File not found

[senthilcaesar]

./pipeline_test.sh Harmonization completed IITmean_FA_skeleton.nii.gz file not found error I tried to download the data, but its downloading IITmean_FA.nii.gz file

[tashrifbillah]

As we saw, due to network problem, the file can't be downloaded in your computer. So, I have copied the file in /tmp/IIT_mean_FA_skeleton.nii.gz. Copy the file in IITAtlas/ directory and then run test with previous outputs:

cd lib/tests/connectom_prisma/ \
../../harmonization.py \
--template ./template/ \
--ref_list connectom.txt.modified \
--tar_list prisma.txt \
--harm_list prisma.txt.modified.harmonized \
--ref_name CONNECTOM \
--tar_name PRISMA \
--nshm 4 \
--nproc -1 \
--debug

@SenthilCaesar , let me know how it goes.

[senthilcaesar]

I ran the above command Traceback (most recent call last): File "/rfanfs/pnl-zorro/home/sq566/Downloads/conda/envs/dMRIharmonization/lib/python3.6/site-packages/nibabel/loadsave.py", line 40, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: '/home/sq566/dMRIharmonization/lib/tests/connectom_prisma/prisma/A/dti/dwi_A_prisma_st_b1200_InMNI_FA.nii.gz'

I checked inside the directory for the file name and its not there @tashrifbillah

[tashrifbillah]

Hi @SenthilCaesar , I ran the debug test starting from your output. However, I couldn't reproduce the error. The only thing I realized was, antsRegistration didn't run correctly. I re-ran the registration and now the results are as expected:

Printing statistics :
CONNECTOM mean FA:  0.6799283760230598
PRISMA mean FA before harmonization:  0.8020249146122524
PRISMA mean FA after harmonization:  0.6374742090078741

Anyways, can you run the unittests one last time? We just completed the whole pipeline test. Running unittests should need 5 minutes.

[tashrifbillah]

Fixed by https://github.com/pnlbwh/dMRIharmonization/commit/f2e3d3da2d736b595180729ad7dbfd074aff015a

[tashrifbillah]

Tests ran fine!