New Homer pipeline

[sbastiaens]

No description provided.

[JohnGriffiths]

I ran into a few errors trying to run this.

First: should this line

[rp_atlas, rp_subj] = findCorrespondingRefpts(refpts, digpts); 

actually be this

[rp_atlas, rp_subj] = findCorrespondingRefpts(refpts, digpts.refpts);

?

[JohnGriffiths]

Ok update:

Still erroring.

Possible that the above issue is from running Homer_Atlas.m not Homer_Atlas_2.m.

Anyways, I wrote out instructions for how to test on SCC.

Please go to

`/external/rprshnas01/netdata_kcni/jglab/TestingSpaces/homer_kftools_testing'

and work follow the instructions there until this is working.

---

JG Instructions for making homer pipeline code:

ZW, SB - please modify the code so that the following runs successfully on SCC:

Clone three repos

git clone https://github.com/griffithslab/kernel-flow-tools kftools_test_X
cd kftools_test_X/kftools/homer

rm Homer_Atlas.m

ADD NEW Homer_Atlas_2.m FILE HERE now

cp /external/rprshnas01/netdata_kcni/jglab/TestingSpaces/homer_kftools_testing/snic_sub001_ft_ses01_0909-1523_kp-snf
-mom.snirf .

git clone https://github.com/BUNPC/Homer3
git clone https://github.com/BUMPS/AtlasViewer

Load matlab module

module load math/MATLAB/R2020a
matlab -nodesktop

*** Now we are in matlab ***
cd homer3
setpaths

cd ../

avpath = fullfile(pwd, 'atlasviewer'))
addpath(genpath(avpath))
dirname_atlas_viewer = fullfile(pwd, avpath)

currFolder = pwd

snirfFileName = fullfile(pwd, 'snic_sub001_ft_ses01_0909-1523_kp-snf-mom.snirf')

[dc,fwmodel] = Homer_Atlas(snirfFileName,dirname_atlas_viewer,currFolder)

*** *** ... this is as far as I've got so far