Dear Paul and fatcat expert users,

I am using the command:

fat_proc_dwi_to_dt \
-in_dwi dwi_proc/dwi_DMC.nii \
-in_col_matT dwi_proc/dwi_DMC.bmtxt \
-prefix dwi_DMC2dt \
-in_struc_res dwi_proc/dwi_DMC_structural.nii \
-in_ref_orig imit2w.nii \
-mask dwi_proc/dwi_DMC_structural_brain_mask.nii \
${my_flip}

that generate good output for me, but I get a strange side effect in Geometry string of output, e.g.:

$ 3dinfo dt_FA.nii.gz|grep Geometry
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
Geometry String: "MATRIX(1.5,0,0,-94.74982,0,1.5,0,-99.7506,0,0,1.5,-72.75083):128,157,115"

while the Geometry of input files are "rounded":

3dinfo dwi_proc/dwi_DMC.nii|grep Geometry
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
Geometry String: "MATRIX(1.5,0,0,-94.75,0,1.5,0,-99.75,0,0,1.5,-72.75):128,157,115"

the same Geometry for dwi_DMC_structural.nii and dwi_DMC_structural_brain_mask.nii while of course the imit2w.nii Geometry is different:

$ 3dinfo imit2w.nii|grep Geometry
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
Geometry String: "MATRIX(1,0,0,-95,0,1,0,-100,0,0,1,-73):192,236,172"

the different dt_FA.nii.gz Geometry create errors for successive group analysis with SPM.

Note that if I use 3dAutomask:

fat_proc_dwi_to_dt \
-in_dwi dwi_proc/dwi_DMC.nii \
-in_col_matT dwi_proc/dwi_DMC.bmtxt \
-prefix dwi_DMC2dt \
${my_flip}

the output Geometry is correctly "rounded":

3dinfo dt_FA.nii.gz|grep Geometry
++ 3dinfo: AFNI version=AFNI_18.3.15 (Dec 5 2018) [64-bit]
Geometry String: "MATRIX(1.5,0,0,-94.75,0,1.5,0,-99.75,0,0,1.5,-72.75):128,157,115"

and I have no issues on SPM group analisys, but Automasking is not optimal!

Do you have any suggestion on how to solve my problem?

Cheers,

Giuseppe