Thanks Doug, I tried, but it didn't work (misplaced when visualized in fslview), BUT I tried today again and it worked (don't know what the original error was), so... here it is the final command line for reference for others:

mri_label2vol --label label/lh.th13labels-001.label --temp dmri/dtifit_FA.nii.gz --reg dmri/xfms/anatorig2diff.bbr.dat --fillthresh .5 --o mri/onestep_lh.th13labels-001.nii

thanks! Gari

On Tue, Feb 4, 2014 at 6:08 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

Why not just do it in one step? If you have the registration from dti space to FS anatomical space, the just run mri_label2vol to bring aseg into the dti space. doug

On 02/02/2014 05:24 AM, Garikoitz Lerma-Usabiaga wrote:

...

Hi Doug, I've been reading the list and I ended with 4 steps to move from a label to a mask in diffusion space (below). Is this correct? Is there any other more straightforward way? It should end with a binary mask in diffusion space (I am using the anatorig2diff.bbr.dat created in the Tracula process).

tkregister2 --mov mri/rawavg.mgz --targ mri/aseg.mgz --regheader --reg mri/rawreg.dat --noedit

Create volume (it does it in LPS ): mri_label2vol --label label/lh.th13labels-001.label --temp mri/rawavg.mgz --reg mri/rawreg.dat --fillthresh .5 --o mri/fromlabel_lh.th13labels-001.nii

Move volume to anatorig (LIA) : mri_vol2vol --mov mri/fromlabel_lh.th13labels-001.nii --targ /mri/brainmask.mgz --regheader --o mri/anatorig_lh.th13labels-001.nii --no-save-reg

Move to diffusion space (LAS): mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ /mri/anatorig_lh.th13labels-001.nii --inv --interp nearest --o mri/diff_fromlabel_lh.th13labels-001.nii --reg dmri/xfms/anatorig2diff.bbr.dat --no-save-reg

thanks! Gari

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