Fix space other use and correct json sidecars #170
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NathanMolinier
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Description
This PR fixes:
space-otherintroduced in this former PR.
Miss use of the BIDS entity
space-otherThe entity
space-XXXshould only be used on a label if the space of the latter is different from the one of the corresponding image (see our documentation).To fix this, I iterated through all the labels in the derivative folder
labelswith thespace-otherentity using this script:the entity
space-otherwas removed from the label and the corresponding json sidecar if the array size was the same as the corresponding raw image.the entity
space-otherwas moved after the first suffix for the label and the corresponding json sidecar if the array size was different between the raw image and the label. (e.g. labels were renamed fromsub-subject001_space-other_T1w_label-SC_seg.nii.gz-->sub-subject001_T1w_space-other_label-SC_seg.nii.gz)Potential underlying problem
In this PR , it looks like all the T1w images were resampled to 1mm3, all the T2w images were resampled to 0.8mm3... without considering the resolution of the raw image. Even though this was true for most of the labels, it is actually not true for some images.
RPIorientation.Fixing JSON sidecars
JSON sidecars were modified as well to follow our convention. The script used is here.
Examples
Manual + Resampling (same space)
Before
{ "Author": "Sandrine Bedard", "Date": "2021-07-25 13:39:39", "SpatialReference": { "Resampling": "1x1x1", "Reorientation": "RPI" }After
{ "SpatialReference": "orig", "GeneratedBy": [ { "Name": "Manual", "Author": "Sandrine Bedard", "Date": "2021-07-25 13:39:39" }, { "Name": "sct_resample", "Flags": "-mm", "Resolution": "1x1x1", "Version": "SCT v6~", "Date": "2024-02-20 00:00:00" }, { "Name": "sct_image", "Flags": "-setorient", "Orientation": "RPI", "Version": "SCT v6~", "Date": "2024-02-20 00:00:00" } ] }Manual + Root Mean Square (same space)
Before
{ "Author": "Sandrine Bedard", "Date": "2021-06-08 15:05:54", "SpatialReference": { "Reorientation": "RPI", "Other": "root-mean square across 4th dimension (if it exists)" }After
{ "SpatialReference": "orig", "GeneratedBy": [ { "Name": "Manual", "Author": "Sandrine Bedard", "Date": "2021-06-08 15:05:54" }, { "Name": "sct_maths", "Flags": "-rms", "Axis": "t", "Version": "SCT v6~", "Date": "2024-02-20 00:00:00" }, { "Name": "sct_image", "Flags": "-setorient", "Orientation": "RPI", "Version": "SCT v6~", "Date": "2024-02-20 00:00:00" } ] }Manual + Resampling (different space)
Before
{ "Author": "Etienne Bergeron", "Date": "2021-06-14 09:47:22", "SpatialReference": { "Resampling": "0.8x0.8x0.8", "Reorientation": "RPI" }After
{ "SpatialReference": { "Resampling": "0.8x0.8x0.8", "Reorientation": "RPI" }, "GeneratedBy": [ { "Name": "Manual", "Author": "Etienne Bergeron", "Date": "2021-06-14 09:47:22" }, { "Name": "sct_resample", "Flags": "-mm", "Resolution": "0.8x0.8x0.8", "Version": "SCT v6~", "Date": "2024-02-20 00:00:00" }, { "Name": "sct_image", "Flags": "-setorient", "Orientation": "RPI", "Version": "SCT v6~", "Date": "2024-02-20 00:00:00" } ] }