Hi @Steven, I am a collaborator of Imola’s and wanted to ask you a few follow-up questions related to the confound regression step and PLS analyses.
Just to give you some background, we have decided to try to first regress out the 6 motion parameters (trans x,y,z rot x,y,z) and then complete a 5mm smooth. (ignore format)
for reg in trans_x trans_y trans_z rot_x rot_y rot_z ; do
awk -v col=$reg 'NR==1{for(i=1;i<=NF;i++){if($i==col){c=i;break}} print $c} NR>1{print $c}' sub-005_ses-01_task-NAME_desc-confounds_timeseries.tsv > ${reg}_all_tmp.txt;
sed '1d' ${reg}_all_tmp.txt > ${reg}_noHead_tmp.txt
sed '1!d' ${reg}_all_tmp.txt > ${reg}_Head_tmp.txt
done
paste *_noHead_tmp.txt >> desired_confounds_sub-XXX_ses-XX_TASKNAME_6mot.txt
sed -i 's|n\/a|1|g' desired_confounds_sub-XXX_ses-XX_TASKNAME_6mot.txt
Text2Vest desired_confounds_sub-XXX_ses-XX_TASKNAME_6mot.txt confound_design_sub-XXX_ses-XX_TASKNAME__6mot.mat
fsl_glm -i sub-XXX_ses-XX_TASKNAME_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz -d confound_design_sub-XXX_ses-XX_TASKNAME_6mot.mat --out_res=sub-XXX_ses-XX_TASKNAME_space-MNI152NLin2009cAsym_desc-preproc_noconfounds_bold_6mot.nii.gz
And then we smooth (ignore below format)
fslmaths sub-${i}_ses-01_task-NAME_space-MNI152NLin2009cAsym_desc-preproc_noconfounds_bold.nii.gz -s 2.12 sub-${i}_ses-01_task-NAME_space-MNI152NLin2009cAsym_desc-preproc_noconfounds_smooth_bold.nii.gz
After that, we went into getting the datamat files ready for PLS.
We set the brain_region to 0.15 but have also tried using a personalized brain mask for each participant (just choosing the same task for each participant and using the generated brain mask from fMRIprep).
When we run batch_plsgui with our analysis txt file, we get the error:
ERROR: no common coords among datamats!
Output argument "num_behav_subj" (and possibly others) not assigned a value in the execution with
"fmri_pls_analysis>concat_st_datamat" function.
Error in fmri_pls_analysis (line 156)
concat_st_datamat(behavdata, singleanalysis, ...
Error in batch_pls_analysis (line 543)
fmri_pls_analysis(PLSoptions.profiles, PLSoptions.ContrastFile, ...
Error in batch_plsgui (line 41)
batch_pls_analysis(fid)
We have figured out that we can run the PLS without regressing out the confounds, but once we do any confound regression, no common coordinates are found.
Any help would be appreciated! Thank you.
Kristina