rotated gradient
table. The FA maps were identical as u said.
BUT ! - when I used the rotated gradient table in FSL and tried to create
the FA MD maps (as in the first step of tracula), I got the attached
results: http://tinypic.com/r/skzwqa/8
Does this map seems ok to u ? I think that something is wrong but can't
specify what.
I will appreciate your help here again:)
Hi Rotem - The FA values are actually invariant to a rotation of the
gradient vectors. You can test that yourself. If, however, you get
different FA maps with the different gradient tables, then something else
is going on and not a simple rotation.
a.y
On Wed, 23 Jul 2014, Rotem Saar wrote:
Dear Anastasia Michael,
Thank u for your answers (I attached my last email and your answers at the
end of this email.
I still want to specify my question. If I only want to extract FA values
using the following script (see script below), and I know that an angle
was
applied during the dMRI scans, should I use the rotated gradient matrix ?
When I first analyzed 20 subjects with the gradient matrix that is
published
for a T3 Philips magnet (I also read the gradients from the dicom header -
they were the same) I got reasonable results - but now I don't know what
to
think of them...
source ~/Desktop/fs_script
dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s
Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b
/usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval
/usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec
To check results, run:
tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii
--reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf
tkregister2 --s fsaverage --surf white --reg
/usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov
/usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii
tkregister2 --s fsaverage --surf white --reg
/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov
/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii
freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii
/usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii
freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/
brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg=
register.dat:colo
rmap=heat:heatscale=.2,.2,1
tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg
/usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay
/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1
mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii
\
??? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/
wmparc.mgz
\
??? --inv --interp nearest --o
/usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \
??? --reg
/usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg
mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii
\
??? --targ
/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \
??? --inv --interp nearest --o
/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \
??? --reg
/usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg
freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \
???/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+
aseg2diff.mgz:colormap
=lut
mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \
/usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \
/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz
freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-
masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+
aseg2diff.mgz:colormap
=lut
mri_segstats --seg
/usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --i
/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum
/usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked
It'd be nice if things were that simple, but!
Although the pre-processing is done with FSL tools, tractography is done
with locally written code. Some gradient sets may appear to work with FSL,
but they won't work for us. For example, some dicom converters may perform
a L-R flip as preparation for feeding the gradient vectors into FSL. We
need the unflipped vectors because, instead of flipping vectors, we
convert both vectors and images to LAS orientation. This ensures that they
work both for FSL and for us, and that you can view things correctly in
both freeview and fslview, without the
