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Do some runs have a different number of timepoints?
On 23 Jun 2016 16:03, "Pranish Kantak" <[log in to unmask]> wrote:
>
> Hi Eugene,
>
> Thanks for your response. I originally tried to run this using MELODIC GUI and got the same type of errors, so then I decided to run FEAT in the GUI and then run MELODIC from the command line, but I got the attached errors.
>
> Thanks!
>
> Pranish
>
> Sent from my iPhone
>
> On Jun 23, 2016, at 8:09 AM, Eugene Duff <[log in to unmask]> wrote:
>
>> Hi Pranish -
>>
>> I'm not exactly sure what is causing the problem, but are you aware you can use Melodic to run the ICA including preprocessing? As you have a repeated measures model, you would then want to try to implement this model using dual_regression or NetMats with the ICA network components.
>>
>> Cheers
>>
>> Eugene
>>
>> On 23 June 2016 at 14:35, Pranish Kantak <[log in to unmask]> wrote:
>>>
>>> Dear FSL Experts,
>>>
>>> I'm pre-processing some data for ICA. I've set up FEAT for the following:
>>>
>>> 1) 52 BET-completed inputs (26 subjects, 2 runs, repeated measures)
>>> 2) 150s High Pass Filtering (with the High Pass Temporal Filtering option)
>>> 3) 6mm FWHM Smoothing
>>> 4) Motion Correction using MCFLIRT
>>> 5) Registration to the main structural images (using Normal Search/BBR) --> With this option however, we only have one structural image per subject, where each subject has two runs. So I've copied the files, named them something different, and then added them to FEAT
>>> 6) Standard Space Registration - 2mm MNI (Using Normal Search/12DOF)
>>>
>>> First question is: from the papers I've been reading, this is all I need to do for ICA. No Slice-timing etc. Is that true?
>>>
>>> I also get the following error in the attached file.
>>>
>>> Thanks in advance to anyone who can tell me what this error means!
>>>
>>> Regards,
>>>
>>> Pranish Kantak
>>>
>>>
>>>
>>>
>>>
>>> Progress Report / Log
>>> Started at Thu Jun 23 03:47:45 EDT 2016
>>>
>>> Feat main script
>>>
>>> /bin/cp /Volumes/PRANISH/bfast_club/subjects/bf02/fed/rest/bf02fed_feat_forica.feat/design.fsf design.fsf
>>>
>>> /usr/local/fsl/bin/feat_model design
>>>
>>> mkdir .files;cp /usr/local/fsl/doc/fsl.css .files;cp -r /usr/local/fsl/doc/images .files/images
>>>
>>> /usr/local/fsl/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/local/fsl/bin/feat /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/design.fsf -D /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat -I 5 -init
>>> 53448
>>>
>>> /usr/local/fsl/bin/fsl_sub -T 50 -l logs -N feat2_pre -j 53448 /usr/local/fsl/bin/feat /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/design.fsf -D /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat -I 5 -prestats
>>> child process exited abnormally
>>> while executing
>>> "if { [ catch {
>>>
>>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>> switch -- [ lindex $argv $argindex ] {
>>>
>>> -I {
>>> incr arginde..."
>>> (file "/usr/local/fsl/bin/feat" line 309)
>>>
>>> FATAL ERROR ENCOUNTERED:
>>> COMMAND:
>>> /usr/local/fsl/bin/fsl_sub -T 50 -l logs -N feat2_pre -j 53448 /usr/local/fsl/bin/feat /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/design.fsf -D /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat -I 5 -prestats
>>> ERROR MESSAGE:
>>> child process exited abnormally
>>> END OF ERROR MESSAGE
>>>
>>> ________________________________
>>> Initialisation
>>>
>>> /usr/local/fsl/bin/fslmaths /Volumes/PRANISH/bfast_club/subjects/bf03/fasted/rest/bf03fasted prefiltered_func_data -odt float
>>> Total original volumes = 192
>>> Error - prefiltered_func_data has a different number of time points to that in FEAT setup
>>>
>>> ________________________________
>>> Preprocessing:Stage 1
>>>
>>> /usr/local/fsl/bin/mainfeatreg -F 6.00 -d /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat -l /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/logs/feat2_pre -R /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/report_unwarp.html -r /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/report_reg.html -i /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/example_func.nii.gz -h /Volumes/PRANISH/bfast_club/subjects/bf03/rage/bragebf03 -w BBR -x 90 -s /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -y 12 -z 90
>>> Option -F ( FEAT version parameter ) selected with argument "6.00"
>>> Option -d ( output directory ) selected with argument "/Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat"
>>> Option -l ( logfile )input with argument "/Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/logs/feat2_pre"
>>> Option -R ( html unwarping report ) selected with argument "/Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/report_unwarp.html"
>>> Option -r ( html registration report ) selected with argument "/Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/report_reg.html"
>>> Option -i ( main input ) input with argument "/Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/example_func.nii.gz"
>>> Option -h ( high-res structural image ) selected with argument "/Volumes/PRANISH/bfast_club/subjects/bf03/rage/bragebf03"
>>> Option -w ( highres dof ) selected with argument "BBR"
>>> Option -x ( highres search ) selected with argument "90"
>>> Option -s ( standard image ) selected with argument "/usr/local/fsl/data/standard/MNI152_T1_2mm_brain"
>>> Option -y ( standard dof ) selected with argument "12"
>>> Option -z ( standard search ) selected with argument "90"
>>>
>>> ________________________________
>>> Registration
>>>
>>> /bin/mkdir -p /Volumes/PRANISH/bfast_club/subjects/bf03/Fasted/rest/bf03fasted_feat_forica.feat/reg
>>>
>>>
>>> /usr/local/fsl/bin/fslmaths /Volumes/PRANISH/bfast_club/subjects/bf03/rage/bragebf03 highres
>>>
>>>
>>> /usr/local/fsl/bin/fslmaths /Volumes/PRANISH/bfast_club/subjects/bf03/rage/bragebf03 highres_head
>>>
>>>
>>> /usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard
>>>
>>> did not find file: example_func2highres.mat. Generating transform.
>>>
>>> /usr/local/fsl/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres
>>> Image Exception : #22 :: ERROR: Could not open image example_func
>>> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
>>> /usr/local/fsl/bin/epi_reg: line 326: 54431 Abort trap: 6 $FSLDIR/bin/flirt -ref ${vrefbrain} -in ${vepi} -dof 6 -omat ${vout}_init.mat
>>> Image Exception : #22 :: ERROR: Could not open image example_func
>>> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
>>> /usr/local/fsl/bin/epi_reg: line 378: 54433 Abort trap: 6 $FSLDIR/bin/flirt -ref ${vrefhead} -in ${vepi} -dof 6 -cost bbr -wmseg ${vout}_fast_wmseg -init ${vout}_init.mat -omat ${vout}.mat -out ${vout} -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
>>> Could not open matrix file example_func2highres.mat
>>> Image Exception : #22 :: ERROR: Could not open image example_func
>>> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
>>> /usr/local/fsl/bin/epi_reg: line 378: 54434 Abort trap: 6 $FSLDIR/bin/applywarp -i ${vepi} -r ${vrefhead} -o ${vout} --premat=${vout}.mat --interp=spline
>>> Running FAST segmentation FLIRT pre-alignment Running BBR
>>>
>>> /usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres1.png ; /usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2highres2.png ; /usr/local/fsl/bin/pngappend example_func2highres1.png - example_func2highres2.png example_func2highres.png; /bin/rm -f sl?.png exam
>>> ple_func
>>> 2highres2.png
>>> Image Exception : #22 :: ERROR: Could not open image example_func2highres
>>>
>>> Cannot open sla.png for reading
>>>
>>> Cannot open example_func2highres1.png for reading
>>> Error in slicer input, exiting...
>>>
>>> /bin/rm example_func2highres1.png
>>> rm: example_func2highres1.png: No such file or directory
>>>
>>> did not find file: highres2standard.mat. Generating transform.
>>>
>>> /usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear
>>>
>>>
>>> /usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
>>>
>>>
>>> /usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard1.png ; /usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png highres2standard2.png ; /usr/local/fsl/bin/pngappend highres2standard1.png - highres2standard2.png highres2standard.png; /bin/rm -f sl?.png highres2standard2.png
>>>
>>>
>>> /bin/rm highres2standard1.png
>>>
>>>
>>> /usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat
>>> Could not open matrix file example_func2highres.mat
>>> Cannot read input-matrix
>>>
>>> did not find file: example_func2standard.mat. Generating transform.
>>>
>>> /usr/local/fsl/bin/flirt -in example_func -ref standard -out example_func2standard -omat example_func2standard.mat -cost corratio -dof -searchrx - -searchry - -searchrz - -interp trilinear
>>> Unrecognised option -
>>>
>>>
>>> /usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard1.png ; /usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png ; /usr/local/fsl/bin/pngappend sla.png + slb.png + slc.png + sld.png + sle.png + slf.png + slg.png + slh.png + sli.png + slj.png + slk.png + sll.png example_func2standard2.png ; /usr/local/fsl/bin/pngappend example_func2standard1.png - example_func2standard2.png example_func2standard.png; /bin/rm -f sl?
>>> .png exa
>>> mple_func2standard2.png
>>> Image Exception : #22 :: ERROR: Could not open image example_func2standard
>>>
>>> Cannot open sla.png for reading
>>>
>>> Cannot open example_func2standard1.png for reading
>>> Error in slicer input, exiting...
>>>
>>> ________________________________
>>> Preprocessing:Stage 2
>>>
>>> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final
>>> Image Exception : #22 :: ERROR: Could not open image example_func
>>> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
>>>
>>> /bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
>>> mv: rename prefiltered_func_data_mcf.mat to mc/prefiltered_func_data_mcf.mat: No such file or directory
>>> mv: rename prefiltered_func_data_mcf.par to mc/prefiltered_func_data_mcf.par: No such file or directory
>>> mv: rename prefiltered_func_data_mcf_abs.rms to mc/prefiltered_func_data_mcf_abs.rms: No such file or directory
>>> mv: rename prefiltered_func_data_mcf_abs_mean.rms to mc/prefiltered_func_data_mcf_abs_mean.rms: No such file or directory
>>> mv: rename prefiltered_func_data_mcf_rel.rms to mc/prefiltered_func_data_mcf_rel.rms: No such file or directory
>>> mv: rename prefiltered_func_data_mcf_rel_mean.rms to mc/prefiltered_func_data_mcf_rel_mean.rms: No such file or directory
>>>
>>> FATAL ERROR ENCOUNTERED:
>>> COMMAND:
>>> /bin/mkdir -p mc ; /bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc
>>> ERROR MESSAGE:
>>> child process exited abnormally
>>> END OF ERROR MESSAGE
>>> child process exited abnormally
>>> while executing
>>> "if { [ catch {
>>>
>>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>> switch -- [ lindex $argv $argindex ] {
>>>
>>> -I {
>>> incr arginde..."
>>> (file "/usr/local/fsl/bin/feat" line 309)
>>> Error encountered while running in main feat script, halting.
>>> child process exited abnormally
>>>
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