AnalyzepRF on volume

doi  10.25663/brainlife.app.177
   Registered  4/10/2019    4  Users    176  Requests    1.6 - 13.6 hour

An app to do a population receptive field analysis on HCP 7T retinotopy fMRI data

62.2% Success Rate


This App uses the following input/output datatypes

Input
fmri
Validator
func/task
(multi)

fMRI Task

fmri: bold.nii.gz • events: events.tsv • events_json: events.json • sbref: sbref.nii.gz • sbref_json: sbref.json • physio: physio.tsv.gz • physio_json: physio.json
stim
stimulus
(multi)

stimulus movie

stim: stim.nii.gz
freesurfer
Validator
freesurfer

Used to generate .vtk surfaces

Folder structure generated by FreeSurfer recon-all process.

output: output/
mask
Validator
mask
optional

Volume Mask

mask: mask.nii.gz
Output
prf
prf

Nifti files containing various pRF measures

r2: r2.nii.gz • polarAngle: polarAngle.nii.gz • eccentricity: eccentricity.nii.gz • rfWidth: rfWidth.nii.gz • varea: varea.nii.gz • surfaces: surfaces/ • prf_surfaces: prf_surfaces/

Configuration
frontal: boolean

Include frontal cortex in analysis

parietal: boolean

Include parietal cortex in analysis

temporal: boolean

Include temporal cortex in analysis

occipital: boolean = true

Include occipital cortex in analysis

preprocess: boolean = true

Perform slice-timing and head motion correction on fMRI if not already preprocessed

TR?: number

Repetition time of fMRI (read from the nii header if unspecified)

pxtodeg: number = 0.08

Conversion factor from pixels to degrees subtended for visual stimulus (16 deg / 200 px for HCP data)

gsr: enum = none
  • none no GSR Default
  • per-voxel normalization (pvn) regresses out mean signal per voxel
  • grand-mean scaling (gms) regresses out global mean

Specifies whether global signal regression (GSR) on input fMRI should be done, conversion to % change from baseline

wantquick: boolean

Use seedmode -2 and perform very quick PRF analysis % - When <seedmode> is -2, optimization is not performed and instead the best seed based on the super-grid is returned as the final estimate.

seedmode0: boolean = true

seedmode 0: % - The first seed is a generic large pRF that is centered with respect to the stimulus, has a pRF size equal to 1/4th of the stimulus extent (thus, +/- 2 pRF sizes matches the stimulus extent), and has an exponent of 0.5.

seedmode1: boolean = true

seedmode 1: % - The second seed is a generic small pRF that is just like the first seed except has a pRF size that is 10 times smaller.

seedmode2: boolean = true

seedmode 2: % - The third seed is a "supergrid" seed that is identified by performing a quick grid search prior to optimization (similar in spirit to methods described in Dumoulin and Wandell, 2008). In this procedure, a list of potential seeds is constructed by % exploring a range of eccentricities, angles, and exponents. For each potential % seed, the model prediction is computed, and the seed that produces the closest % match to the data is identified.

Maintainers

List of users who currently maintains this App.

Brad Caron

David Hunt


Contributors

List of code contributors.(davhunt/app-analyzePRF).

David Hunt