spinal-cord-7t coil-qc-code issues

spinal-cord-7t / coil-qc-code

7T Spinal Cord Coil QC Analysis Code

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Unified labels to only use that on TFLTB1 image

#90 jcohenadad opened 5 days ago
2
Normalize snr plots

#89 evaalonsoortiz closed 1 week ago
1
Normalize SNR plots with average B1+ along the cord

#88 evaalonsoortiz closed 1 week ago
1
Why redefining the labels for DREAM and SNR is they already exist for TFL?

#87 jcohenadad opened 1 week ago
2
Simplify code and use variables

#86 jcohenadad opened 1 week ago
0
Linear interpolation might not be appropriate for the mask

#85 jcohenadad opened 1 week ago
0
Confusing code for labeling, mask creation and registration

#84 jcohenadad closed 1 week ago
1
sct_flatten_sagittal changes the dynamic range of the image

#83 evaalonsoortiz opened 1 week ago
1
Registration issues: `acq-coilQaSagLarge_SNR_T0000`

#82 jcohenadad opened 1 week ago
0
Registration issues: `DREAMTB1avgB1map`

#81 jcohenadad opened 1 week ago
0
Add section that generate a GIF animation to assess the quality of co-registration

#80 jcohenadad opened 1 week ago
1
RuntimeError: ../../sub-CRMBM/fmap/mask_spinalcord_DREAM.nii.gz does not exist

#79 jcohenadad closed 1 week ago
3
Make sure extraction does include values interpolated close to zero values

#78 jcohenadad opened 1 week ago
1
Add coil element layout across coils

#77 jcohenadad opened 2 weeks ago
0
Generate approximate mask of spinal cord

#76 jcohenadad closed 3 weeks ago
5
Co-register phantom fmap across sites

#75 jcohenadad closed 3 weeks ago
1
Error: SCT's Matplotlib interaction when used in interactive mode

#74 jcohenadad opened 4 weeks ago
0
Co-register phantom fmap across sites

#73 jcohenadad closed 3 weeks ago
1
Co-register phantom fmap across sites

#72 jcohenadad closed 3 weeks ago
1
Generate an approximate spinal cord mask for the phantom data

#71 jcohenadad closed 3 weeks ago
4
Special if case for `acq-coilQaSagLarge_SNR_T0000` is overwritten

#70 jcohenadad closed 1 week ago
5
Converted notebook to script for processing phantom data

#69 jcohenadad closed 4 weeks ago
1
Consider moving notebook to python script

#68 jcohenadad opened 4 weeks ago
0
FileNotFoundError: [Errno 2] No such file or directory: '/Users/julien/code/coil-qc-code/data-phantom/derivatives/labels/sub-UCL/fmap/sub-UCL_acq-coilQaSagSmall_GFactor_mask.nii.gz'

#67 jcohenadad closed 2 weeks ago
1
openneuro-py download error: No such option: --target_dir

#66 jcohenadad closed 4 weeks ago
2
Flatten the spinal cord in SNR and B1+ maps to better visualization

#65 evaalonsoortiz opened 1 month ago
0
Co-register in-vivo and phantom B1+ and SNR maps for visualisation purposes

#64 evaalonsoortiz opened 1 month ago
7
Consider quantifying g-factor within a mask, or overlaying an anatomical image

#63 dpapp86 closed 2 weeks ago
4
Consider cropping the g-factor map

#62 jcohenadad closed 3 weeks ago
3
Phantom sub-MSSM_acq-coilQaTra_GFactor file appears to be corrupt

#61 evaalonsoortiz opened 2 months ago
1
Phantom dataset json files have incorrect format/information

#60 evaalonsoortiz closed 2 months ago
2
Key to link sub1/2/3 to D/L/R needed

#59 evaalonsoortiz opened 2 months ago
1
Dynamic range of coilQA 1/g factor map

#58 evaalonsoortiz closed 2 months ago
2
lack of documentation on the coilQA sequence

#57 evaalonsoortiz opened 2 months ago
4
Consider cropping the SNR maps

#56 jcohenadad opened 2 months ago
1
Review of SNR registration to MP2RAGE scan

#55 jcohenadad closed 2 months ago
0
Review of DREAM registration to MP2RAGE scan

#54 jcohenadad opened 2 months ago
0
Add QC report for `sct_deepseg` command

#53 jcohenadad closed 2 months ago
0
Review of TB1TFL segmentations

#52 jcohenadad closed 2 months ago
0
Projection of vertebral levels should be done orthogonally to the cord centerline

#51 jcohenadad opened 2 months ago
0
QC for vertebral labeling is showing the segmentation instead of the image

#50 jcohenadad closed 2 months ago
0
`sub-MPI1: Manual segmentation not found`

#49 jcohenadad closed 2 months ago
0
`sub-MPI2_inv-1_part-mag_MP2RAGE.nii.gz` is missing

#48 jcohenadad closed 1 month ago
11
Review of automatic MP2RAGE segmentation

#47 jcohenadad closed 2 months ago
2
Issue downloading with openneuro-py

#46 jcohenadad closed 2 months ago
3
`openneuro-py` CLI to add in requirements

#45 jcohenadad opened 2 months ago
0
Remove `dataset_description.json`

#44 jcohenadad closed 2 months ago
2
TB1TFL anat scans for site MSSM do not exist

#43 evaalonsoortiz closed 1 month ago
4
Make data public?

#42 jcohenadad opened 2 months ago
1
Change homo sapiens for something more relevant for the phantom data

#41 jcohenadad opened 2 months ago
7