dmriprep IMAGE_Filter module does not remove DWI volumes

[markwfoster]

I am using version DTIPlayground VERSION : 0.5.7b5. I am having trouble getting DMRI Prep to remove volumes that have high b-values using the IMAGE_Filter module. I have tried to change many of the parameters in the config file to no avail. DMRI Prep changes the header according to what you specify but does not actually remove DWIs. (i.e. When you visualize the DWI output by dmriprep, all volumes are still there.)

Here is the path on longleaf to the folder where I have been testing dmriprep:

/work/users/m/w/mwfoster/TestExcludeUpperShells_13Mar2023

Here is the command with a parameters file that I have used:

dmriprep run -i BEE-1127-2wk-DWI_6shell_PA_select-padded_eddy_openmp_corrected_noneg_QCed.nrrd -p protocol_RemoveShellsAbove1700.json -o /work/users/m/w/mwfoster/TestExcludeUpperShells_13Mar2023/Output_Test_DMRI_Playground_Latest

[scalphunters]

There might be compromised parameter from a bug. Can you try v0.5.7b9? ($pip install dtiplayground==0.5.7b9)

[markwfoster]

I deleted the comment I made yesterday. I thought I was using v0.5.7b9, but the log file showed another version. I apologize for any confusion. I have tried it again with version v0.5.7b9, but it is still not removing DWI volumes.

Here is the command I used with v0.5.7b9 :

dmriprep run -i /work/users/m/w/mwfoster/TestExcludeUpperShells_13Mar2023/BEE-1127-2wk-DWI_6shell_PA_select-padded_eddy_openmp_corrected_noneg_QCed.nrrd -p /work/users/m/w/mwfoster/TestExcludeUpperShells_13Mar2023/protocol_RemoveShellsAbove1700.txt -o /work/users/m/w/mwfoster/TestExcludeUpperShells_13Mar2023/Output_Test_DMRI_Playground0.5.7b9_22Mar2023

[scalphunters]

No problem, thanks for reporting the issue. I've checked that the IMAGE_Filter module has some problem. I'll rewrite the code and get back to you.

[scalphunters]

IMAGE_Filter module rewritten. Please try v0.5.7b10

$pip install dtiplayground==0.5.7b10

[scalphunters]

Problem fixed with version 0.5.7b10