Open tjhendrickson opened 2 years ago
@tjhendrickson , could you show an example of the DICOM folder organization? Is it something like this?:
my_DICOMs \
|- run_1 \
| |- run_1_volume_1.dcm
| |- run_1_volume_2.dcm
| | ...
|- run_2 \
| |- run_2_volume_1.dcm
| |- run_2_volume_2.dcm
| | ...
| ...
|- run_1_PhysioLog \
| |- run_1_PhysioLog.dcm
|- run_2_PhysioLog \
| |- run_2_PhysioLog.dcm
| ...
Also, can you post the contents of the .heudiconv/<subID>/info/dicominfo.tsv
and .heudiconv/<subID>/info/<subID>.auto.txt
files (at the root of the output folder)?
@pvelasco Thanks for getting back to me. Yes, the DICOMs are organized in the way you suspected. Here is an example: `20211001-ST001-SUB1000101ses1/MR-SE030-rest_ep2d_bold_ME_16MIN_PhysioLog: MR-ST001-SE030-0001.dcm
20211001-ST001-SUB1000101ses1/MR-SE031-rest_ep2d_bold_ME_16MIN2_SBRef: MR-ST001-SE031-0001.dcm MR-ST001-SE031-EC3-0001.dcm MR-ST001-SE031-EC5-0001.dcm MR-ST001-SE031-EC2-0001.dcm MR-ST001-SE031-EC4-0001.dcm ` Attached are the files you asked for.
Actually, the physio data extraction has not been added yet to the master
branch. PR #446 addresses it, but it is still under review. You can test that PR, to see if it works with your data (still, your heuristic.py
file will need some changes, like adding an extra argument (outtype = ('physio',)
) to all the create_key
calls for physio files.
Looking at the dicominfo
file, it didn't "see" series number 30 (the one with the PhysioLog DICOM). I'm not sure why.
Do you mind posting the full heudiconv
call?
I assume these DICOMs with the physio in them come from the CMRR SMS sequence. Is that correct?
I'm checking in to see if there has been any update on this. I guess since #446 is still open, the best way to convert physio is directly through bidsphysio, right? I'm thinking to run heudiconv on everything except physio, and then on top of it run bidsphysio
Summary
I cannot seem to figure out how to convert physiological recordings present within the DICOM folder from a neuroimaging dataset. The physiological recordings are organized as one DICOM file within its own folder and with the same naming scheme as the BOLD it relates to with "PhysioLog" suffixed. The heuristic script below failed to find this and even when I run
convertall.py
as the heuristic the physiological recordings are not found.Any ideas?
def create_key(template, outtype=('nii.gz','dicom'), annotation_classes=None): #), annotation_classes=None): if template is None or not template: raise ValueError('Template must be a valid format string') return (template, outtype, annotation_classes)
def infotodict(seqinfo): """Heuristic evaluator for determining which runs belong where