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neuropoly
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template
A framework for creating unbiased MRI templates of the spinal cord
MIT License
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Template generation pipeline crashing on the Compute Canada cluster
#86
rohanbanerjee
opened
6 months ago
6
Creation of `subjects.csv` in the correct path and fixing minor bugs in the path name
#85
rohanbanerjee
closed
11 months ago
0
Straighten spinal cord now includes all disc levels as mentioned in the `last_disc` parameter in the `configuration.json` file
#84
rohanbanerjee
closed
11 months ago
0
Creation of `subjects.csv` under the parent folder and not in the subject derivative folder
#83
rohanbanerjee
closed
11 months ago
1
Fixes bugs in the `generate_template.py` pipeline
#82
rohanbanerjee
closed
11 months ago
1
Adding the preprocessing code back
#81
rohanbanerjee
closed
1 year ago
0
Adding the code back to `preprocess_segment.sh`
#80
rohanbanerjee
closed
1 year ago
0
Updated documentation for running the `template generation pipeline` in Alliance Canada
#79
rohanbanerjee
closed
1 year ago
0
Error while running `generate_template.py` for template generation after following the current documentation
#78
rohanbanerjee
closed
11 months ago
1
Clearer documentation of creating jobs and job files in Alliance Canada
#77
rohanbanerjee
closed
1 year ago
1
No mention of the data to be used for `template generation` (i.e. Step 2)
#76
rohanbanerjee
closed
1 year ago
0
Removal of hard-coded `configuration` file in `preprocess_segment.sh` script and extraction of `include_list` from the `configuration` file directly
#75
rohanbanerjee
closed
1 year ago
0
The derivatives are not copied after the `preprocess_segment.sh` runs
#74
rohanbanerjee
opened
1 year ago
1
Removal of `preprocess_segment.sh` requirement of mentioning the names of the subjects in the `--include-list` flag
#73
rohanbanerjee
closed
1 year ago
0
Fix the hard-coding of `configuration.json` or modify `preprocess_segment.sh`
#72
NadiaBlostein
closed
1 year ago
0
Updates the `centerline` as a derivative in the `preprocess_normalize.py` and `README`
#71
rohanbanerjee
closed
1 year ago
1
Listing the `centerline` as a possible derivative
#70
rohanbanerjee
closed
1 year ago
0
Fixing issue #68 by generating a centerline NIFTI file for subjects who do not have a SC mask NIFTI file
#69
NadiaBlostein
closed
1 year ago
9
Subject straightening in `preprocess_normalize.py` requires either SC mask NIFTI file or centerline NIFTI file
#68
NadiaBlostein
closed
1 year ago
1
Fixing issue #66
#67
NadiaBlostein
closed
1 year ago
0
`ParamCenterline` on line 143 of `preprocessing_normalize.py` missing `contrast` argument
#66
NadiaBlostein
closed
1 year ago
1
Straightened spinal cord does not include all the disc levels
#65
rohanbanerjee
closed
11 months ago
6
Add `first_disc` option to `configuration_default.json`
#64
NadiaBlostein
opened
1 year ago
0
Update to stable version of SCT
#63
NadiaBlostein
opened
1 year ago
0
Fixing issues related to output file management (#57), documentation (#58), QC procedure (#59, #61), template max range (#41, #60)
#62
NadiaBlostein
closed
1 year ago
0
Currently used file suffixes are not consistent with what is described in the SCT manual-correction module
#61
NadiaBlostein
closed
1 year ago
1
`sct_straighten_spinalcord` cannot seem to straighten a spinal cord that is too short?
#60
NadiaBlostein
closed
1 year ago
9
Update the format of `preprocess_segment.sh` outputs
#59
NadiaBlostein
closed
1 year ago
1
Better document how to do manual QC and keep provenance of who did the QC
#58
jcohenadad
closed
1 year ago
3
`sub-XXX_T1w_label-SC_seg_labeled.nii.gz` is not needed
#57
jcohenadad
closed
1 year ago
1
Why can't `sct_run_batch` use the `include-list` from `configuration.json`?
#56
NadiaBlostein
closed
11 months ago
1
figure out what is going with ICBM152 in `preprocess_normalize.py`
#55
NadiaBlostein
opened
1 year ago
0
Make sure the comments description each function in `preprocess_normalize` are correct
#54
NadiaBlostein
opened
1 year ago
0
Make the code more generalizable to non-human template
#53
NadiaBlostein
closed
1 year ago
1
Figure out how to make `sct_run_batch` (step 1.3) use `include-list` from `configuration.json` file
#52
NadiaBlostein
closed
1 year ago
1
Remove redundancy: `list_labels` in `preprocess_normalize.py` (lines 18-19)
#51
NadiaBlostein
closed
1 year ago
1
Add explanation at the beginning of `preprocess_normalize.py`
#50
NadiaBlostein
closed
1 year ago
1
pep-8 python code style convention
#49
rohanbanerjee
opened
1 year ago
0
Make schematic of worflow
#48
jcohenadad
opened
1 year ago
1
Remove redundant lists `labels_regions` and `regions_labels`
#47
NadiaBlostein
closed
1 year ago
1
Rb/rename files
#46
rohanbanerjee
closed
1 year ago
0
Rb/remove contrast param
#45
rohanbanerjee
closed
1 year ago
1
Rb/remove_save_centerline
#44
rohanbanerjee
closed
1 year ago
1
Removal of loading npz centerline file
#43
rohanbanerjee
closed
1 year ago
0
Make sure to create the centerline under derivatives/labels
#42
rohanbanerjee
closed
1 year ago
0
Take into account min and max disc label option from configuration file into code
#41
NadiaBlostein
closed
1 year ago
4
Merging template_preprocessing.py and template_preprocessing_pipeline.py into one file
#40
rohanbanerjee
closed
1 year ago
1
Rename preprocessing files for clarity
#39
jcohenadad
closed
1 year ago
1
Renaming files according to which preprocessing step it belongs to
#38
rohanbanerjee
closed
1 year ago
1
In `segment_sc_discs_deepseg.sh`, create the segmentation and labels directly in `derivatives/labels`
#37
jcohenadad
closed
1 year ago
1
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