jessedesimone / fmri_proc

shell script package for (pre)processing fmri data

fmri_proc

A shell script package for (pre)processing task or resting-state functional MRI data

preproc

fMRI preprocessing package to prepare data for afni_proc.py processing with deoblique and skullstrip (brain extraction) options
./preproc/s0_driver -h for help

proc

fMRI processing pipeline to generate an afni_proc.py tcsh script for an AFNI process stream and prepare data for analysis
./proc/s1_driver -h for help

Change Log

fmri_proc's Issues

QC s0_driver.sh function

review output directories and files; make sure that all required directories and folders were created:

• job file
• deoblique file/resample
• skull strip file

afni_proc.py package

proc.py test run on test subject failed; issue may be related to oblique EPI raw dataset

potential solution: include deoblique option for EPI dataset in the s0 preproc pipeline
for test subject, deoblique epi raw data and copy to data_proc/test; then re-run proc.py

3dbucket -DAFNI_NIFTI_VIEW=tlrc -prefix test.spgr2 awpy/test.spgr2.aw.nii
++ 3dbucket: AFNI version=AFNI_22.1.06 (Apr 24 2022) [64-bit]
mv awpy/anat.un.aff.Xat.1D .
mv awpy/anat.un.aff.qw_WARP.nii .
if ( ! -f test.spgr2+tlrc.HEAD ) then
foreach run ( 01 )
3dvolreg -verbose -zpad 4 -base vr_base_min_outlier+orig -1Dfile dfile.r01.1D -prefix rm.epi.volreg.r01 heptic -1Dmatrix_save mat.r01.vr.aff12.1D pb02.test.r01.tshift+orig
++ 3dvolreg: AFNI version=AFNI_22.1.06 (Apr 24 2022) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./vr_base_min_outlier+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./vr_base_min_outlier+orig.BRIK is 14.691048 degrees from plumb.
++ Reading in base dataset ./vr_base_min_outlier+orig.BRIK
** FATAL ERROR: Too many arguments?! Dataset=heptic?

run deoblique and skullstrip for all subjects; QC data

run test of -d and -s driver options for 1 subject; modify code for efficiency

then,
run driver with -d and -s options for all subjects
QC data - confirm plumb orientation; confirm brain extraction

s0_driver.sh bug fix

issue

double loop
driver is looping through each subject, calling deoblique.sh and bet.sh
deoblique.sh and bet.sh also have a subject loop, the loop to occur for the number of subjects in the id list (the loop only needs to happen once)

fix

remove the loop function from deoblique.sh and bet.sh -> this should make the script only run once for each subject

s0_deoblique.sh

include deoblique option for EPI dataset in the s0_preproc pipeline
proc.py pipeline threw error related to oblique epi dataset (see issue 5)

update code according to BIDS data structure

use BIDS data structure in raw data directory (anat, func)
pull data for preproc using BIDS structure
should be an easy implementation

anat
-sub-${sub#}_T1w.nii.gz
func
-sub-${sub#}_task-${task}_run-${run#}_bold.nii.gz

add driver options for multiple scans (i.e., run 1, run 2, ... run n)

add handle option for multiple scans

• user input number of runs
• if more than 1 run is input change -dsets input to epi_r??

participants script

review subject list creation script; edit and revise to liking

brainextract.sh