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Technical: re-run with the latest dcm2niix #8

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opened 2025-05-23 16:34:40 +00:00 by msz · 0 comments
msz commented 2025-05-23 16:34:40 +00:00
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The conversion to NIfTI was done with dcm2niiX v1.0.20240202. The latest version currently available is v1.0.20241211.

As discovered in #6 (comment) dcm2niix v1.0.20241211 has some kludges for processing data saved with Syngo MR XA60 (software version used in Aachen, Frankfurt, and Mannheim); see dcm2niix issue 870

That issue is about MultibandAccelerationFactor and slice timing. Reading the thread suggests that our older version also handles those correctly due to fixes for unrelated issues. I ran both versions on a single rsfMRI series and checked sidecar jsons; indeed both have "MultibandAccelerationFactor": 3 and identical slice timing. Diff of these sidecars below:

11c11
<       "BodyPartExamined": "HEADNECK",
---
>       "BodyPart": "HEADNECK",
15a16
>       "StudyDescription": "Kopf Q01",
22c23
<       "ImageType": ["ORIGINAL", "PRIMARY", "FMRI", "NONE"],
---
>       "ImageType": ["ORIGINAL", "PRIMARY", "FMRI", "NONE", "MAGNITUDE"],
29a31,34
>       "TablePosition": [
>               0,
>               0,
>               13      ],
52a58
>       "ConsistencyInfo": "66010002",
154c160
<       "ConversionSoftwareVersion": "v1.0.20240202"
---
>       "ConversionSoftwareVersion": "v1.0.20241211"

Outputs from running the two dcm2niix versions side by side on the Aachen rsfMRI series:

old ("CMRR bug"):

Chris Rorden's dcm2niiX version v1.0.20240202  (JP2:OpenJPEG) GCC12.2.0 x86-64 (64-bit Linux)
Found 741 DICOM file(s)
Convert 1 DICOM as /tmp/aaa-aaa/Q01_func_task-rest_7_MR_Q01_fmap_se_ap_20250120132533_8 (104x104x72x1)
270 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.
CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..4347.5, TR=1500 ms)
Convert 470 DICOM as /tmp/aaa-aaa/Q01_func_task-rest_7_MR_Q01_func_task-rest_20250120132533_7 (104x104x72x470)
Conversion required 2.166813 seconds (2.166440 for core code).

new ("Issue870"):

Chris Rorden's dcm2niiX version v1.0.20241211  (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux)
Found 741 DICOM file(s)
Convert 1 DICOM as /tmp/aaa-dec/Q01_func_task-rest_7_MR_Q01_fmap_se_ap_20250120132533_8 (104x104x72x1)
270 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED.
Warning: Issue870: Slice timing range of first volume: range 0..4347.5, TA= 4347.5, TR=1500 ms)
Warning: Issue870: Slice timing range of 2nd volume: range 14845..16262.5, TA= 1417.5, TR=1500 ms)
Convert 470 DICOM as /tmp/aaa-dec/Q01_func_task-rest_7_MR_Q01_func_task-rest_20250120132533_7 (104x104x72x470)
Conversion required 2.207800 seconds (2.207232 for core code).

This goes to show that either version handles these DICOMs correctly, but it would probably be prudent to use the one which is currently latest. The only reason for using 20240202 was that I had it installed from Neurodebian.

The conversion to NIfTI was done with dcm2niiX v1.0.20240202. The latest version currently available is v1.0.20241211. As discovered in https://hub.trr379.de/q02/phantom-mri-bids/issues/6#issuecomment-121 dcm2niix v1.0.20241211 has some kludges for processing data saved with Syngo MR XA60 (software version used in Aachen, Frankfurt, and Mannheim); see [dcm2niix issue 870](https://github.com/rordenlab/dcm2niix/issues/870) That issue is about `MultibandAccelerationFactor` and slice timing. Reading the thread suggests that our older version also handles those correctly due to fixes for unrelated issues. I ran both versions on a single rsfMRI series and checked sidecar jsons; indeed both have `"MultibandAccelerationFactor": 3` and identical slice timing. Diff of these sidecars below: ``` diff 11c11 < "BodyPartExamined": "HEADNECK", --- > "BodyPart": "HEADNECK", 15a16 > "StudyDescription": "Kopf Q01", 22c23 < "ImageType": ["ORIGINAL", "PRIMARY", "FMRI", "NONE"], --- > "ImageType": ["ORIGINAL", "PRIMARY", "FMRI", "NONE", "MAGNITUDE"], 29a31,34 > "TablePosition": [ > 0, > 0, > 13 ], 52a58 > "ConsistencyInfo": "66010002", 154c160 < "ConversionSoftwareVersion": "v1.0.20240202" --- > "ConversionSoftwareVersion": "v1.0.20241211" ``` Outputs from running the two dcm2niix versions side by side on the Aachen rsfMRI series: old ("CMRR bug"): ``` Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) GCC12.2.0 x86-64 (64-bit Linux) Found 741 DICOM file(s) Convert 1 DICOM as /tmp/aaa-aaa/Q01_func_task-rest_7_MR_Q01_fmap_se_ap_20250120132533_8 (104x104x72x1) 270 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED. CSA slice timing based on 2nd volume, 1st volume corrupted (CMRR bug, range 0..4347.5, TR=1500 ms) Convert 470 DICOM as /tmp/aaa-aaa/Q01_func_task-rest_7_MR_Q01_func_task-rest_20250120132533_7 (104x104x72x470) Conversion required 2.166813 seconds (2.166440 for core code). ``` new ("Issue870"): ``` Chris Rorden's dcm2niiX version v1.0.20241211 (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux) Found 741 DICOM file(s) Convert 1 DICOM as /tmp/aaa-dec/Q01_func_task-rest_7_MR_Q01_fmap_se_ap_20250120132533_8 (104x104x72x1) 270 images have identical time, series, acquisition and instance values. DUPLICATES REMOVED. Warning: Issue870: Slice timing range of first volume: range 0..4347.5, TA= 4347.5, TR=1500 ms) Warning: Issue870: Slice timing range of 2nd volume: range 14845..16262.5, TA= 1417.5, TR=1500 ms) Convert 470 DICOM as /tmp/aaa-dec/Q01_func_task-rest_7_MR_Q01_func_task-rest_20250120132533_7 (104x104x72x470) Conversion required 2.207800 seconds (2.207232 for core code). ``` This goes to show that either version handles these DICOMs correctly, but it would probably be prudent to use the one which is currently latest. The only reason for using 20240202 was that I had it installed from Neurodebian.
msz self-assigned this 2025-05-23 16:34:40 +00:00
msz removed their assignment 2025-08-14 13:48:17 +00:00
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