CREST sub-ACT6210: Nuisance Regression Error

[ariveradompenciel]

Seeding Script

for sub in $(cat /Volumes/vosslabhpc/Projects/CREST/derivatives/sublists/ardlifespan_act_ahseeding_sublist.txt); do 
   docker run -it -v /Volumes/vosslabhpc/Projects/CREST:/data hbclab/restingstate:v0.3.1 \
        --epi=/data/${sub}/func/${sub}_task-rest_bold.nii.gz \
        --t1=/data/${sub}/anat/${sub}_T1w.nii.gz \
        --t1_mask=/data/derivatives/fmriprep/${sub}/anat/${sub}_desc-brain_mask.nii.gz \
        --roiList=/data/derivatives/roilists/AHseedingROIlist_docker.txt \
        --compcor_global
done

Command Line Output

Running /opt/RestingState/removeNuisanceRegressor.sh ...
/opt/RestingState/ROIs/global.nii.gz is in MNI space
/data/derivatives/rsOut/sub-ACT6210/SNR/CSF_pve_to_RS_thresh.nii.gz is in native space
/data/derivatives/rsOut/sub-ACT6210/SNR/WM_pve_to_RS_thresh_ero.nii.gz is in native space
Performing a 'bandpass' filter.  Frequencies between .08 & .008 will be filtered.
++ 3dTproject: AFNI version=Debian-18.0.05+git24-gb25b21054~dfsg.1-1~nd90+1 (Jan 23 2018) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
*+ WARNING:   If you are performing spatial transformations on an oblique dset, 
  such as /data/derivatives/rsOut/sub-ACT6210/preproc/nonfiltered_smooth_data.nii.gz,
  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:/data/derivatives/rsOut/sub-ACT6210/preproc/nonfiltered_smooth_data.nii.gz is 7.902490 degrees from plumb.
++ Oblique dataset:/data/derivatives/rsOut/sub-ACT6210/mcImgMean_mask.nii.gz is 7.902490 degrees from plumb.
++ Setting up regressors
++ setting up stopband frequency mask
 + run #0 has 48 time points
 +  stopband 0.0000..0.0079 = indexes 0..1 = 0.0000..0.0104
 +  stopband 0.0801..0.2510 = indexes 8..24 = 0.0833..0.2500
 + Block #0: 48 time points -- 35 stopband regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
 + -- 17 other fixed ort regressors
** ERROR: total number of fixed regressors (55) is too many for 48 retained time points!
** FATAL ERROR: Cannot continue after above errors :-( :-( :-( !!
** Program compile date = Jan 23 2018
...Scaling data by 1000
cp: cannot stat '/data/derivatives/rsOut/sub-ACT6210/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d.nii.gz': No such file or directory
...Copy Brain mask
...Normalize Data
Cannot open volume /data/derivatives/rsOut/sub-ACT6210/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d for reading!
Cannot open volume /data/derivatives/rsOut/sub-ACT6210/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d for reading!
Cannot open volume /data/derivatives/rsOut/sub-ACT6210/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d for reading!
Cannot open volume /data/derivatives/rsOut/sub-ACT6210/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d_dmean for reading!
Cannot open volume /data/derivatives/rsOut/sub-ACT6210/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d_normed for reading!
/opt/RestingState/removeNuisanceRegressor.sh Complete

From here on out, continued errors.

[jdkent]

when I ran nib-ls on sub-ACT6210_task-rest_bold.nii.gz I got:

sub-ACT6210_task-rest_bold.nii.gz int16 [ 64, 64, 35, 48] 3.44x3.44x4.00x2.00 sform

The error is expected since the number of regressors/predictors is greater than the number of time points/observations (this creates problems with standard linear regression).

I would suspect the participant has more than 48 volumes collected for resting state, my guess is that the file was not completely copied over, so recopying the file over to CREST could work, or if the file from the original project also only has 48 volumes then something weird happened to that original file and warrants further investigation.

find and check the original file and see if it also has 48 volumes or a different number.