editing convert_dicom.py & rename_nifti.py to deal with T2space scans

[cacoughlin]

As of right now, T2space scans (e.g., T2spaces010a1001.nii.gz & oT2spaces010a1001.nii.gz) are moved to the "raw" subdirectory. I'm manually moving them to the "anatomy" directory, but am wondering if it would be possible to build this into the existing scripts. As a side note - I'm planning on using the images that have been moved to standard orientation for preprocessing purposes (I can add this to the wiki if everyone is in agreement). Thanks for any help!

[mortonne]

This will take a little work to get right. The main thing will be to edit dicom_filetype in skyra.py, so that the T2space scans are correctly recognized as anatomical scans (it sounds like they're being treated as localizer scans or something now). You'll need to look at the header information using ipython on the virtual login or on idev. In ipython, something like:

import dicom
hdr = dicom.read_file('path_to_t2space_dicom')
hdr

Look at ProtocolName, SequenceName, and SeriesDescription for strings that could be added to the scan_protocols['anatomy'] list in dicom_filetype.

We could also modify rename_nifti.py, but it isn't necessary. I really just included the anatomical renaming part to match setup_subject.py, but in the standard naming system I use, highres001.nii.gz gets renamed to highres1.nii.gz (or highres.nii.gz) anyway. run_freesurfer.sh expects the FLAIR to be called [subjectdir]/anatomy/flair.nii.gz, so move it there in your data organization script. Or I guess that could be built into rename_nifti.py if you want to take a crack at that.