lyman
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mwaskom
Data pipelines and analysis library for functional MRI
Presently one gets this unhelpful message ``` (lyman-dev) [kianilab-cs1 data]$ lyman template -s s1 171025-10:41:43,806 workflow INFO: Workflow template settings: ['check', 'execution', 'logging'] 171025-10:41:43,815 workflow INFO: Running in parallel. Traceback...
The idea is to do something like ```python >>> template = lyman.SubjectTemplate("subj01") >>> template.seg_fname /home/user/study/proc/subj01/template.seg.nii.gz >>> template.seg_img ``` where the attributes are properties with caching of the image objects. Makes...
We're going to need to add wholly-new anatomical pre- and post-processing. This will include: - T1w/T2w registration, averaging, and bias-field removal. This work is mostly done here: https://github.com/mwaskom/prisma_preproc/blob/master/prisma_anat.py - Executing...
Easy to do and a nice check for cross-run alignment.
This should be added while remaining optional. A few thoughts: - Probably easier to do in Python with spline interpolation than calling out to FSL. - Need to determine the...
When analyzing ROIs we want a function that takes matrix-form BOLD data and fits the film_gls model for each voxel using autocorrelation estimates that are averaged across the voxels (for...
This will probably require a completely separate preprocessing workflow (but using many of the custom interfaces developed in #106). Should this workflow be oriented towards non-SMS acquisitions and thus also...
The HCP does this using the gradient echo/spin echo EPI pair: https://github.com/Washington-University/Pipelines/blob/master/fMRIVolume/scripts/ComputeSpinEchoBiasField.sh It's also possible to acquire dedicated scans to do this.
Now that is is [possible](https://github.com/mwaskom/lyman/commit/25347dfe77c1a2bfb8d79c1a461391fc9bc85f2d) to turn off the FSL highpass filter, it could be nice to make polynomial regressor detrending an option in the design matrix. This probably would...