Description:
I’m trying to process stimulus-evoked BOLD runs using preprocess_conc. I did a few trials, and it seems to not like when the parameter --event_string is used as “assumed modelling” and it contains only the fidl_code and hrf, as I do not have behavioral measures to regress. I copied the command call and the error log file. I attached the respective conc and fidl files.
Estephan
Call:
msi_resources_time=02:00:00; msi_resources_nodes=1; msi_resources_ntaskspernode=2; msi_resources_mem=32000; msi_queue=agsmall; msi_resources_jobname=BOLD5; \
study_sharedfolder=/home/moanae/shared/project_K99_ChrTMDHCP_qunex02; \
subjID_list="10001,10002,10004,10005,10006,10007,10009,10011,10012,10013,10014,10015,10016,10018,10019,10021,10022,10023,10024,10030,10031,10033,10034,10035,10037,10038,10039,10041,10042,11004,11006,11009,11015,20001,20004,20005,20006,20008,20010,20011,20012,20013,20015,20016,20017,20018,20019,20021,20022"; \
conc_name="bold3-bold4_dtseries_dentalvpress"; fidl_name="BlockOnOff-30s"; \
qunex_container preprocess_conc \
--batchfile=${study_sharedfolder}/processing/batch_K99Aim2.txt --sessionsfolder=${study_sharedfolder}/sessions -sessions=${subjID_list} --parsessions=1 --parelements=2 \
--event_file="${conc_name}_${fidl_name}" --bolds="${conc_name}" --bold_actions="s,h,r0,l" --pignore="hipass=spline|regress=spline|lopass=spline" --bold_nuisance="e" --event_string="dentalvpress_ON:SPM-uni" --glm_matrix="both" --glm_residuals="all" --glm_name="" --image_target='dtseries' --nifti_tail="_hp0_clean_tclean" --cifti_tail="_Atlas_MSMAll_hp0_clean_tclean" --overwrite=yes \
--scheduler=SLURM,time=${msi_resources_time},nodes=${msi_resources_nodes},cpus-per-task=${msi_resources_ntaskspernode},mem=${msi_resources_mem},partition=${msi_queue},jobname=${msi_resources_jobname} \
--bind=${study_sharedfolder}:${study_sharedfolder} --container=${HOME}/qunex/qunex_suite-0.98.0.sif
Logs:
# Generated by QuNex 0.98.0 on 2023-06-10_17.33.00.054937
#
------------------------------------------------------------
Running external command via QuNex:
octave -q --no-init-file --eval "try fc_preprocess_conc('/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10004', [3 4], 's,h,r0,l', 0.937, 0, 'e', [], 'bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s.fidl', 'dentalvpress_ON:SPM-uni>dentpress', '', true, '.dtseries.nii', 'radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.50|after:2|before:1|reject:dvarsme', 'hipass=spline|regress=spline|lopass=spline', 'boldname=bold|fidlname=bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s|concname=bold3-bold4_dtseries_dentalvpress|surface_smooth=2.000000|volume_smooth=2.000000|voxel_smooth=1.000000|hipass_filter=0.008000|lopass_filter=0.090000|omp_threads=0|framework_path=|wb_command_path=|smooth_mask=false|dilate_mask=false|glm_matrix=both|glm_residuals=all|glm_results=c,r|glm_name=|bold_tail=_Atlas_MSMAll_hp0_clean_tclean|ref_bold_tail=_hp0_clean_tclean|bold_variant=|img_suffix=', '/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10004/images/functional/concs/bold_Atlas_MSMAll_hp0_clean_tclean_dtseries_bold3-bold4_dtseries_dentalvpress_bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s_s_hpss_res-e_lpss.conc.ok'); catch ME, general_report_crash(ME); exit(1), end; exit;"
Test file:
/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10004/images/functional/concs/bold_Atlas_MSMAll_hp0_clean_tclean_dtseries_bold3-bold4_dtseries_dentalvpress_bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s_s_hpss_res-e_lpss.conc.ok
------------------------------------------------------------
Running preproces conc script v0.9.16 [.dtseries.nii]
-------------------------------------
Parameters:
---------------
sessionf: /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10004
bolds: [3 4]
doIt: s,h,r0,l
tr: 0.94
omit: 0
rgss: e
task: [0 0]
efile: bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s.fidl
eventrstring: dentalvpress_ON:SPM-uni>dentpress
variant:
overwrite: 1
tail: .dtseries.nii
scrub: radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.50|after:2|before:1|reject:dvarsme
ignores: hipass=spline|regress=spline|lopass=spline
done: /home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10004/images/functional/concs/bold_Atlas_MSMAll_hp0_clean_tclean_dtseries_bold3-bold4_dtseries_dentalvpress_bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s_s_hpss_res-e_lpss.conc.ok
options: boldname=bold|fidlname=bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s|concname=bold3-bold4_dtseries_dentalvpress|surface_smooth=2.000000|volume_smooth=2.000000|voxel_smooth=1.000000|hipass_filter=0.008000|lopass_filter=0.090000|omp_threads=0|framework_path=|wb_command_path=|smooth_mask=false|dilate_mask=false|glm_matrix=both|glm_residuals=all|glm_results=c,r|glm_name=|bold_tail=_Atlas_MSMAll_hp0_clean_tclean|ref_bold_tail=_hp0_clean_tclean|bold_variant=|img_suffix=
Options used:
----------------
boldname: bold
concname: bold3-bold4_dtseries_dentalvpress
fidlname: bold3-bold4_dtseries_dentalvpress_BlockOnOff-30s
surface_smooth: 2
volume_smooth: 2
voxel_smooth: 1
lopass_filter: 0.09
hipass_filter: 0.008
framework_path:
wb_command_path:
omp_threads: 0
smooth_mask: false
dilate_mask: false
glm_matrix: both
glm_residuals: all
glm_results: c,r
glm_name:
bold_tail: _Atlas_MSMAll_hp0_clean_tclean
ref_bold_tail: _hp0_clean_tclean
bold_variant:
img_suffix:
=========================================
Execution error! Processing failed!
Please check arguments and/or try running the command in Matlab or Octave directly.
The exact error reported:
-----------------------------------------
Error identifier:
Error message: @binopdf: no function and no method found
Error stack: /usr/local/share/octave/packages/statistics-1.4.2/pdf.m -> pdf [line: 59]
/opt/qunex/matlab/qx_mri/general/general_hrf.m -> general_hrf [line: 153]
/opt/qunex/matlab/qx_mri/general/general_create_task_regressors.m -> general_create_task_regressors [line: 378]
/opt/qunex/matlab/qx_mri/fc/fc_preprocess_conc.m -> fc_preprocess_conc [line: 910]
=========================================
conc file
number_of_files: 2
file:/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/images/functional/bold3_Atlas_MSMAll_hp0_clean_tclean.dtseries.nii
file:/home/moanae/shared/project_K99_ChrTMDHCP_qunex02/sessions/10001/images/functional/bold4_Atlas_MSMAll_hp0_clean_tclean.dtseries.nii
fidl file
0.937 dentalvpress_OFF dentalvpress_ON
0 0 9
9 1 30
39 0 30
69 1 30
99 0 30
129 1 30
159 0 30
189 1 30
219 0 30
249 1 30
279 0 30
309 1 30
339 0 54
393 0 9
402 1 30
432 0 30
462 1 30
492 0 30
522 1 30
552 0 30
582 1 30
612 0 30
642 1 30
672 0 30
702 1 30
732 0 54
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