Hi Juan - You can see usage info for dt_recon if you run it without arguments: USAGE: dt_recon
Required Aruments: --i invol --b bvals bvecs --s subjectid --o outputdir ...
So --b takes both bvals and bvecs one after the other, and --s is the subject name as found under $SUBJECTS_DIR.
Best, a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Juan Rivas jcrn12@gmail.com Sent: Friday, October 4, 2019 4:13 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula
External Email - Use Caution
Hi, I am trying to make the recon with diffusion images for running tracula. I gave this command:
set cmd = dt_recon
set cmd = ($cmd --b $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvals
set cmd = ($cmd --b $SUBJECTS_DIR/esq-15 hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/31190669_bvecs)
set cmd = ($cmd --i $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing/esq-15-hc_dwi.nii.gz)
set cmd = ($cmd --s $SUBJECTS_DIR/esq-15-hc/)
set cmd = ($cmd --o $SUBJECTS_DIR/esq-15-hc/0122816811_007_ep2d_diff_mddw_20_3mm_p2_20190405/processing)
echo $cmd
$cmd
But ir marks two kinds of error: can´t fin bvals.dat or Eddy/Motion correct and stops.
Could yo help me?
Thanks,
JC.