neuropoly/template

Issues

• Template generation pipeline crashing on the Compute Canada cluster

  #86 opened 5 months ago by rohanbanerjee
  6

• Straightened spinal cord does not include all the disc levels

  #65 opened 10 months ago by rohanbanerjee
  6

• Creation of `subjects.csv` under the parent folder and not in the subject derivative folder

  #83 opened 10 months ago by rohanbanerjee
  1

• Issue while straightening spinal cord

  #22 opened 10 months ago by rohanbanerjee
  4

• Why can't `sct_run_batch` use the `include-list` from `configuration.json`?

  #56 opened 10 months ago by NadiaBlostein
  1

• Error while running `generate_template.py` for template generation after following the current documentation

  #78 opened 10 months ago by rohanbanerjee
  1

• Clearer documentation of creating jobs and job files in Alliance Canada

  #77 opened a year ago by rohanbanerjee
  1

• No mention of the data to be used for `template generation` (i.e. Step 2)

  #76 opened a year ago by rohanbanerjee
  0

• Adding the code back to `preprocess_segment.sh`

  #80 opened a year ago by rohanbanerjee
  0

• `ParamCenterline` on line 143 of `preprocessing_normalize.py` missing `contrast` argument

  #66 opened a year ago by NadiaBlostein
  1

• Removal of `preprocess_segment.sh` requirement of mentioning the names of the subjects in the `--include-list` flag

  #73 opened a year ago by rohanbanerjee
  0

• Fix the hard-coding of `configuration.json` or modify `preprocess_segment.sh`

  #72 opened a year ago by NadiaBlostein
  0

• Subject straightening in `preprocess_normalize.py` requires either SC mask NIFTI file or centerline NIFTI file

  #68 opened a year ago by NadiaBlostein
  1

• Listing the `centerline` as a possible derivative

  #70 opened a year ago by rohanbanerjee
  0

• The derivatives are not copied after the `preprocess_segment.sh` runs

  #74 opened a year ago by rohanbanerjee
  1

• Add `first_disc` option to `configuration_default.json`

  #64 opened a year ago by NadiaBlostein
  0

• Currently used file suffixes are not consistent with what is described in the SCT manual-correction module

  #61 opened a year ago by NadiaBlostein
  1

• Better document how to do manual QC and keep provenance of who did the QC

  #58 opened a year ago by jcohenadad
  3

• Update the format of `preprocess_segment.sh` outputs

  #59 opened a year ago by NadiaBlostein
  1

• `sub-XXX_T1w_label-SC_seg_labeled.nii.gz` is not needed

  #57 opened a year ago by jcohenadad
  1

• `sct_straighten_spinalcord` cannot seem to straighten a spinal cord that is too short?

  #60 opened a year ago by NadiaBlostein
  9

• Take into account min and max disc label option from configuration file into code

  #41 opened a year ago by NadiaBlostein
  4

• Update to stable version of SCT

  #63 opened a year ago by NadiaBlostein
  0

• Figure out how to make `sct_run_batch` (step 1.3) use `include-list` from `configuration.json` file

  #52 opened a year ago by NadiaBlostein
  1

• Add explanation at the beginning of `preprocess_normalize.py`

  #50 opened a year ago by NadiaBlostein
  1

• In `segment_sc_discs_deepseg.sh`, create the segmentation and labels directly in `derivatives/labels`

  #37 opened a year ago by jcohenadad
  1

• Remove loading of npz for centerline

  #34 opened a year ago by jcohenadad
  1

• Change `segment_sc_discs_deepseg.sh` to only accept a single contrast

  #31 opened a year ago by jcohenadad
  1

• Get data suffixes from `configuration.json` file for the `segment_sc_discs_deepseg.sh` script

  #29 opened a year ago by jcohenadad
  1

• Removal of the segment_batching_script

  #25 opened a year ago by rohanbanerjee
  0

• figure out what is going with ICBM152 in `preprocess_normalize.py`

  #55 opened a year ago by NadiaBlostein
  0

• Make sure the comments description each function in `preprocess_normalize` are correct

  #54 opened a year ago by NadiaBlostein
  0

• Make schematic of worflow

  #48 opened a year ago by jcohenadad
  1

• Remove redundancy: `list_labels` in `preprocess_normalize.py` (lines 18-19)

  #51 opened a year ago by NadiaBlostein
  1

• Change the segmentation suffix and the location of the segmentation in the segment_sc_discs_deepseg.sh

  #24 opened a year ago by rohanbanerjee
  1

• pep-8 python code style convention

  #49 opened a year ago by rohanbanerjee
  0

• Rename preprocessing files for clarity

  #39 opened a year ago by jcohenadad
  1

• Merging template_preprocessing.py and template_preprocessing_pipeline.py into one file

  #40 opened a year ago by rohanbanerjee
  1

• Removal of redundancy in the suffix in the configuration file

  #36 opened a year ago by rohanbanerjee
  1

• Remove `contrast` parameter in the `template_preprocessing.py` script

  #30 opened a year ago by jcohenadad
  1

• Adding a configuration_default.json file which is git-tracked

  #28 opened a year ago by rohanbanerjee
  1

• Update code according to new `configuration.json` file

  #35 opened a year ago by NadiaBlostein
  1

• Remove redundant lists `labels_regions` and `regions_labels`

  #47 opened a year ago by NadiaBlostein
  1

• Add the last_disc value to the configuration.json

  #26 opened a year ago by rohanbanerjee
  1

• Renaming files according to which preprocessing step it belongs to

  #38 opened a year ago by rohanbanerjee
  1

• Make the preprocessing pipeline rely on SC segmentation OR centerline

  #33 opened a year ago by jcohenadad
  0

• Make sure to create the centerline under derivatives/labels

  #42 opened a year ago by rohanbanerjee
  0

• Centerline extraction should not be done in `template_preprocessing.py`

  #32 opened a year ago by jcohenadad
  0

• Make data-agnostic versions of scripts have suffix `_default`

  #27 opened a year ago by NadiaBlostein
  0

• SCT version - update to the stable version

  #23 opened a year ago by rohanbanerjee
  0