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CBICA / CaPTk

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
https://www.cbica.upenn.edu/captk
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Perfusion alignment doesn't output nii.gz & please update usage #678

Open chiharusako opened 4 years ago

chiharusako commented 4 years ago

Describe the bug perfusion alignment doesn't output nii.gz

To Reproduce

PerfusionAlignment -i $input -d $inputdcm -c $t1ce -b 15 -a 30 -e 0.045 -o $PWD/out_AAAA

outputs 2 files, original_curve.csv and revised_curve.csv Original_curve.csv seems correct with 45 timepoints but revised_curve.csv only has 2. It also does not output a nii.gz

I have put files for you reference here: /cbica/home/sakoc/comp_space/Saima/20190930_perfalignment

CaPTk Version 1.7.3 Alpha

Desktop (please complete the following information): centos7 on cbica-cluster

** In addition:

Please update the Usage part of the help (1) several say --dicom file. for -d, is this one .dcm file? (2) echo time -- in what unit? (3) do we need to input a t1ce image? if so, any requirements? Does it need to be in the same space as the DSC?

chiharusako commented 4 years ago

Updated file path due to request: /cbica/home/sakoc/comp_space/lab/captk/180a/perfalignment

input perfusion: AAAB_perf.nii.gz input t1ce: AAAB_t1ce.nii.gz input dicom folder AAAB_dicom_anonymized

command run:

PerfusionAlignment -i AAAB_perf.nii.gz \ -d AAAB_dicom_anonymized/1.3.6.1.4.1.14519.5.2.1.99700540694421948465921560797431588453 \ -c AAAB_2006.10.28_t1ce.nii.gz -b 15 -a 17 -e 2 -o ./out

Result: 2 csvs in folder out as well as out16.nii.gz - out31.nii.gz in current folder

ashishsingh18 commented 4 years ago

@saimarathore Could you please take a look at this? I just tried this on windows ( as per @chiharusako earlier comment ) and I see: 1 ) there are multiple output.nii.gz created from 16 - 31 2) 2 csv in output folder. The output revised_curve.csv has 90 entries. The last one is zero.

Is this how it is supposed to work? or are there any bugs? Also tagging @chiharusako