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HBClab / RestingState

Scripts to preprocess resting state data and extract ROI-ROI correlations and voxel-wise ROI seedmaps
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Nuisance ROI issue #65

Closed rachclark closed 6 years ago

rachclark commented 6 years ago

Summary

Actual behavior

Expected behavior

How to replicate the behavior

Script/Workflow details

Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/job_scripts/processRestingStatebids_tester.job Please put URL to code or code here (if not too long). Error log

Restoring modules to user's neuro-packages
find: ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/sub-SEH1001/pre/fmap’: No such file or directory
find: ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/sub-SEH1001/pre/fmap’: No such file or directory
find: ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/sub-SEH1001/pre/fmap/mag1/’: No such file or directory
++ 3dvolreg: AFNI version=AFNI_18.0.09 (Jul  7 2015) [64-bit]
++ Authored by: RW Cox
*+ WARNING:   If you are performing spatial transformations on an oblique dset, 
  such as /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/sub-SEH1001_ses-pre_task-rest_bold.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/sub-SEH1001_ses-pre_task-rest_bold.nii.gz is 12.099993 degrees from plumb.
++ WARNING: -tshift used on a dataset with no time-offsets!
++ Reading input dataset /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/sub-SEH1001_ses-pre_task-rest_bold.nii.gz
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
 + Automask has 27792 voxels
 + 4472 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 180 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..
++ CPU time for realignment=0 s  [=0 s/sub-brick]
++ Min : roll=-0.079  pitch=-0.516  yaw=-0.163  dS=-0.470  dL=-0.137  dP=-0.114
++ Mean: roll=+0.015  pitch=+0.043  yaw=+0.040  dS=-0.071  dL=-0.036  dP=+0.108
++ Max : roll=+0.180  pitch=+0.591  yaw=+0.289  dS=+0.228  dL=+0.090  dP=+0.417
++ Max displacements (mm) for each sub-brick:
 0.66(0.00) 0.66(0.14) 0.62(0.24) 0.60(0.16) 0.60(0.04) 0.63(0.16) 0.68(0.40) 0.70(0.34) 0.64(0.23) 0.64(0.14) 0.61(0.08) 0.63(0.12) 0.67(0.24) 0.57(0.16) 0.59(0.08) 0.59(0.09) 0.54(0.19) 0.63(0.20) 0.55(0.10) 0.56(0.03) 0.61(0.15) 0.51(0.13) 0.60(0.14) 0.71(0.21) 0.52(0.25) 0.65(0.16) 0.73(0.16) 0.79(0.28) 0.94(0.17) 0.78(0.18) 1.00(0.25) 1.12(0.15) 0.84(0.29) 1.09(0.25) 0.88(0.23) 1.04(0.19) 0.93(0.13) 0.91(0.02) 1.30(0.41) 0.91(0.41) 1.12(0.23) 1.11(0.14) 1.07(0.06) 1.14(0.10) 0.84(0.30) 1.01(0.19) 1.14(0.18) 1.00(0.16) 1.08(0.10) 0.86(0.22) 1.02(0.20) 0.99(0.08) 0.90(0.09) 1.08(0.18) 0.87(0.22) 1.19(0.33) 0.98(0.25) 1.01(0.07) 1.03(0.11) 0.91(0.12) 0.91(0.10) 0.97(0.10) 0.72(0.26) 0.93(0.28) 0.64(0.30) 0.87(0.23) 0.83(0.04) 0.73(0.11) 0.83(0.12) 0.85(0.10) 0.73(0.13) 0.84(0.11) 0.67(0.19) 0.80(0.16) 0.72(0.14) 0.62(0.13) 0.60(0.11) 0.22(0.46) 0.36(0.21) 0.36(0.28) 0.55(0.24) 0.47(0.10) 0.43(0.07) 0.47(0.09) 0.29(0.18) 0.37(0.31) 0.20(0.49) 0.24(0.13) 0.07(0.20) 0.22(0.24) 0.00(0.22) 0.37(0.37) 0.16(0.27) 0.23(0.33) 0.23(0.39) 0.52(0.31) 0.19(0.39) 0.13(0.21) 0.16(0.09) 0.12(0.14) 0.15(0.10) 0.35(0.35) 0.40(0.13) 0.41(0.09) 0.33(0.14) 0.30(0.18) 0.37(0.22) 0.44(0.21) 0.49(0.26) 0.59(0.18) 0.61(0.29) 0.54(0.13) 0.50(0.05) 0.62(0.16) 0.59(0.17) 0.65(0.17) 0.70(0.36) 0.56(0.30) 0.45(0.18) 0.46(0.03) 0.59(0.14) 0.49(0.17) 0.47(0.08) 0.50(0.09) 0.52(0.06) 0.57(0.08) 0.66(0.31) 0.71(0.12) 0.79(0.14) 0.81(0.19) 0.85(0.08) 0.85(0.34) 0.81(0.16) 0.77(0.15) 0.84(0.13) 0.91(0.10) 0.73(0.27) 0.78(0.21) 0.70(0.18) 0.67(0.10) 0.72(0.12) 0.73(0.11) 0.74(0.11) 0.74(0.08) 0.68(0.09) 0.75(0.14) 0.64(0.13) 0.68(0.23) 0.61(0.24) 0.61(0.11) 0.66(0.30) 0.58(0.32) 0.51(0.17) 0.51(0.09) 0.56(0.16) 0.65(0.58) 0.39(0.44) 0.40(0.22) 0.37(0.15) 0.44(0.11) 0.73(1.07) 0.82(0.45) 0.49(0.37) 0.39(0.24) 0.38(0.05) 0.45(0.22) 0.36(0.29) 0.45(0.26) 0.39(0.21) 0.37(0.07) 0.48(0.28) 0.41(0.24) 0.44(0.19) 0.40(0.17) 0.42(0.02) 0.63(0.35) 0.64(0.15) 0.62(0.07) 0.62(0.06) 0.62(0.10)
++ Max displacement in automask = 1.30 (mm) at sub-brick 38
++ Max delta displ  in automask = 1.07 (mm) at sub-brick 160
++ Wrote dataset to disk in ./mcImg.nii.gz
++ 3dmerge: AFNI version=AFNI_18.0.09 (Jul  7 2015) [64-bit]
*+ WARNING:   If you are performing spatial transformations on an oblique dset, 
  such as /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/SNR/RestingState_GM.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/SNR/RestingState_GM.nii.gz is 12.099993 degrees from plumb.
++ default -1dindex = 0
++ default -1tindex = 1
++ Oblique dataset:/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/SNR/RestingState_GM.nii.gz is 12.099993 degrees from plumb.
-- Wrote edited dataset: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/SNR/RestingState_GMsmooth.nii.gz
++ 3dTqual: AFNI version=AFNI_18.0.09 (Jul  7 2015) [64-bit]
*+ WARNING:   If you are performing spatial transformations on an oblique dset, 
  such as nonfilteredImg.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:nonfilteredImg.nii.gz is 12.099993 degrees from plumb.
++ Autoclip value = 419.849
++ 26628 out of 126976 voxels survive the clip
++ Median=0.00842059  Median-3.5*MAD=0.00276114  Median+3.5*MAD=0.01408
{Error using cd
Cannot CD to
/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats
(Name is nonexistent or not a directory).

Error in motionscrub (line 22)
cd(mypath);

Error in run_motionscrub (line 6)
motionscrub('/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre','nuisancereg.feat',funcvoldim)

Error in run (line 96)
evalin('caller', [script ';']);
} 
ERROR: Could not open file
cat: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/deleted_vols.txt: No such file or directory
awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted
cat: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/deleted_vols.txt: No such file or directory
find: ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg*.feat’: No such file or directory
cp: cannot stat ‘/Volumes/vosslabhpc/UniversalSoftware/RestingState2014a/ROIs/BamHippo_Blessing_14mm.nii.gz’: No such file or directory
Image Exception : #22 :: ERROR: Could not open image /Volumes/vosslabhpc/UniversalSoftware/RestingState2014a/ROIs/BamHippo_Blessing_14mm
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 221: 48191 Aborted                 applywarp --ref=${epiData} --in=${roi} --out=${nuisancefeat}/stats/${roiName}_mask.nii.gz --warp=${MNItoEPIWarp} --mask=${nuisancefeat}/stats/mask.nii.gz --datatype=float
Cannot open volume nuisancereg.feat/stats/BamHippo_Blessing_14mm_mask for reading!
Cannot open volume nuisancereg.feat/stats/BamHippo_Blessing_14mm_mask for reading!
Image Exception : #22 :: ERROR: Could not open image nuisancereg.feat/stats/BamHippo_Blessing_14mm_mask
Image Exception : #22 :: ERROR: Could not open image nuisancereg.feat/stats/res4d_normandscaled
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 221: 48197 Aborted                 fslmeants -i ${nuisancefeat}/stats/res4d_normandscaled -o ${nuisancefeat}/stats/${roiName}_residvol_ts.txt -m ${roiMask}
Image Exception : #22 :: ERROR: Could not open image nuisancereg.feat/stats/res4d_normandscaled_motionscrubbed
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 221: 48198 Aborted                 fslmeants -i ${nuisancefeat}/stats/res4d_normandscaled_motionscrubbed -o ${nuisancefeat}/stats/${roiName}_residvol_ms_ts.txt -m ${roiMask}
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 279: nuisancereg.feat/stats/temp_BamHippo_Blessing_14mm_residvol_ts.txt: No such file or directory
cat: nuisancereg.feat/stats/BamHippo_Blessing_14mm_residvol_ts.txt: No such file or directory
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 280: nuisancereg.feat/stats/temp_BamHippo_Blessing_14mm_residvol_ms_ts.txt: No such file or directory
cat: nuisancereg.feat/stats/BamHippo_Blessing_14mm_residvol_ms_ts.txt: No such file or directory
mv: cannot stat ‘nuisancereg.feat/stats/temp_BamHippo_Blessing_14mm_residvol_ts.txt’: No such file or directory
mv: cannot stat ‘nuisancereg.feat/stats/temp_BamHippo_Blessing_14mm_residvol_ms_ts.txt’: No such file or directory
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/overlay_split_sagittal for reading!
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cp: omitting directory ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/’
cp: omitting directory ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/’
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 107: [: =: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 115: [: -gt: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_underlay_sagittal for reading!
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 107: [: =: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 115: [: -gt: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_overlay_sagittal for reading!
gzip: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_underlay_sagittal.nii.gz: No such file or directory
gzip: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_overlay_sagittal.nii.gz: No such file or directory
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/overlay_split_coronal for reading!
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cp: omitting directory ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/’
cp: omitting directory ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/’
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 107: [: =: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 115: [: -gt: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_underlay_coronal for reading!
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_underlay_coronal for reading!
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 107: [: =: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 115: [: -gt: unary operator expected
ERROR: Could not open file
/Users/rachclark/packages/FSL/5.0.10/bin/fslswapdim: line 117: [: -gt: unary operator expected
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_overlay_coronal for reading!
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_overlay_coronal for reading!
gzip: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_underlay_coronal.nii.gz: No such file or directory
gzip: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_overlay_coronal.nii.gz: No such file or directory
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/overlay_split_axial for reading!
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cp: omitting directory ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/’
cp: omitting directory ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/temp/’
gzip: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_underlay_axial.nii.gz: No such file or directory
gzip: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/seedQC/BamHippo_Blessing_14mm_overlay_axial.nii.gz: No such file or directory
{Error using load_nii_hdr (line 32)
Cannot find file "BamHippo_Blessing_14mm_underlay_coronal.nii".

Error in load_untouch_nii (line 103)
   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);

Error in seedregistrationcheck (line 69)
    useedhdr=load_untouch_nii(uinput);

Error in run_seedregistrationcheck (line 15)
seedregistrationcheck(seedDir,roiList,imageDir)

Error in run (line 96)
evalin('caller', [script ';']);
} 
{Error using load_nii_hdr (line 32)
Cannot find file "res4d_normandscaled.nii".

Error in load_untouch_nii (line 103)
   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);

Error in firstlevelseeding_parallel (line 82)
funcon=load_untouch_nii(input);

Error in run_firstlevelseeding_parallel (line 14)
firstlevelseeding_parallel('/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre',roiList,'nuisancereg.feat',funcvoldim,input,motion_scrub,doFisherZ)

Error in run (line 96)
evalin('caller', [script ';']);
} 
{Error using load_nii_hdr (line 32)
Cannot find file "res4d_normandscaled_motionscrubbed.nii".

Error in load_untouch_nii (line 103)
   [nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);

Error in firstlevelseeding_parallel (line 82)
funcon=load_untouch_nii(input);

Error in run_firstlevelseeding_parallel_ms (line 14)
firstlevelseeding_parallel('/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre',roiList,'nuisancereg.feat',funcvoldim,input,motion_scrub,doFisherZ)

Error in run (line 96)
evalin('caller', [script ';']);
} 
cp: cannot stat ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres.nii.gz’: No such file or directory
cp: cannot stat ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres2standard.nii.gz’: No such file or directory
cp: cannot stat ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/standard.nii.gz’: No such file or directory
Image Exception : #22 :: ERROR: Could not open image /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 667: 49027 Aborted                 flirt -in $indir/${nuisancefeat}/stats/${roi}/cope1.nii -ref $indir/${nuisancefeat}/reg/highres.nii.gz -out ${seedcorrDir}/${roi}_highres_zmap.nii.gz -applyxfm -init $indir/${nuisancefeat}/reg/example_func2highres.mat -datatype float
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres for reading!
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/seedCorrelation/BamHippo_Blessing_14mm_highres_zmap for reading!
Image Exception : #22 :: ERROR: Could not open image /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/BamHippo_Blessing_14mm/cope1
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 667: 49030 Aborted                 applywarp --in=$indir/${nuisancefeat}/stats/${roi}/cope1.nii --ref=$indir/${nuisancefeat}/reg/standard.nii.gz --out=${seedcorrDir}/${roi}_standard_zmap.nii.gz --warp=$indir/${nuisancefeat}/reg/example_func2standard_warp.nii.gz --datatype=float
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/seedCorrelation/BamHippo_Blessing_14mm_standard_zmap for reading!
Image Exception : #22 :: ERROR: Could not open image /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/seedCorrelation/BamHippo_Blessing_14mm_standard
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 667: 49032 Aborted                 applywarp --in=${seedcorrDir}/${roi}_standard.nii.gz --ref=$indir/${nuisancefeat}/reg/highres.nii.gz --out=${seedcorrDir}/${roi}_highres.nii.gz --warp=$indir/${nuisancefeat}/reg/standard2highres_warp.nii.gz --interp=nn
Image Exception : #22 :: ERROR: Could not open image /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 667: 49033 Aborted                 flirt -in $indir/${nuisancefeat}/stats/${roi}_ms/cope1.nii -ref $indir/${nuisancefeat}/reg/highres.nii.gz -out ${seedcorrDir}/${roi}_ms_highres_zmap.nii.gz -applyxfm -init $indir/${nuisancefeat}/reg/example_func2highres.mat -datatype float
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres for reading!
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/seedCorrelation/BamHippo_Blessing_14mm_ms_highres_zmap for reading!
rm: cannot remove ‘/Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/reg/highres_mask.nii.gz’: No such file or directory
Image Exception : #22 :: ERROR: Could not open image /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/BamHippo_Blessing_14mm_ms/cope1
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh: line 667: 49037 Aborted                 applywarp --in=$indir/${nuisancefeat}/stats/${roi}_ms/cope1.nii --ref=$indir/${nuisancefeat}/reg/standard.nii.gz --out=${seedcorrDir}/${roi}_ms_standard_zmap.nii.gz --warp=$indir/${nuisancefeat}/reg/example_func2standard_warp.nii.gz --datatype=float
Cannot open volume /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/seedCorrelation/BamHippo_Blessing_14mm_ms_standard_zmap for reading!
cat: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/deleted_vols.txt: No such file or directory
cat: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/BamHippo_Blessing_14mm_residvol_ts.txt: No such file or directory
cat: /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/nuisancereg.feat/stats/BamHippo_Blessing_14mm_residvol_ts.txt: No such file or directory

Part of FSL (ID: 5.0.10)
fsl_tsplot 
Copyright(c) 2007, University of Oxford (Christian F. Beckmann)

Usage: 
fsl_tsplot [options] 

Compulsory arguments (You MUST set one or more of):
    -i,--in         comma-separated list of input file names (ASCII text matrix, one column per timecourse)
    -o,--out    output filename for the PNG file

Optional arguments (You may optionally specify one or more of):
    -t,--title  plot title
    -l,--legend file name of ASCII text file, one row per legend entry
    -a,--labels comma-separated list of labels
    --ymin          minimum y-value
    --ymax          maximum y-value
    -x,--xlabel X-axis label
    -y,--ylabel Y-axis label
    -h,--height plot height in pixels (default 150)
    -w,--width  plot width in pixels (default 600)
    -u,--unit   scaling units for x-axis (default 1...length of infile
    --precision precision of x-axis labels
    --sci           switch on sientific notation
    --start         Position of first column to plot
    --finish    Position of final column to plot

--ymin: Missing non-optional argument!
which: no ICA_AROMA.py in (/Users/rachclark/.linuxbrew/bin:/Users/rachclark/.linuxbrew/sbin:/Users/rachclark/.linuxbrew/bin:/opt/apps/matlab/R2016b/bin:/opt/apps/python/2.7.13/bin:/opt/apps/tiff/4.0.7/bin:/opt/apps/sqlite/3.16.2/bin:/opt/apps/readline/7.0/bin:/opt/apps/ncurses/6.0/bin:/opt/apps/proj/4.9.3/bin:/opt/apps/pcre/8.40/bin:/opt/apps/openjpeg/2.1.2/bin:/opt/apps/libpng/1.6.28/bin:/opt/apps/jpeg/9b/bin:/opt/apps/freetype/2.7.1/bin:/opt/apps/fontconfig/2.12.1/bin:/opt/apps/libxml2/2.9.4/bin:/opt/apps/xz/5.2.3/bin:/opt/apps/expat/2.2.0/bin:/opt/apps/c-blosc/1.11.2/bin:/opt/apps/pkg-config/0.29.1/bin:/opt/apps/glib/2.51.1/bin:/opt/apps/bzip2/1.0.6/bin:/opt/apps/netcdf/4.4.1.1/bin:/opt/apps/hdf5/1.8.18/bin:/opt/apps/grib_api/1.19.0/bin:/opt/apps/hdf/4.2.12/bin:/opt/apps/curl/7.52.1/bin:/opt/apps/jasper/1.900.1/bin:/Users/rachclark/packages/FSL/5.0.10/bin:/Users/rachclark/packages/AFNI/abin:/Users/rachclark/packages/FreeSurfer/6.0.0/bin:/Users/rachclark/packages/FreeSurfer/6.0.0/fsfast/bin:/Users/rachclark/packages/FreeSurfer/6.0.0/tktools:/Users/rachclark/packages/FreeSurfer/6.0.0/mni/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/localscratch/7687045.1.UI:/Users/rachclark/.linuxbrew/bin:/Users/rachclark/.linuxbrew/sbin:/Users/rachclark/.linuxbrew/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/Shared/vosslabhpc/UniversalSoftware/ICA-AROMA/ICA_AROMA:/usr/local/sbin:/usr/sbin:/Shared/vosslabhpc/UniversalSoftware/ICA-AROMA/ICA_AROMA:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Shared/vosslabhpc/UniversalSoftware/ICA-AROMA/ICA_AROMA:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Users/rachclark/packages/AFNI/abin)
which: no ICA_AROMA.py in (/Users/rachclark/.linuxbrew/bin:/Users/rachclark/.linuxbrew/sbin:/Users/rachclark/.linuxbrew/bin:/opt/apps/matlab/R2016b/bin:/opt/apps/python/2.7.13/bin:/opt/apps/tiff/4.0.7/bin:/opt/apps/sqlite/3.16.2/bin:/opt/apps/readline/7.0/bin:/opt/apps/ncurses/6.0/bin:/opt/apps/proj/4.9.3/bin:/opt/apps/pcre/8.40/bin:/opt/apps/openjpeg/2.1.2/bin:/opt/apps/libpng/1.6.28/bin:/opt/apps/jpeg/9b/bin:/opt/apps/freetype/2.7.1/bin:/opt/apps/fontconfig/2.12.1/bin:/opt/apps/libxml2/2.9.4/bin:/opt/apps/xz/5.2.3/bin:/opt/apps/expat/2.2.0/bin:/opt/apps/c-blosc/1.11.2/bin:/opt/apps/pkg-config/0.29.1/bin:/opt/apps/glib/2.51.1/bin:/opt/apps/bzip2/1.0.6/bin:/opt/apps/netcdf/4.4.1.1/bin:/opt/apps/hdf5/1.8.18/bin:/opt/apps/grib_api/1.19.0/bin:/opt/apps/hdf/4.2.12/bin:/opt/apps/curl/7.52.1/bin:/opt/apps/jasper/1.900.1/bin:/Users/rachclark/packages/FSL/5.0.10/bin:/Users/rachclark/packages/AFNI/abin:/Users/rachclark/packages/FreeSurfer/6.0.0/bin:/Users/rachclark/packages/FreeSurfer/6.0.0/fsfast/bin:/Users/rachclark/packages/FreeSurfer/6.0.0/tktools:/Users/rachclark/packages/FreeSurfer/6.0.0/mni/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/localscratch/7687045.1.UI:/Users/rachclark/.linuxbrew/bin:/Users/rachclark/.linuxbrew/sbin:/Users/rachclark/.linuxbrew/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/Shared/vosslabhpc/UniversalSoftware/ICA-AROMA/ICA_AROMA:/usr/local/sbin:/usr/sbin:/Shared/vosslabhpc/UniversalSoftware/ICA-AROMA/ICA_AROMA:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Shared/vosslabhpc/UniversalSoftware/ICA-AROMA/ICA_AROMA:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Users/rachclark/.local/bin:/Users/rachclark/bin:/Users/rachclark/packages/AFNI/abin)

Output file

subDir is /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/sub-SEH1001.
MBA_dir is /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/MBA/sub-SEH1001.

Mon Feb 19 19:39:02 CST 2018
Beginning preprocesssing (classic mode)...
no fieldmap found.Running /Users/rachclark/git_clones/RestingState/qualityCheck.sh ...
...Applying motion correction.
...SNR mask creation.
...Creating Tissue class segmentations.
...Optimizing EPI (func) to T1 (highres) registration.
......Registration Without FieldMap Correction.
FLIRT pre-alignment
Running BBR
0.562812 0.999986 0.002395 -0.004699 0.000000 -0.002303 0.999805 0.019601 0.000000 0.004745 -0.019590 0.999797 0.000000 -0.580023 3.417209 2.683061 1.000000 
...Estimating SNR.
...Warping GM/WM/CSF mask to EPI space
Program 3dmerge 
3dmerge: edit and combine 3D datasets, by RW Cox
++ editing input dataset in memory (0.1 MB)
.
...Calculating SNR measurements per TR.
...Calculating signal to noise measurements
...Detecting time series spikes
Image mean is 211.891344 
Image standard deviation is 1.027400423
/Users/rachclark/git_clones/RestingState/qualityCheck.sh Complete

Running /Users/rachclark/git_clones/RestingState/restingStatePreprocess.sh ...
...Running FEAT (preproc)
To view the FEAT progress and final report, point your web browser at /Shared/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/derivatives/rsOut_legacy/sub-SEH1001/pre/preproc.feat/report_log.html
...Guassian Smoothing
...Fixing FEAT registration QC images.
......func2highres
......highres2standard
......func2standard
/Users/rachclark/git_clones/RestingState/restingStatePreprocess.sh Complete

Error: Invalid Nuisance ROI specified (global)
Valid Nuisance ROIs: wmroi
Running /Users/rachclark/git_clones/RestingState/motionScrub.sh ...
...Scrubbing data

                            < M A T L A B (R) >
                  Copyright 1984-2016 The MathWorks, Inc.
                   R2016b (9.1.0.441655) 64-bit (glnxa64)
                             September 7, 2016

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> ...Summarizing Results
/Users/rachclark/git_clones/RestingState/motionScrub.sh Complete

Running /Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh ...
...Transforming ROIs to EPI space
......Mapping BamHippo_Blessing_14mm from MNI (standard) to subject EPI (func) space
...QC Image Setup
BamHippo_Blessing_14mm
......Preparing BamHippo_Blessing_14mm (x)
......Preparing BamHippo_Blessing_14mm (y)
......Preparing BamHippo_Blessing_14mm (z)
...Creating QC Images of ROI/Seed Registration To Functional Space

                            < M A T L A B (R) >
                  Copyright 1984-2016 The MathWorks, Inc.
                   R2016b (9.1.0.441655) 64-bit (glnxa64)
                             September 7, 2016

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

>> ...Seed Voxel Correlation Setup
...Creating Octave script
...Creating Octave script (motionscrubbed data)
...Correlating Seeds With Time Series Data

                            < M A T L A B (R) >
                  Copyright 1984-2016 The MathWorks, Inc.
                   R2016b (9.1.0.441655) 64-bit (glnxa64)
                             September 7, 2016

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

[Warning: Undefined function 'matlabpool' for input arguments of type 'char'.] 
[> In firstlevelseeding_parallel (line 71)
  In run_firstlevelseeding_parallel (line 14)
  In run (line 96)] 
>> 
                            < M A T L A B (R) >
                  Copyright 1984-2016 The MathWorks, Inc.
                   R2016b (9.1.0.441655) 64-bit (glnxa64)
                             September 7, 2016

To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.

[Warning: Undefined function 'matlabpool' for input arguments of type 'char'.] 
[> In firstlevelseeding_parallel (line 71)
  In run_firstlevelseeding_parallel_ms (line 14)
  In run (line 96)] 
>> ...Creating zstat Results Directory
...Mapping Correlation For BamHippo_Blessing_14mm To Subject T1, MNI
/Users/rachclark/git_clones/RestingState/seedVoxelCorrelation.sh Complete
Please make sure that the ROI folders were created in the nuisancereg.feat/stats/ folder.
If resultant warped seeds (to MNI) were too small, they were NOT processed.  Check nuisancereg.feat/stats/seedsTooSmall for exclusions.
If motionscrubbing was set to 1 or 2, make sure that motionscrubbed data was created.
OCTAVE/Matlab wouldn't give an error even if this step was not successfully done.

Mon Feb 19 19:46:35 CST 2018
Beginning reproc nuisance regression (ica_aroma + compcor)...
ICA_AROMA is either not downloaded or not defined in your path, exiting script
tbweng commented 6 years ago

Have you pulled from master recently? Does this file exist in your cloned repository: /Users/rachclark/git_clones/RestingState/ROIs/global.nii.gz Appears that global and latvent are missing from the ROIs in your repository.

tbweng commented 6 years ago

Fixed with Pull Request #68