Closed cpdavis closed 4 years ago
a3sha2
commented
5 years ago you have to include -r ${HOME}/results like :
singularity run -B ${DATA_ROOT}:${HOME}/results \ \ ${SIMG} \ \ -d ${HOME}/results/fc-36p.dsn \ \ -c ${HOME}/results/cohort_test.csv \ \ -o ${HOME}/results/xcp_output \ \ -t 2 \ -r ${HOME}/results
NB; pls change prestats_rerun[1]=0 to prestats_rerun[1]=1
cpdavis
commented
5 years ago thanks for your quick reply, but I still seem to be getting the same error. is there any other info I can provide to better diagnose the issue?
in case it helps, here is a subject tree under ./results/fmriprep
|-- sub-1017SP
| |-- anat
| | |-- sub-1017SP_T1w_brainmask.nii.gz
| | |-- sub-1017SP_T1w_class-CSF_probtissue.nii.gz
| | |-- sub-1017SP_T1w_class-GM_probtissue.nii.gz
| | |-- sub-1017SP_T1w_class-WM_probtissue.nii.gz
| | |-- sub-1017SP_T1w_dtissue.nii.gz
| | |-- sub-1017SP_T1w_inflated.L.surf.gii
| | |-- sub-1017SP_T1w_inflated.R.surf.gii
| | |-- sub-1017SP_T1w_label-aparcaseg_roi.nii.gz
| | |-- sub-1017SP_T1w_label-aseg_roi.nii.gz
| | |-- sub-1017SP_T1w_midthickness.L.surf.gii
| | |-- sub-1017SP_T1w_midthickness.R.surf.gii
| | |-- sub-1017SP_T1w_pial.L.surf.gii
| | |-- sub-1017SP_T1w_pial.R.surf.gii
| | |-- sub-1017SP_T1w_preproc.nii.gz
| | |-- sub-1017SP_T1w_smoothwm.L.surf.gii
| | |-- sub-1017SP_T1w_smoothwm.R.surf.gii
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
| | |-- sub-1017SP_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
| | |-- sub-1017SP_T1w_target-MNI152NLin2009cAsym_warp.h5
| | |-- sub-1017SP_T1w_target-fsnative_affine.txt
| | |-- sub-1017SP_run-01_T1w_space-orig_target-T1w_affine.txt
| | `-- sub-1017SP_run-02_T1w_space-orig_target-T1w_affine.txt
| |-- figures
| | |-- sub-1017SP_T1w_reconall.svg
| | |-- sub-1017SP_T1w_seg_brainmask.svg
| | |-- sub-1017SP_T1w_t1_2_mni.svg
| | |-- sub-1017SP_task-rest_run-01_bold_bbr.svg
| | |-- sub-1017SP_task-rest_run-01_bold_carpetplot.svg
| | |-- sub-1017SP_task-rest_run-01_bold_rois.svg
| | `-- sub-1017SP_task-rest_run-01_bold_sdc_syn.svg
| `-- func
| |-- sub-1017SP_task-rest_run-01_bold_confounds.tsv
| |-- sub-1017SP_task-rest_run-01_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz
| |-- sub-1017SP_task-rest_run-01_bold_space-MNI152NLin2009cAsym_preproc.nii.gz
| |-- sub-1017SP_task-rest_run-01_bold_space-T1w_brainmask.nii.gz
| |-- sub-1017SP_task-rest_run-01_bold_space-T1w_label-aparcaseg_roi.nii.gz
| |-- sub-1017SP_task-rest_run-01_bold_space-T1w_label-aseg_roi.nii.gz
| `-- sub-1017SP_task-rest_run-01_bold_space-T1w_preproc.nii.gz
Hi there,
I'm running into an issue at the confound2/regress stage (probably multiple issues) running the 36p resting state functional connectivity pipeline on preprocessed fmriprep data. I have a sense it might be a binding issue but multiple attempts at solutions have failed. Any insight would be appreciated.
Cohort File
Design File
Error Message
Runtime Information
Singularity on HPC
Sorry if this is naive!