Need help extracting roi_timeseries_masked"

I need to extract (and plot) timeseries from concatenated bolds (rest1->task->rest2) for a specific ROI.
As a start, I try to extract the timeseries from rest1 only. I use the following call

qunex fc_extract_roi_timeseries_masked \
     --flist='/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/lists/pb1047.list' \
     --roiinfo='/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/selectedROIs/SN.names' \
     --inmask=0 \
     --targetf='/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/DMN_SN/' \
     --options='mt' \
     --method='mean' \
     --ignore='udvarsme'

The error message is

Starting ...
 ... listing files to process
 ... reading file list:
     - session id: pb1047
       ... found image file (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1047/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii)
       ... found GLM file (/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1047/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d_coeff.dtseries.nii)
 done.
 ... done.
Matlab Error! Processing Failed!
Index exceeds the number of array elements. Index must not exceed 1.

ERROR: fc_extract_roi_timeseries_masked failed! Please check output / log!

My list file is:

session id: pb1047 
	file:/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1047/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d.dtseries.nii
	glm:/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/sessions/pb1047/images/functional/bold1_Atlas_s_hpss_res-mVWMWB1d_coeff.dtseries.nii

I cannot locate the log anywhere. Please advise.

Hi Helen,

Someone will take a look at this over the next couple of days and let you know what is happening.

Best, Jure

Hi Helen,

there is a bug related to the parsing of the inmask parameter. You can run the command via matlab, e.g.

addpath(genpath('/gpfs/gibbs/pi/n3/software/qunex'))
fc_extract_roi_timeseries_masked('/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/lists/pb1047.list', '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/selectedROIs/SN.names', 0, '/gpfs/gibbs/pi/n3/Studies/Pushkarskaya.RA/analysis/DMN_SN/test', 'mt', 'mean', 'udvarsme', '', '', '')

Note that 0 (inmask) should be a number, not a string. We will fix this in the next qunex release so that it works with a string as well.
Next, the targetf parameter should be a filename, not a folder name (in the example above I changed it to test).
However, this function call will result in an error due to an inappropriate naming of the function img_scrub (in the master branch, the function is currently called img_sscrub). We will fir this in the next days.

Also, in the next qunex release fc_extract_roi_timeseries_masked will be superseeded by fc_extract_timeseries, a more general function.

Thank you! Please let me know when I can try running this again.

Hi Andraz, Just checking when do you think the “img_scrub” error might be fixed.

It will be released in the 0.100.0 version that is coming out over the next 10 days or so.

1 Like