Hi Tawfik, 

Thanks very much for your help with this - much appreciated. 

Please find a point-by-point response to your previous email: 

First to your question, yes you have to run mica for all subfolders generated by split-half (number of mica commands = 2 x number of dimensionalities). One can use a bash script to schedule them all using fsl_sub if your fsl setup uses parallel processing. Or call mica one by one for each folder.

What do you mean by run mica for all subfolders generated by split-half?

Doesn't the mica script in the bin directory already do this when you supply the folder generated by split-half as the input? Could you provide an example? Thanks! 

To provide some clarity, I have outlined all the steps I have run below according to your suggestions in a previous email:

STEP 1: Generate all the relevant subfolders using py/splithalf.py script: 

  ./splithalf.py $working_dir/input_list 50 $working_dir/results/out_50

input_list is a text file of absolute paths to each .nii file like so: 

/Volumes/ImagingData_WillKhan/HCP_Data2018/raw_data/100307/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean.nii.gz
/Volumes/ImagingData_WillKhan/HCP_Data2018/raw_data/100307/MNINonLinear/Results/rfMRI_REST1_RL/rfMRI_REST1_RL_hp2000_clean.nii.gz
/Volumes/ImagingData_WillKhan/HCP_Data2018/raw_data/100307/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean.nii.gz
/Volumes/ImagingData_WillKhan/HCP_Data2018/raw_data/100307/MNINonLinear/Results/rfMRI_REST2_RL/rfMRI_REST2_RL_hp2000_clean.nii.gz

STEP 2: Run group ICA on PCC mask using bin/mica script:

export MICADIR=/Users/wasimkhan/Documents/mICA_Toolbox

./mica $working_dir/input_list $working_dir/results/out_50 -mask $working_dir/masks/PCC_and_Precuneus_mask_thr20_Harvard.nii.gz -dim 2 -extra -a concat -- sep_vn --nobet --bgthreshold=10 --tr=1 --report --mmthresh=0.5 --Oall -o $working_dir/results/mica_test_2comp

Note this command was run a total of 5 times for 2, 4, 6, 8 and 10 components.

Therefore, in the $working_dir/results directory I have the following directory structure: 

melodic_test_2comp....melodic_test_4comp....melodic_test_6comp and so on.

STEP 3: calculate a correlation using py/ic_corr.py script. Here I changed the relevant lines of code from your previous email and renamed the script py/ic_corr_updated.py. 

Usage: ic_corr.r in_prefix samples dims [just_read]
in_prefix path of the folder that contains samples folders
samples number of samplings
dims dimensionality range
[just_read] 0 is default. 1 will not perform fsl_cc and just reads any previously calculated cross-correlation file

./ic_corr_updated.py $working_dir/results/out_50 50 2-10 0

in_prefix:  I supply the folder generated by py/splithalf.py
samples: is this the number of permutations run in splithalf? I provide 50
dims: I supply 2-10 as I have already produced 5 different group ICA's (2,4,6,8,10) using the mica script  .

I get this error: 

File "./ic_corr_updated.py", line 102, in
if int(proc1.stdout.read().rstrip('\n')) != 1 or int(proc2.stdout.read().rstrip('\n')) != 1 or int(n1.stdout.read().rstrip('\n')) != int(dim) or int(n2.stdout.read().rstrip('\n')) != int(dim):
TypeError: a bytes-like object is required, not 'str'

line 102 reads like so: 

if int(proc1.stdout.read().rstrip('\n')) != 1 or int(proc2.stdout.read().rstrip('\n')) != 1 or int(n1.stdout.read().rstrip('\n'))!= int(dim) or int(n2.stdout.read().rstrip('\n')) != int(dim):



Could you please advise if all the following steps are correct or if I have made a mistake somewhere? 

Apologies for the rather long email - I wanted to be as detailed as possible so that it is easier in the debugging process :) 


Thanks so much!

Cheers, 

Will



Originally posted by Tawfik Moher Alsady: