Hi Fred - What program are you using to display these? Any chance that the volumes are not actually all zero but that they're just not displayed correctly for whatever reason?

Have you tried opening these two volumes in freeview at the same time?

/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain.nii.gz

/media/freds/LinuxData2/FIS_ESTHERCUBO_RESO/Tractografia_FIS_CUBO/TractHipoResult//T1_GONZALEZ_DE_LAS_HERAS_TERESA_NeuroNavegador_Sag_FSPGR_3D_geometry_activo_GD_177643_NeuroNavegador_Sag_FSPGR_3D_geometry_activo_GD_20190403164820_3/dmri/brain_anat_mni.nii.gz

a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fred Sampedro fredsampedro@gmail.com Sent: Thursday, August 8, 2019 5:35:50 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA empty bbr maps after trac-all -prep

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Dear TRACULA experts, dear Anastasia,

I've been successfully using TRACULA for a while with different DTI images from different scanners (siemens, philips...). Now I am working with GE DTI data and whereas the trac-all -prep command went well, and $subject/dmri/dtifit_FA.nii.gz and dtifit_MD.nii.gz look fine, $subject/dmri/mni/dtifit_FA.bbr.nii.gz and all mni-space maps are empty (see pictures attached). I also attach the trac-all.log file. and bvals/bvecs that were generated by trac-all directly from the dicom images.

What could have gone wrong?