neuropoly template issues

neuropoly / template

A framework for creating unbiased MRI templates of the spinal cord

MIT License

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issues

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Template generation pipeline crashing on the Compute Canada cluster

#86 rohanbanerjee opened 3 months ago
6
Creation of `subjects.csv` in the correct path and fixing minor bugs in the path name

#85 rohanbanerjee closed 8 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 8 months ago
0
Creation of `subjects.csv` under the parent folder and not in the subject derivative folder

#83 rohanbanerjee closed 8 months ago
1
Fixes bugs in the `generate_template.py` pipeline

#82 rohanbanerjee closed 8 months ago
1
Adding the preprocessing code back

#81 rohanbanerjee closed 9 months ago
0
Adding the code back to `preprocess_segment.sh`

#80 rohanbanerjee closed 9 months ago
0
Updated documentation for running the `template generation pipeline` in Alliance Canada

#79 rohanbanerjee closed 9 months ago
0
Error while running `generate_template.py` for template generation after following the current documentation

#78 rohanbanerjee closed 8 months ago
1
Clearer documentation of creating jobs and job files in Alliance Canada

#77 rohanbanerjee closed 9 months ago
1
No mention of the data to be used for `template generation` (i.e. Step 2)

#76 rohanbanerjee closed 9 months 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 10 months ago
0
The derivatives are not copied after the `preprocess_segment.sh` runs

#74 rohanbanerjee opened 11 months ago
1
Removal of `preprocess_segment.sh` requirement of mentioning the names of the subjects in the `--include-list` flag

#73 rohanbanerjee closed 10 months ago
0
Fix the hard-coding of `configuration.json` or modify `preprocess_segment.sh`

#72 NadiaBlostein closed 10 months ago
0
Updates the `centerline` as a derivative in the `preprocess_normalize.py` and `README`

#71 rohanbanerjee closed 11 months ago
1
Listing the `centerline` as a possible derivative

#70 rohanbanerjee closed 10 months 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 10 months ago
9
Subject straightening in `preprocess_normalize.py` requires either SC mask NIFTI file or centerline NIFTI file

#68 NadiaBlostein closed 10 months ago
1
Fixing issue #66

#67 NadiaBlostein closed 10 months ago
0
`ParamCenterline` on line 143 of `preprocessing_normalize.py` missing `contrast` argument

#66 NadiaBlostein closed 10 months ago
1
Straightened spinal cord does not include all the disc levels

#65 rohanbanerjee closed 8 months ago
6
Add `first_disc` option to `configuration_default.json`

#64 NadiaBlostein opened 11 months ago
0
Update to stable version of SCT

#63 NadiaBlostein opened 11 months ago
0
Fixing issues related to output file management (#57), documentation (#58), QC procedure (#59, #61), template max range (#41, #60)

#62 NadiaBlostein closed 11 months ago
0
Currently used file suffixes are not consistent with what is described in the SCT manual-correction module

#61 NadiaBlostein closed 11 months ago
1
`sct_straighten_spinalcord` cannot seem to straighten a spinal cord that is too short?

#60 NadiaBlostein closed 11 months ago
9
Update the format of `preprocess_segment.sh` outputs

#59 NadiaBlostein closed 11 months ago
1
Better document how to do manual QC and keep provenance of who did the QC

#58 jcohenadad closed 11 months ago
3
`sub-XXX_T1w_label-SC_seg_labeled.nii.gz` is not needed

#57 jcohenadad closed 11 months ago
1
Why can't `sct_run_batch` use the `include-list` from `configuration.json`?

#56 NadiaBlostein closed 8 months ago
1
figure out what is going with ICBM152 in `preprocess_normalize.py`

#55 NadiaBlostein opened 12 months 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 12 months ago
1
Figure out how to make `sct_run_batch` (step 1.3) use `include-list` from `configuration.json` file

#52 NadiaBlostein closed 11 months 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 12 months 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 11 months ago
0
Rb/remove contrast param

#45 rohanbanerjee closed 11 months ago
1
Rb/remove_save_centerline

#44 rohanbanerjee closed 11 months ago
1
Removal of loading npz centerline file

#43 rohanbanerjee closed 11 months 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 11 months 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 12 months ago
1