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 subject looking like it's hanging
> upside down from its bat cave or some such awkward arrangement.
>
> In the end, the best way of knowing that the gradient table is correct is
> to run one example subject through and view the eigenvectors of the
> tensors as lines to see if they're pointing in the right direction. (Even
> though the tensors themselves aren't used for tractography, they're good
> for troubleshooting.)
>
> On Mon, 21 Jul 2014, Harms, Michael wrote:
>
> >
> > FS uses FSL tools under the hood, so you want to use the bvecs that are
> > rotated into the axes of the scan.
> >
> > cheers,
> > -MH
> >
> > --?
> > Michael Harms, Ph.D.
> > -----------------------------------------------------------
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > 660 South Euclid Ave. Tel: 314-747-6173
> > St. Louis, MO ?63110 Email:?mharms@wustl.edu
> >
> > From: Rotem Saar <saar.rotem@gmail.com>
> > Reply-To:?Freesurfer?support list <freesurfer@nmr.mgh.harvard.edu>
> > Date: Monday, July 21, 2014 1:54 PM
> > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> > Subject: [Freesurfer] Diffusion analysis qs - gradient matrix
> >
> > Dear?freesurfer?experts,
> >
> > For diffusion analysis in?freesurfer?- I want to know which gradient
> matrix
> >?freesurfer?expects.
> >
> > The thing is - when I look at the gradient matrix created using a MATLAB
> > script that reads the directions from the dicom header - I get one table,
> > but the bvecs file created in MRIconvert (for converting dicoms to nifti)
> > looks different.
> >
> > This is the situation when an angle is applied during the acquisition of
> the
> > dMRI scans, which means that each subject has its own gradient matrix.
> >
> > So my question is which table should I use for diffusion analysis in
> >?freesurfer? The one that was created from the dicom header or the one
> > created for NIFTI format using MRIconvert ??

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work

Ashkelon Academic College, Ashkelon, 78211

Israel