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pnlbwh / pnlpipe

A Python-based framework for processing anatomical (T1, T2) and diffusion weighted images
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Clarification on adding more than one subject #54

Closed vzeng97 closed 3 years ago

vzeng97 commented 3 years ago

Hi Tashrif, this is a continuation of the email chain we had, where I would like clarification on adding more than one subject:

Previously for pnlpipe I put something like:

ABC = { 'caseid_placeholder': '3TB6312','3TB6371', 'dwi': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPDTI_jones30_b1000_SPIRweakSENSE_15.nrrd', '/users/vzeng/smu_transfer/3TB6371/3TB6371_WIPDTI_jones30_b1000_SPIRweakSENSE_16.nrrd', 't1': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPMPRAGE2100-MPRinto_4.nrrd', '/users/vzeng/smu_transfer3TB6371/3TB6371​_WIPMPRAGE2100-MPRinto_4.nrrd' } INPUT_KEYS = ABC

and that crashed, so you specified putting:

ABC = { 'caseid_placeholder': '3TB6312', 'dwi': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPDTI_jones30_b1000_SPIRweakSENSE_15.nrrd', 't1': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPMPRAGE2100-MPRinto_4.nrrd' }

and I was wondering how it would recognize the address of 3TB6371 for example?

Should I have it like this?:

ABC1 = { 'caseid_placeholder': '3TB6312', 'dwi': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPDTI_jones30_b1000_SPIRweakSENSE_15.nrrd', 't1': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPMPRAGE2100-MPRinto_4.nrrd' } ABC2 = { 'caseid_placeholder': '3TB6371', 'dwi': '/users/vzeng/smu_transfer/3TB6371/3TB6371_WIPDTI_jones30_b1000_SPIRweakSENSE_16.nrrd', 't1': '/users/vzeng/smu_transfer/3TB6371/3TB6371_WIPMPRAGE2100-MPRinto_4.nrrd' }

tashrifbillah commented 3 years ago

I was wondering how it would recognize the address of 3TB6371 for example?

You provide just one block:

ABC = {
'caseid_placeholder': '3TB6312',
'dwi': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPDTI_jones30_b1000_SPIRweakSENSE_15.nrrd',
't1': '/users/vzeng/smu_transfer/3TB6312/3TB6312_WIPMPRAGE2100-MPRinto_4.nrrd'
}

Then, as long as your case ids in caselist consist of equal number of characters as of 3TB6312, the pipeline will obtain the location of the other ids magically!

vzeng97 commented 3 years ago

Wow... ummm I'll assume it does that although its not consistently named "_WIPDTI_jones30_b1000_SPIRweakSENSE_15.nrrd"

tashrifbillah commented 3 years ago

Aha ... now I see your confusion. First of all, your assumption is right.

See my example, the program would substitute 3TB6312, wherever that occurs, with each line of the caselist.

vzeng97 commented 3 years ago

I understand now. I'll just rename the dti/t1 files so that it can be replaced with the new id automatically for pnlpipe