Recap

So from the other day, I was able to get ALFF/fALFF working with QC turned off. Now let me try reho.

REHO

1st Attempt

First run got an error of course.

from nipype.utils.filemanip import loadflat
crashinfo = loadflat('/home2/data/Projects/ABIDE_Initiative/CPAC/test_qp/crash/crash-20131024-150154-milham-reho_map.a0.a0.npz')
crashinfo['node'].run()

The error is related to reno map and need more than 3 values to unpack in line 55 of compute_reho. If we look at the inputs:

crashinfo['node'].inputs.in_file

Then it seems that the functional_brain_mask_to_standard.nii.gz (a 3D image) is being input when it should be a 4D functional image such as functional_mni.nii.gz. This leads to a failure later when the shape of the input image is expected to have 4 dimensions but instead gets 3 with the mask.

So investigating the input to reho in cpac_pipeline.py, we see that it calls the following command that gets whatever the last node was saved:

node, out_file = strat.get_leaf_properties()
workflow.connect(node, out_file,
	reho, 'inputspec.rest_res_filt')

Whoops seems like a coding error in my part where the brain mask was being set as the leaf but shouldn’t be.

2nd Attempt

This ran through without issue but the REHO maps weren’t transformed to standard space. This is because the run register option is off. As a workaround, I’m creating another auto-set apply register option. This is the same thing I did with ALFF. It’s possible that I should include the apply register option into the config file instead of always assuming you want to apply it. I also change this for all the other derivates (i.e., use an apply register option).

QC Fix

Cameron suggested to gravely continue after a failure in QC when running quick pack. Looking at the offending code again with this mindset, I realize that this approach could easily work. The following two lines get called to help create the html page which throw an error message:

meanFD, meanDvars = get_power_params(qc_path, file_)
mean_rms, max_rms = get_motion_params(qc_path, file_)

Those variables are then used in the html pages to indicate motion values. Since I haven’t actually re-run preprocessing or given it those values, an error is thrown. To get around this, I put a try/except statement and when an exception is thrown I set all the values to ‘NA’.

Excellent! The QC page looks good when running it now for REHO! Gives the REHO maps and a histogram!