a3sha2
commented
5 years ago Hi
You dont need structural processing anymore to run functional processing Azeez
Closed mitchem890 closed 5 years ago
a3sha2
commented
5 years ago Hi
You dont need structural processing anymore to run functional processing Azeez
mitchem890
commented
5 years ago Thanks Azeez, So I've moved on to directly running the functional pipeline and it seems like the expected naming convention is not the same as what is output from fmriprep. Is this because xcp-engine is expecting a different version of fmriprep output, or is there a way to configure the expected filenames for xcp?
Cohort File
id0,img
sub-155938,fmriprep/sub-155938/ses-wave1bas/func/sub-155938_ses-wave1bas_task-Rest_acq-mb4AP_run-1_bold_space-MNI152NLin2009cAsym_preproc.nii.gzDesign File
#!/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/fc-36p.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]=1
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=1
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=0
confound2_past[2]=0
confound2_dx[2]=1
confound2_sq[2]=2
confound2_custom[2]=
confound2_censor[2]=0
confound2_censor_contig[2]=0
confound2_framewise[2]=rmss:0.083,fds:0.167,dv:2
confound2_rerun[2]=0
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]=all
fcon_metric[4]=corrcoef
fcon_thr[4]=N
fcon_pad[4]=FALSE
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]=all
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]=1Error Message
cp /data/fmriprep/sub-155938/ses-wave1bas/func/sub-155938_ses-wave1bas_task-Rest_acq-mb4AP_run-1_desc-confounds_regressors.tsv /data/xcp-engine/xcp_output/sub-155938/prestats/sub-155938_fmriconf.tsv
cp: cannot stat '/data/fmriprep/sub-155938/ses-wave1bas/func/sub-155938_ses-wave1bas_task-Rest_acq-mb4AP_run-1_desc-confounds_regressors.tsv': No such file or directory
ls: cannot access '/data/fmriprep/sub-155938/ses-wave1bas/..//anat/*from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5': No such file or directory
ls: cannot access '/data/fmriprep/sub-155938/ses-wave1bas/..//anat/*from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5': No such file or directory
ls: cannot access '/data/fmriprep/sub-155938/ses-wave1bas/..//anat/*MNI*desc-preproc_T1w.nii.gz': No such file or directory
ls: cannot access '/data/fmriprep/sub-155938/ses-wave1bas/..//anat/*MNI*dseg.nii.gz': No such file or directory
ls: cannot access '/data/fmriprep/sub-155938/ses-wave1bas/..//anat/*MNI*desc-brain_mask.nii.gz': No such file or directory
Runtime Information Running Through Singularity using the following command:
singularity run -B /data/nil-bluearc/ccp-hcp/CCPLinux2testing/fmriprep/sub-155938/output:/data /data/nil-bluearc/ccp-hcp/SingularityImages/xcpengine-latest.simg -d /data/fc-36p.dsn -c /data/func_cohort.csv -o /data/xcp-engine/xcp_output -t 1 -r /dataAdditional Information My anat files look like the files below:
sub-155938_T1w_brainmask.nii.gz
sub-155938_T1w_class-CSF_probtissue.nii.gz
sub-155938_T1w_class-GM_probtissue.nii.gz
sub-155938_T1w_class-WM_probtissue.nii.gz
sub-155938_T1w_dtissue.nii.gz
sub-155938_T1w_inflated.L.surf.gii
sub-155938_T1w_inflated.R.surf.gii
sub-155938_T1w_label-aparcaseg_roi.nii.gz
sub-155938_T1w_label-aseg_roi.nii.gz
sub-155938_T1w_midthickness.L.surf.gii
sub-155938_T1w_midthickness.R.surf.gii
sub-155938_T1w_pial.L.surf.gii
sub-155938_T1w_pial.R.surf.gii
sub-155938_T1w_preproc.nii.gz
sub-155938_T1w_smoothwm.L.surf.gii
sub-155938_T1w_smoothwm.R.surf.gii
sub-155938_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz
sub-155938_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz
sub-155938_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz
sub-155938_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz
sub-155938_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz
sub-155938_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz
sub-155938_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5
sub-155938_T1w_target-fsnative_affine.txt
sub-155938_T1w_target-MNI152NLin2009cAsym_warp.h5I found this issue which is essentially the same: https://github.com/PennBBL/xcpEngine/issues/141 I'll have to update fmriprep to at least version 1.2.0 and rerun my subject. Then I'll give xcp-engine another shot.
Describe the bug Not able to complete the anat pipeline to move onto the func analysis.
Cohort file
Design File
Error message
Runtime Information
running through singularity using the following command:
Additional context Subject was ran through fmriprep using the following command: