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preprocessing with SCT #5

Merged
merged 30 commits into from
Dec 2, 2022
Merged

preprocessing with SCT #5

merged 30 commits into from
Dec 2, 2022

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kiristern
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@kiristern kiristern commented Nov 17, 2022 •
edited by valosekj
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initial preprocess .sh script

Fixes: #1 #2 #3

@kiristern kiristern changed the title create new branch preprocessing with SCT Nov 17, 2022
@kiristern kiristern marked this pull request as draft November 17, 2022 17:21
@valosekj
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valosekj commented Nov 18, 2022 •
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@kiristern I just pushed commits with updated preprocessing for the T2w image. Please, could you run the script across the whole dataset? Thanks!

Update: done; see #3 (comment) for details

valosekj and others added 16 commits November 19, 2022 13:36
@valosekj
Allow kernel specification (2d, 3d) for segment_if_does_not_exist fun…
1b1b4f8 
…ction
@valosekj
Add info how to run analysis in virtual terminal
1639353
@valosekj
Keep only sct_deepseg_sc 2d.
9bb41b7
@sandrinebedard
initial commit
5b1300b
@valosekj
Keep only sct_deepseg_sc within the segment_if_does_not_exist function.
493c47d
@sandrinebedard
adjust manual correction script for sc segmentation
a62a266
@sandrinebedard
add instructions for manual corrections
59197c6
@sandrinebedard
add pycache
3b5e73c
@sandrinebedard
add script to package data to correct
478b363
@sandrinebedard
Merge branch 'sb/manual_correction_script' of github.com:ivadomed/can…
f8503f3 
…proco into sb/manual_correction_script
@valosekj
Allow specifying deepseg/propseg for the segment_if_does_not_exist fu…
4769f16 
…nction
@valosekj
Implement _raw suffix to have BIDS compliant derivatives
0bd91d6
@valosekj
Comment out T2w labeling and lesion seg
d309326
@valosekj
Add check if T2w file exists
20776e6
@valosekj
Remove unused processing steps for T2w
6d8b48a
@valosekj
Add PSIR, STIR and T2star preprocessing (reorientation, segmentation).
a00b02b
@valosekj valosekj mentioned this pull request Nov 28, 2022
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jcohenadad
jcohenadad reviewed Nov 28, 2022
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@valosekj valosekj marked this pull request as ready for review December 2, 2022 15:47
@valosekj valosekj merged commit aa3b963 into main Dec 2, 2022
@valosekj valosekj mentioned this pull request Dec 2, 2022
Closed
@valosekj valosekj deleted the ks/preprocess branch February 3, 2023 20:10
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Create code and doc for preprocessing of spinal cord data
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@kiristern @valosekj @jcohenadad @sandrinebedard