Hi Rob,
I will be extremely excited to learn about such a pipeline if you are indeed planning to implement it in future versions
QN1) Do I use maksfilter to dilate the brain mask? Is there a general ACT recommendation for the -npass value?
QN2) For now, when I tried to run 5ttgen with FSL, I ran into the following error:
Command: mrconvert /Users/MacPro/Documents/NIMROD_Mrtrix/dlb_mrtrix/22995_T1.nii /tmp/5ttgen-tmp-3O4SZI/input.mif
5ttgen: Changing to temporary directory (/tmp/5ttgen-tmp-3O4SZI/)
Command: mrconvert input.mif T1.nii -stride -1,+2,+3
Command: maskfilter /usr/local/fsl/data/standard/MNI152_T1_1mm_brain_mask_dil.nii.gz dilate mni_mask.nii -npass 4
Command: standard_space_roi T1.nii T1_preBET.nii.gz -maskMASK mni_mask.nii -roiFOV
5ttgen: [WARNING] FSL command standard_space_roi appears to have failed; passing T1 directly to BET
Command: mrconvert input.mif T1_preBET.nii.gz -stride -1,+2,+3
Command: bet T1_preBET.nii.gz T1_BET.nii.gz -f 0.15 -R
Command: fast T1_BET.nii.gz
5ttgen:
5ttgen: [ERROR] Command failed: fast T1_BET.nii.gz
5ttgen: Output of failed command:
Image Exception : #22 :: ERROR: Could not open image T1_BET
terminate called after throwing an instance of âRBD_COMMON::BaseExceptionâ<
To investigate further, I tried to manually run standard_space_roi with the following command. Why is there an unrecognised option m?
standard_space_roi 22995_T1.nii -maskMASK mni_mask.nii -roiFOV
Unrecognised option m
Lacking argument to option -maskMASK_tmp_to_std.mat
Could not open matrix file -maskMASK_tmp_to_std_inv.mat
terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
/usr/local/fsl/bin/standard_space_roi: line 229: 68194 Abort trap: 6 ${FSLDIR}/bin/flirt -ref $in -in ${out}_tmp_standard_mask -o ${out}_tmp_standard_mask_to_in -applyxfm -init ${out}_tmp_to_std_inv.mat
Cannot open volume -maskMASK_tmp_standard_mask_to_in for reading!
Image Exception : #22 :: ERROR: Could not open image -maskMASK_tmp_standard_mask_to_in
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/usr/local/fsl/bin/standard_space_roi: line 229: 68197 Abort trap: 6 ${FSLDIR}/bin/fslmaths $inapply -mas ${out}_tmp_standard_mask_to_in ${out}_tmp_masked
Could not open matrix file -maskMASK_tmp_to_std_inv.mat
terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
/usr/local/fsl/bin/standard_space_roi: line 242: 68199 Abort trap: 6 ${FSLDIR}/bin/flirt -ref $in -in ${out}_tmp_standard_roi -o ${out}_tmp_standard_roi_to_in -applyxfm -init ${out}_tmp_to_std_inv.mat
Image Exception : #22 :: ERROR: Could not open image -maskMASK_tmp_standard_roi_to_in`indent preformatted text by 4 spaces`indent preformatted text by 4 spaces``
QN3 ) Regarding ACT, it is stated that T1 image should be rigidly registered to the DWI series before running 5ttgen and tckgen. I was wrongly under the impression that the registration was being done under the hood of tckgen. How can I do that with MRTrix? When I tried the following:
mrregister 22995_T1.mif 22995.mif (my DTI series) -type rigid
mrregister: [100%] preloading data for â22995_T1.mifâ
mrregister: [100%] preloading data for â22995.mifâ
mrregister: [ERROR] input images do not have the same number of dimensions
Image: â22995_T1.mifâ
Dimensions: 176 x 240 x 256 x 1
Voxel size: 1 x 1 x 1 x 0
Data strides: [ -3 -1 -2 4 ]
Format: MRtrix
Data type: signed 16 bit integer (big endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 0.9993 0.01697 -0.03344 -84.88
-0.006881 0.9596 0.2814 -128.6
0.03687 -0.281 0.959 -109.5
mrtrix_version: 0.3.15-179-g77ed15eb
Image: â22995.mifâ
Dimensions: 96 x 96 x 63 x 64
Voxel size: 2 x 2 x 2 x 11.7
Data strides: [ -1 2 3 4 ]
Format: MRtrix
Data type: signed 16 bit integer (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 0.9998 -0.02094 0.001451 -91.66
0.02078 0.9775 -0.2098 -93.95
0.002975 0.2098 0.9777 -53.58
comments: TE=106;sec=47865.0775;phaseDir=+;dwell=0.475
dw_scheme: [ 64 entries ]
mrtrix_version: 0.3.15-179-g77ed15eb
Thanks!