T1w to DWI alignment errors in 5tt ACT

1

Dear MRtrix3 users and developers,
I’m trying to adapt the preprocessing pipeline available at OSF (B.A.T.M.A.N) to my data in order to perform Anatomically Constrained Tractography (OSF | B.A.T.M.A.N.: Basic and Advanced Tractography with MRtrix for All Neurophiles). Unfortunately I encounter some form of image registration error between T1 and DWI images.

Here’s a picture of my dwi_b0 image with the 5tt_nocoreg.mif image overlayed onto it (almost perfectly aligned):

5tt_nocoreg0001
5tt_nocoreg00011537×979 177 KB

Here’s a picture of my dwi_b0 image with the 5tt_nocoreg.mif image overlayed onto it (crazy stuff here!):

5tt_coreg0000
5tt_coreg00001537×979 235 KB

Here’s my bit of code for five tyssue type generation and then registration to dwi images:

…
#converting DICOM T1 directory to T1 image in .mif format
mrconvert /T1 T1_raw.mif

#preparing data for anatomically constrained tractography (ACT) to increase biological plausibility of stramlines
5ttgen fsl T1_raw.mif 5tt_nocoreg.mif -nocleanup

#compute mean of b0 images
dwiextract dwi_den_unr_preproc.mif - -bzero | mrmath - mean mean_b0_preprocessed.mif -axis 3

mrconvert mean_b0_preprocessed.mif mean_b0_preprocessed.nii.gz
bet mean_b0_preprocessed.nii.gz mean_b0_preprocessed_BET.nii.gz

#getting images for registration
cp 5ttgen-tmp-*/T1_BET.nii.gz ./
cp 5ttgen-tmp-*/T1_BET_pve_2.nii.gz ./
mrconvert T1_raw.mif T1.nii.gz

#register dwi to T1 and then apply inverse transform to register 5tt image to dwi
epi_reg --epi=mean_b0_preprocessed_BET.nii.gz --t1=T1.nii.gz --t1brain=T1_BET.nii.gz --wmseg=T1_BET_pve_2.nii.gz --out=diff2struct_fsl

transformconvert diff2struct_fsl.mat mean_b0_preprocessed_BET.nii.gz T1.nii.gz flirt_import diff2struct_mrtrix.txt

mrtransform 5tt_nocoreg.mif -linear diff2struct_mrtrix.txt -inverse 5tt_coreg.mif

#check results with:
mrview dwi_den_unr_preproc.mif -overlay.load 5tt_nocoreg.mif -overlay.colourmap 2 -overlay.load 5tt_coreg.mif -overlay.colourmap 1

Here there is mrinfo’s output of 5tt_nocoreg.mif and 5tt_coreg.mif

> ************************************************
> Image:               "5tt_nocoreg.mif"
> ************************************************
>   Dimensions:        192 x 245 x 195 x 5
>   Voxel size:        0.700521 x 0.700521 x 0.7 x ?
>   Data strides:      [ 2 3 4 1 ]
>   Format:            MRtrix
>   Data type:         32 bit float (little endian)
>   Intensity scaling: offset = 0, multiplier = 1
>   Transform:               0.9998    -0.01169     0.01318      -59.43
>                           0.01551      0.9388     -0.3442      -70.12
>                         -0.008352      0.3444      0.9388      -79.66
>   command_history:   /home/duzzo/mrtrix3/bin/mrcalc "T1_BET_pve_1.nii.gz" "multiplier_noNAN.mif" "-mult" "remove_unconnected_wm_mask.mif" "-mult" "cgm.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>                      /home/duzzo/mrtrix3/bin/mrcat "cgm.mif" "sgm.mif" "wm.mif" "csf.mif" "path.mif" "-" "-axis" "3" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>                      /home/duzzo/mrtrix3/bin/mrconvert "-" "combined_precrop.mif" "-strides" "+2,+3,+4,+1" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>                      /home/duzzo/mrtrix3/bin/mrcrop "combined_precrop.mif" "result.mif" "-mask" "-" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>                      /home/duzzo/mrtrix3/bin/mrconvert "result.mif" "/mnt/226AE1226AE0F407/DTI/pipeline_test/Duzzo/5tt_nocoreg.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>   comments:          6.0.1
>   mrtrix_version:    3

************************************************
Image:               "5tt_coreg.mif"
************************************************
  Dimensions:        192 x 195 x 245 x 5
  Voxel size:        0.700521 x 0.7 x 0.700521 x ?
  Data strides:      [ 2 -4 3 1 ]
  Format:            MRtrix
  Data type:         32 bit float (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:               0.9962    -0.08495     0.01874      -3.205
                          0.05217      0.7558      0.6527      -155.2
                         -0.06962     -0.6493      0.7574      -35.24
  command_history:   /home/duzzo/mrtrix3/bin/mrcalc "T1_BET_pve_1.nii.gz" "multiplier_noNAN.mif" "-mult" "remove_unconnected_wm_mask.mif" "-mult" "cgm.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
  [6 entries]        /home/duzzo/mrtrix3/bin/mrcat "cgm.mif" "sgm.mif" "wm.mif" "csf.mif" "path.mif" "-" "-axis" "3" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
                     ...
                     /home/duzzo/mrtrix3/bin/mrconvert "result.mif" "/mnt/226AE1226AE0F407/DTI/pipeline_test/Duzzo/5tt_nocoreg.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
                     mrtransform "5tt_nocoreg.mif" "-linear" "diff2struct_mrtrix.txt" "-inverse" "5tt_coreg.mif"  (version=3.0_RC3-137-g5d6b3a6f)
  comments:          6.0.1
                     transform modified
  mrtrix_version:    3.0_RC3-137-g5d6b3a6f
.0_RC3-137-g5d6b3a6f

Does anyone have an idea of why this is happening or where my pipeline is wrong?

thanks for your kind help and support
Davide

2

Hi,

I think the problem is here:

You should rename your WM mask as T1_BET_wmseg.nii.gz, and waht I don’t know is if it uses partial volume effect or binary images, you could try with both and see what happens.

Best regards,

Manuel

3

Dear Manuel,
many thanks for the quick answer!
I tried remaming the partial volume mask as T1_BET_wmseg.nii.gz but unfortunately the error still remained (blue is 5tt_nocoreg.mif, orange is 5tt_coreg.mif

wmseg0001
wmseg00011464×979 321 KB

mrinfo says:

>  ************************************************
> Image:               "5tt_coreg_wmseg.mif"
> ************************************************
>  Dimensions:        192 x 195 x 245 x 5
>   Voxel size:        0.700521 x 0.7 x 0.700521 x ?
>   Data strides:      [ 2 -4 3 1 ]
>   Format:            MRtrix
>   Data type:         32 bit float (little endian)
>   Intensity scaling: offset = 0, multiplier = 1
>   Transform:               0.9962    -0.08495     0.01874      -3.205
>                           0.05217      0.7558      0.6527      -155.2
>                          -0.06962     -0.6493      0.7574      -35.24
>   command_history:   /home/duzzo/mrtrix3/bin/mrcalc "T1_BET_pve_1.nii.gz" "multiplier_noNAN.mif" "-mult" "remove_unconnected_wm_mask.mif" "-mult" "cgm.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>   [6 entries]        /home/duzzo/mrtrix3/bin/mrcat "cgm.mif" "sgm.mif" "wm.mif" "csf.mif" "path.mif" "-" "-axis" "3" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>                      ...
>                      /home/duzzo/mrtrix3/bin/mrconvert "result.mif" "/mnt/226AE1226AE0F407/DTI/pipeline_test/Duzzo/5tt_nocoreg.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
>                      mrtransform "5tt_nocoreg.mif" "-linear" "diff2struct_mrtrix_wmseg.txt" "-inverse" "5tt_coreg_wmseg.mif" "-force"  (version=3.0_RC3-137-g5d6b3a6f)
>   comments:          6.0.1
>                      transform modified
>   mrtrix_version:    3.0_RC3-137-g5d6b3a6f

I then tried with a binary mask from 5tt image itself:

mrconvert 5tt_nocoreg.mif 5tt_nocoreg.nii.gz
fslsplit 5tt_nocoreg.nii.gz vol -t
mv vol0002..nii.gz T1_BET_wmseg.nii.gz
....

and the alignment improved (still not optimal):

wmseg_binary0001
wmseg_binary00011537×979 461 KB

mrinfo says:

Image:               "5tt_coreg_wmseg.mif"
************************************************
  Dimensions:        192 x 245 x 195 x 5
  Voxel size:        0.700521 x 0.700521 x 0.7 x ?
  Data strides:      [ 2 3 4 1 ]
  Format:            MRtrix
  Data type:         32 bit float (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:               0.9959    -0.03314    -0.08453         -63
                        -0.003852      0.9147      -0.404      -56.37
                          0.09071      0.4027      0.9108      -77.84
  command_history:   /home/duzzo/mrtrix3/bin/mrcalc "T1_BET_pve_1.nii.gz" "multiplier_noNAN.mif" "-mult" "remove_unconnected_wm_mask.mif" "-mult" "cgm.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
  [6 entries]        /home/duzzo/mrtrix3/bin/mrcat "cgm.mif" "sgm.mif" "wm.mif" "csf.mif" "path.mif" "-" "-axis" "3" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
                     ...
                     /home/duzzo/mrtrix3/bin/mrconvert "result.mif" "/mnt/226AE1226AE0F407/DTI/pipeline_test/Duzzo/5tt_nocoreg.mif" "-nthreads" "4"  (version=3.0_RC3-137-g5d6b3a6f)
                     mrtransform "5tt_nocoreg.mif" "-linear" "diff2struct_mrtrix_wmseg.txt" "-inverse" "5tt_coreg_wmseg.mif" "-force"  (version=3.0_RC3-137-g5d6b3a6f)
  comments:          6.0.1
                     transform modified
  mrtrix_version:    3.0_RC3-137-g5d6b3a6f

so this surely has helped but has not solved the issue.
I’m also wondering why the 5tt_nocoreg.mif image is so similar to the mean_b0_preprocessed_BET.mif reference

4

Hi,

I think the 5tt file is builded with the probability maps, so unless there is an extra command after that, the wm should be a pve.

Could you check that the T1, T1_BET and T1_BET_wmseg are in the same space? and the output of epi_reg is aligned to the T1? maybe the B0 mask is not good enough?

Best regards,

Manuel

5

Dear Manuel,
you were right in checking the T1_BET image. As always, looking at the data is the best thing to do.
Now the registration works perfectly.
Using mean_b0_preprocessed.nii.gz (instead of the BET image) and hard segmentation (non pve) wmseg image also improves the alignment

here the final result:

screenshot_optimal0002
screenshot_optimal00021537×979 254 KB

thanks for your kind help and support
Davide

6

Hi all,

I wanted to align 5tt_nocoreg.mif to the subjects’ DWI space and saw this thread. However, I realized that using epi_reg results in alignment errors whatever I do so I came up with a simpler solution and I wonder was there a reason that you haven’t used it? Any comments are appreciated.

5ttgen fsl t1.nii.gz 5tt_nocoreg.mif -nocleanup
dwiextract preproc_dwi.mif - -bzero | mrmath - mean preproc_b0.nii.gz -axis 3
bet preproc_b0.nii.gz preproc_b0_brain.nii.gz #I had to change -f option
flirt -in preproc_b0_brain.nii.gz -ref T1_BET.nii.gz -cost normmi -dof 6 -omat dwi_to_t1.mat -out dwi_to_t1.nii.gz
transformconvert dwi_to_t1.mat preproc_b0_brain.nii.gz T1_BET.nii.gz flirt_import dwi_to_t1.txt
mrtransform 5tt_nocoreg.mif -linear dwi_to_t1.txt -inverse 5tt_coreg.mif
5tt2vis 5tt_coreg.mif 5tt_coreg_vis.mif

The result can be viewed:
image

Bests,
Amir