Description:
I’ve been using QuNex preprocess_conc command using one of the recent versions of the container (qunex_suite-0.96.2.sif). However I just noticed that the TR value that is passed to the fc_preprocess_conc function is TR=2.5 which is the default value, instead of .7 which is the correct value in the batch file and the stats files in the corresponding …/sessionID/images/functional/movement/ directory.
It seems that up to qunex_suite-0.93.6.sif version, the TR value is read in correctly, but for the later versions, the TR value in the log file is always TR=2.5.
Call:
< Provide the qunex or qunexContainer command that was executed.
In order to make the issue reproducible, please include all relevant
information such as where the command was executed from, which
version of the container was used, and full paths to all files. >
Logs:
Generated by QuNex 0.96.2 on 2023-01-11_18.40.15.595469
#
------------------------------------------------------------
Running external command via QuNex:
octave -q --no-init-file --eval "try fc_preprocess_conc('/gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698', [2 3 4 5 6 7 8], 'mshr', 2.500, 0, 'm,m1d,mSq,m1dSq,e', [], 'AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C.fidl', 'cue:boynton|delay1:boynton|distractor:boynton|delay2:boynton|probe:boynton|cue:boynton>cue_rbf1:1:w:z|cue:boynton>cue_rbf2:2:w:z|cue:boynton>cue_rbf3:3:w:z|cue:boynton>cue_rbf4:4:w:z|cue:boynton>cue_rbf5:5:w:z|cue:boynton>cue_rbf6:6:w:z|cue:boynton>cue_rbf7:7:w:z', '', true, '.dtseries.nii', 'radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme', 'splin', 'boldname=bold|fidlname=AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C|concname=Atlas_AllExps_noL1RO_pl|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=nonzero|dilate_mask=/gpfs/gibbs/pi/n3/software/MNAP/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz|glm_matrix=both|glm_residuals=save|glm_name=|bold_tail=_Atlas|ref_bold_tail=|bold_variant=|img_suffix=', '/gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698/images/functional/concs/bold_Atlas_dtseries_Atlas_AllExps_noL1RO_pl_AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C_s_hpss_res-mm1dmSqm1dSqe.conc.ok'); catch ME, general_report_crash(ME); exit(1), end; exit;"
Test file:
/gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698/images/functional/concs/bold_Atlas_dtseries_Atlas_AllExps_noL1RO_pl_AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C_s_hpss_res-mm1dmSqm1dSqe.conc.ok
------------------------------------------------------------
Running preproces conc script v0.9.16 [.dtseries.nii]
-------------------------------------
Parameters:
---------------
sessionf: /gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698
bolds: [2 3 4 5 6 7 8]
doIt: mshr
TR: 2.50
omit: 0
rgss: m,m1d,mSq,m1dSq,e
task: [0 0]
efile: AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C.fidl
eventrstring: cue:boynton|delay1:boynton|distractor:boynton|delay2:boynton|probe:boynton|cue:boynton>cue_rbf1:1:w:z|cue:boynton>cue_rbf2:2:w:z|cue:boynton>cue_rbf3:3:w:z|cue:boynton>cue_rbf4:4:w:z|cue:boynton>cue_rbf5:5:w:z|cue:boynton>cue_rbf6:6:w:z|cue:boynton>cue_rbf7:7:w:z
variant:
overwrite: 1
tail: .dtseries.nii
scrub: radius:50|fdt:0.50|dvarsmt:3.00|dvarsmet:1.60|after:0|before:0|reject:udvarsme
ignores: splin
done: /gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698/images/functional/concs/bold_Atlas_dtseries_Atlas_AllExps_noL1RO_pl_AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C_s_hpss_res-mm1dmSqm1dSqe.conc.ok
options: boldname=bold|fidlname=AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C|concname=Atlas_AllExps_noL1RO_pl|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=nonzero|dilate_mask=/gpfs/gibbs/pi/n3/software/MNAP/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz|glm_matrix=both|glm_residuals=save|glm_name=|bold_tail=_Atlas|ref_bold_tail=|bold_variant=|img_suffix=
Options used:
----------------
boldname: bold
concname: Atlas_AllExps_noL1RO_pl
fidlname: AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C
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: nonzero
dilate_mask: /gpfs/gibbs/pi/n3/software/MNAP/library/data/atlases/MNITemplates/MNI152_T1_2mm_brain_mask.nii.gz
glm_matrix: both
glm_residuals: save
glm_name:
bold_tail: _Atlas
ref_bold_tail:
bold_variant:
img_suffix:
---> removing old files:
... /gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698/images/functional/bold8_Atlas_s.dtseries.nii
... /gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698/images/functional/concs/bold_Atlas_dtseries_AllExpsTasks_noL1RO_evRegNum35_PL_ring7_sz20_C_s.conc--> starting the loop
---> saving conc file ... done!
Smoothing
---> /gpfs/gibbs/pi/n3/Studies/Anticevic.DP5/GLM_EM/sessions/ta6698/images/functional/bold2_Atlas.dtseries.nii
---> running wb_command -cifti-smoothing
... smoothing ... done!
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