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This repository has been archived by the owner on Apr 19, 2023. It is now read-only.
Cohort file
Paste cohort file between the triple backticks
Design File
Paste your entire design (.dsn) file between the triple backticks
#!/usr/bin/env bash
###################################################################
# ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ ⊗ #
###################################################################
###################################################################
# This design file stores the values of all variables required to
# execute a complete neuroimage processing pipeline. You may
# execute the analysis specified in this design file by calling
# (in any v4 or higher bash terminal):
#
# xcpEngine -d <design> -c <cohort> -o <output> <options>
#
# Variables fall into five general categories:
# * ANALYSIS VARIABLES are used at all stages of this analysis.
# * PIPELINE specifies the modules that comprise the analysis.
# * MODULE VARIABLES are used during one stage of the analysis.
# These are typically array variables with array
# indices equal to the index of the module that
# calls them.
# * OUTPUT VARIABLES may be used at all stages of the analysis.
# These are typically array variables with array
# indices equal to the value of the primary
# subject identifier. They will appear only in
# localised design files.
###################################################################
###################################################################
# ANALYSIS VARIABLES
###################################################################
analysis=fc_$(whoami)
design=/data/jux/BBL/projects/testACT/script/designfiles/fc-acompcor.dsn
sequence=anatomical
standard=MNI%2x2x2
###################################################################
# PIPELINE
###################################################################
pipeline=prestats,confound2,regress,fcon,reho,alff,roiquant,norm,qcfc
###################################################################
# 1 PRESTATS
###################################################################
prestats_rerun[1]=1
prestats_cleanup[1]=1
prestats_process[1]=FMP
###################################################################
# 2 CONFOUND2
###################################################################
confound2_rps[2]=0
confound2_rms[2]=0
confound2_wm[2]=0
confound2_csf[2]=0
confound2_gsr[2]=0
confound2_acompcor[2]=1
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=0
confound2_sq[2]=0
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_rerun[2]=1
confound2_cleanup[2]=1
###################################################################
# 3 REGRESS
###################################################################
regress_tmpf[3]=butterworth
regress_hipass[3]=0.01
regress_lopass[3]=0.08
regress_tmpf_order[3]=1
regress_tmpf_pass[3]=2
regress_tmpf_ripple[3]=0.5
regress_tmpf_ripple2[3]=20
regress_dmdt[3]=2
regress_1ddt[3]=1
regress_smo[3]=6
regress_sptf[3]=susan
regress_usan[3]=default
regress_usan_space[3]=
regress_rerun[3]=0
regress_cleanup[3]=1
regress_process[3]=DMT-TMP-REG
###################################################################
# 4 FCON
###################################################################
fcon_atlas[4]=power264
fcon_metric[4]=corrcoef
fcon_rerun[4]=0
fcon_cleanup[4]=1
###################################################################
# 5 REHO
###################################################################
reho_nhood[5]=vertices
reho_roikw[5]=0 # does nothing at the moment
reho_sptf[5]=susan
reho_smo[5]=6
reho_rerun[5]=0
reho_cleanup[5]=1
###################################################################
# 6 ALFF
###################################################################
alff_hipass[6]=0.01
alff_lopass[6]=0.08
alff_sptf[6]=susan
alff_smo[6]=6
alff_rerun[6]=0
alff_cleanup[6]=1
###################################################################
# 7 ROIQUANT
###################################################################
roiquant_atlas[7]=power264
roiquant_globals[7]=1
roiquant_vol[7]=0
roiquant_rerun[7]=0
roiquant_cleanup[7]=1
###################################################################
# 8 NORM
###################################################################
norm_primary[8]=1
norm_rerun[8]=0
norm_cleanup[8]=1
##################################################################
# 9 QCFC
###################################################################
qcfc_atlas[9]=power264
qcfc_sig[9]=fdr
qcfc_rerun[9]=0
qcfc_cleanup[9]=1
Error message
Runtime Information
Tried both of these:
Additional context
I realize that LinAsym6 space is not supported according to the docs. However, 1) my colleague @lollopasquini from #486 was able to run this with the LinAsym6 space images, and 2) I tried this also with fMRIprep generated MNI152NLin2009cAsym space as well with essentially the same problems. This seems to be a problem with Docker binding. All the permissions are open. Any help would be greatly appreciated!
The text was updated successfully, but these errors were encountered:
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Cohort file
![Screen Shot 2022-06-27 at 11 29 08 AM](https://user-images.githubusercontent.com/61159065/176878984-ef13a4a5-dcf3-4c47-9b3b-ad7257db69be.png)
Paste cohort file between the triple backticks
Design File
Paste your entire design (
.dsn
) file between the triple backticksError message
![Screen Shot 2022-06-27 at 11 09 04 AM](https://user-images.githubusercontent.com/61159065/176879285-4911ae15-3c61-4fc8-8c3a-a586b52d813e.png)
Runtime Information
Tried both of these:
Additional context
I realize that LinAsym6 space is not supported according to the docs. However, 1) my colleague @lollopasquini from #486 was able to run this with the LinAsym6 space images, and 2) I tried this also with fMRIprep generated MNI152NLin2009cAsym space as well with essentially the same problems. This seems to be a problem with Docker binding. All the permissions are open. Any help would be greatly appreciated!
The text was updated successfully, but these errors were encountered: