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:?mha...@wustl.edu > > > > From: Rotem Saar <saar.ro...@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
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