Julien Cohen-Adad

Update PAM50 with the spinal label files produced by the University of Calgary's Philips Lab

3

A [group in Calgary](https://cumming.ucalgary.ca/labs/phillips/home) has improved the spinal labeling of the PAM50 template. An article is under review, but the label files are already available at https://github.com/PhillipsLab/pam50. It would be...

Resampling resets the q/sform codes to their default values of `0`/`2`

4

with SCT version: git-lr/missing_disc_label_vertebrae-d5bd44bc312de4db31d1556bea66f15b917e9b7c When resampling a data to a fixed resolution (specified in mm), the qform_code changes, which is not expected behaviour and could have [consequences down the line](https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html)....

`chunk` entity not covered by validator?

7

Hello! I have a dataset that contains the `chunk` entity, which is valid in v1.8.0 (see [here](https://bids-specification.readthedocs.io/en/stable/appendices/entities.html#chunk)). However, I am getting a bids-validator error: [test_bids_errors.txt](https://github.com/bids-standard/bids-validator/files/10397495/test_bids_errors.txt) Dummy dataset for testing: [test_bids.zip](https://github.com/bids-standard/bids-validator/files/10397493/test_bids.zip)...

### Description of Problem / Inefficiency: When there is a slice gap, eg: slice thickness 4mm, slice gap 50%, the output NIfTI file will have slices that are 6mm thick....

### Feature Description: After running shimming toolbox, the coefficients for external and/or MR coils are calculated, and then the user runs the experiment. In order to assess whether the experiment...

Like in [SCT](https://spinalcordtoolbox.com/overview/testimonials.html), it would be great to create a testimonials page. Pros: - it helps to get grants - it helps attracting more users [Here](https://docs.google.com/forms/d/e/1FAIpQLSdo6uzqlwO_H2XmUwzdAlMiOnpk7ui1jnEYlKrEBBh63GhfYQ/viewform) is the gform that...

### Checklist - 3T and 7T (once AC/DC coil is ready) - system integration (arduino, amplifier, software, MR sequence, etc.) - experimentation ### References - todo ### Contacts - @po09i...

### Context in order to use a 3rd party ACDC coil with realtime shimming (accounting for breathing), we need realtime access to the signal from Siemens' respiratory probe. Few investigations:

Basic idea: - Generate a text file containing the shim weights optimized by ST (similar to what we currently do) - Run `adjvalidate` (Siemens Syngo executable) to read the text...

### Context Implement a shimming algorithm that computes a different set of shim weights for each imaged slice to obtain a better homogeneity. What is needed: - Siemens pulse sequence...