I'm attempting to convert some data from a Siemens Vida running XA20 and producing enhanced DICOMs. I followed the example here for generating the dicominfo.tsv file prior to setting up my heuristic file. I removed all of the derived images (e.g., the TRACEW files) since these cause it to fail with the error in #670. This allows it to run just fine but I get unusual output (see below). Is there a reason that it's not reporting correct dim4/TR/TE fields? Specific to dim4 the DTI SMS and rs-fMRI acquisitions, for example, should be 137 and 942 respectively.
Log:
singularity run /groups/adamraikes/singularity_images/heudiconv_0.13.1.sif -d $PWD/dicoms/{subject}/*/* -c none -b --minmeta -o nifti -s 000052 -f convertall
INFO: Running heudiconv version 0.13.1 latest 0.13.1
INFO: Need to process 1 study sessions
INFO: PROCESSING STARTS: {'subject': '000052', 'outdir': '/xdisk/adamraikes/test/nifti/', 'session': None}
INFO: Processing 1156 dicoms
INFO: Analyzing 1156 dicoms
INFO: Generated sequence info for 12 studies with 1156 entries total
INFO: Populating template files under /xdisk/adamraikes/test/nifti/
INFO: PROCESSING DONE: {'subject': '000052', 'outdir': '/xdisk/adamraikes/test/nifti/', 'session': None}
Summary
I'm attempting to convert some data from a Siemens Vida running XA20 and producing enhanced DICOMs. I followed the example here for generating the dicominfo.tsv file prior to setting up my heuristic file. I removed all of the derived images (e.g., the TRACEW files) since these cause it to fail with the error in #670. This allows it to run just fine but I get unusual output (see below). Is there a reason that it's not reporting correct dim4/TR/TE fields? Specific to
dim4the DTI SMS and rs-fMRI acquisitions, for example, should be 137 and 942 respectively.Log:
Heuristic: `
Platform details:
Choose one:
[ ] Local environment
[ x] Container
Singularity: heudiconv:0.13.1
Heudiconv version:
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total_files_till_now | example_dcm_file | series_id | dcm_dir_name | series_files | unspecified | dim1 | dim2 | dim3 | dim4 | TR | TE | protocol_name | is_motion_corrected | is_derived | patient_id | study_description | referring_physician_name | series_description | sequence_name | image_type -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- 1 | 23062616_53360000_52371909 | 1- | fe07ab9d | 1 | | 512 | 512 | 11 | 1 | -1 | -1 | | FALSE | FALSE | | | | localizer | | ('ORIGINAL', 'PRIMARY', 'M', 'NONE') 2 | 23062616_53360000_52371920 | 2- | a868ce34 | 1 | | 256 | 240 | 160 | 1 | -1 | -1 | | FALSE | FALSE | | | | Sagittal 3D T1 | ('ORIGINAL', 'PRIMARY', 'M', 'NONE') 3 | 23062616_53360000_52371931 | 3- | 6b209f37 | 1 | | 256 | 240 | 160 | 1 | -1 | -1 | | FALSE | FALSE | | | | Sag 3D FLAIR | ('ORIGINAL', 'PRIMARY', 'M', 'NONE') 4 | 23062616_53360000_52371942 | 4- | 0ae812ca | 1 | | 448 | 448 | 33 | 1 | -1 | -1 | | FALSE | FALSE | | | | OBL COR HIPPOCAMPUS T2 | ('ORIGINAL', 'PRIMARY', 'M', 'NONE') 141 | 23062616_53360000_52371953 | 5- | 666e4ef2 | 137 | | 116 | 116 | 72 | 1 | -1 | -1 | | FALSE | FALSE | | | | DTI SMS | | ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE') 148 | 23062616_53360000_52373504 | 9- | 8da03538 | 7 | | 116 | 116 | 72 | 1 | -1 | -1 | | FALSE | FALSE | | | | DTI SMS_PA | ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE') 162 | 23062616_53360000_52373647 | 17- | 2ad12395 | 14 | | 128 | 128 | 32 | 1 | -1 | -1 | | FALSE | FALSE | | | | Axial 3D Arterial Spin Labeling | ('ORIGINAL', 'PRIMARY', 'ASL', 'NONE') 163 | 23062616_53360000_52373812 | 20- | 215fc33d | 1 | | 78 | 78 | 54 | 1 | -1 | -1 | | FALSE | FALSE | | | | gre_field_mapping_3 x 3 x 3 164 | ('ORIGINAL', 'PRIMARY', 'P', 'NONE') 164 | 23062616_53360000_52373823 | 21- | 52639778 | 1 | | 320 | 320 | 39 | 1 | -1 | -1 | | FALSE | FALSE | | | | Axial 2D t2 start | ('ORIGINAL', 'PRIMARY', 'M', 'NONE') 165 | 23062616_53360000_52373834 | 22- | 7aefc563 | 1 | | 320 | 288 | 39 | 1 | -1 | -1 | | FALSE | FALSE | | | | AX T2 FS | | ('ORIGINAL', 'PRIMARY', 'M', 'NONE') 1141 | 23062616_53360000_52373845 | 23- | bdafc35b | 976 | | 88 | 88 | 64 | 1 | -1 | -1 | | FALSE | FALSE | | | | rs-fMRI | | ('ORIGINAL', 'PRIMARY', 'FMRI', 'NONE') 1156 | 23062616_53360002_52384581 | 25- | 647dd794 | 15 | | 88 | 88 | 64 | 1 | -1 | -1 | | FALSE | FALSE | | | | rs-fMRI PA phase | ('ORIGINAL', 'PRIMARY', 'FMRI', 'NONE')