Dear Matt,
So changing that line did fix the error with the 0.7mm brain mask. However,
there seems to be an additional error:
hcp_fix: INFORM: functionmotionconfounds log file is to be named:
.fix.functionmotionconfounds.log instead of .fix.log
hcp_fix: DEBUG: current folder
/home/functionalspinelab/Desktop/Dinal/mystudy/NSI_12/MNINonLinear/Results/rfMRI_REST1_PA/rfMRI_REST1_PA_hp2000.ica/reg
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: 159:
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix:
//MNINonLinear/brainmask_fs.nii.gz: not found
hcp_fix: INFORM: running FIX
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: 171:
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: [[: not found
hcp_fix: INFORM: About to run:
/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/fix
rfMRI_REST1_PA_hp2000.ica
/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData
10 -m -h 2000
FIX Feature extraction for Melodic output directory: rfMRI_REST1_PA_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: rfMRI_REST1_PA_hp2000.ica
using training file:
/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData
and threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_PA_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup
set to 1
Could not find a supported file with prefix
"rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean"
Could not find a supported file with prefix
"rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn"
This is the line in hcp_fix which relates to these two files:
$FSLDIR/bin/immv ${fmri}.ica/filtered_func_data_clean ${fmri}_clean
$FSLDIR/bin/immv ${fmri}.ica/filtered_func_data_clean_vn ${fmri}_clean_vnf
I initially thought the specified path to these two files were incorrect but it
turns out these files were never created. Are these files meant to be created
by hcp_fix?
Kind regards,
Dinal Jayasekera
PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering | Washington University in St. Louis
________________________________
From: Glasser, Matthew
Sent: Friday, November 9, 2018 7:36:59 PM
To: NEUROSCIENCE tim
Cc: Jayasekera, Dinal; Dierker, Donna; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
We should change that line to use this file:
${StudyFolder}/${Subject}/MNINonLinear/brainmask_fs.nii.gz
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, November 9, 2018 at 7:18 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Jayasekera, Dinal"
<dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>, "Dierker,
Donna" <do...@wustl.edu<mailto:do...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
Here is the line from hcp_fix where it uses a 0.7mm mask:
$FSLDIR/bin/fslmaths veins -div `$FSLDIR/bin/fslstats veins -k
${FSL_FIXDIR}/mask_files/hcp_0.7mm_brain_mask -P 50` -mul 2.18 -thr 10 -min 50
-div 50 veins
https://github.com/Washington-University/HCPpipelines/blob/master/ICAFIX/hcp_fix#L159
So, the script hardcodes a path to a 0.7mm mask.
Tim
On Fri, Nov 9, 2018 at 7:13 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Yes you probably need to have bash instead of a non-bash shell. Perhaps fixing
that will solve the problem. As far as the resolution of the T1w and T2w,
presumably so long as they are the same resolution everything should work. We
have tested on 0.8mm human data and 0.5mm monkey data.
Matt.
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Date: Friday, November 9, 2018 at 3:53 PM
To: "Jayasekera, Dinal"
<dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>, Matt Glasser
<glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
This is the first problem I see in the text you pasted in the email:
Mask and image must be the same size
This looks like it will happen whenever your T1w and T2w are not 0.7mm, as it
specifically uses a 0.7mm mask. Someone else (Matt?) will need to say how this
is supposed to work.
Unfortunately, what I recommended was only for solving this error (and related):
flirt: symbol lookup error: flirt: undefined symbol: dgesdd_
I was hoping that the earlier errors were caused by a similar undefined symbol
error that you hadn't seen.
As for this one, for some reason hcp_fix asked for the ancient behavior of
/bin/sh at the top of the file, rather than /bin/bash:
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: 171:
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: [[: not found
Tim
On Fri, Nov 9, 2018 at 3:07 PM, Jayasekera, Dinal
<dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>> wrote:
Dear Tim,
I made the changes you recommended but I continue to receive the same
segmentation error I mentioned before.
Kind regards,
Dinal Jayasekera
PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering | Washington University in St. Louis
________________________________
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Sent: Thursday, November 8, 2018 6:03:10 PM
To: Jayasekera, Dinal
Cc: Dierker, Donna;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
FSL 6 requires openblas, and specifically a build of openblas that contains
lapack symbols, which is not the case for the system-supplied on in ubuntu
14.04. Via instructions on https://www.openblas.net/, clone the source from
github, build manually, and install to /usr/local (it is important to install
it there because of how we deal with matlab changing library paths - if you
don't want to install it there, you will need to resort to wrapper scripts
around fsl binaries, or other trickery), and run "ldconfig" so that it will be
found by default, like this (minorly edited from a container recipe I am
working with):
sudo apt-get install build-essential
git clone https://github.com/xianyi/OpenBLAS.git --branch release-0.3.0 --depth
5
cd OpenBLAS
#you could specify a TARGET to optimize for your cpu here
make
sudo make PREFIX=/usr/local install
sudo ldconfig
Tim
On Thu, Nov 8, 2018 at 1:36 PM, Jayasekera, Dinal
<dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>> wrote:
Dear Donna,
I apologize for the late reply. I've been trying different approaches to solve
the errors I've been receiving. I've attached the updated log files after
re-configuring the R packages. This was the output to stdout and stderr:
rfMRI_REST1_PA_hp2000.ica/mc:
total 32
drwxrwxr-x 2 functionalspinelab functionalspinelab 4096 Oct 31 19:12 .
drwxrwxr-x 6 functionalspinelab functionalspinelab 4096 Nov 7 15:57 ..
-rw-rw-r-- 1 functionalspinelab functionalspinelab 20936 Nov 7 15:57
prefiltered_func_data_mcf.par
rfMRI_REST1_PA_hp2000.ica/reg:
total 41680
drwxrwxr-x 2 functionalspinelab functionalspinelab 4096 Nov 7 15:57 .
drwxrwxr-x 6 functionalspinelab functionalspinelab 4096 Nov 7 15:57 ..
lrwxrwxrwx 1 functionalspinelab functionalspinelab 19 Nov 7 15:57
example_func.nii.gz -> ../mean_func.nii.gz
lrwxrwxrwx 1 functionalspinelab functionalspinelab 36 Nov 7 15:57
highres.nii.gz -> ../../../../T1w_restore_brain.nii.gz
-rw-rw-r-- 1 functionalspinelab functionalspinelab 149 Nov 7 15:57
highres2example_func.mat
-rw-rw-r-- 1 functionalspinelab functionalspinelab 42190921 Nov 7 15:57
veins.nii.gz
-rw-rw-r-- 1 functionalspinelab functionalspinelab 473780 Nov 7 15:57
veins_exf.nii.gz
lrwxrwxrwx 1 functionalspinelab functionalspinelab 25 Nov 7 15:57
wmparc.nii.gz -> ../../../../wmparc.nii.gz
hcp_fix: INFORM: functionmotionconfounds log file is to be named:
.fix.functionmotionconfounds.log instead of .fix.log
hcp_fix: DEBUG: current folder
/home/functionalspinelab/Desktop/Dinal/mystudy/NSI_12/MNINonLinear/Results/rfMRI_REST1_PA/rfMRI_REST1_PA_hp2000.ica/reg
Mask and image must be the same size
Image Exception : #63 :: No image files match: -mul
Image Exception : #22 :: Failed to read volume -mul
Error : No image files match: -mul
terminate called after throwing an instance of 'armawrap::AWException'
what(): Failed to read volume -mul
Error : No image files match: -mul
Aborted (core dumped)
hcp_fix: INFORM: running FIX
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: 171:
/home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: [[: not found
hcp_fix: INFORM: About to run:
/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/fix
rfMRI_REST1_PA_hp2000.ica
/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData
10 -m -h 2000
FIX Feature extraction for Melodic output directory: rfMRI_REST1_PA_hp2000.ica
create edge masks
run FAST
registration of standard space masks
flirt: symbol lookup error: flirt: undefined symbol: dgesdd_
extract features
FIX Classifying components in Melodic directory: rfMRI_REST1_PA_hp2000.ica
using training file:
/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData
and threshold 10
No valid labelling file specified
Could not find a supported file with prefix
"rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean"
Could not find a supported file with prefix
"rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn"
I'm receiving a segmentation error which is causing MATLAB to exit. Any
thoughts?
Kind regards,
Dinal Jayasekera
PhD Candidate | InSITE Fellow
Ammar Hawasli Lab
Department of Biomedical Engineering | Washington University in St. Louis
________________________________
From: Dierker, Donna
Sent: Saturday, November 3, 2018 7:39:51 AM
To: Jayasekera, Dinal
Cc: Glasser, Matthew; Harms, Michael;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
Check not only your standard output file, but also your standard error.
Do either indicate whether it is finding matlab/octave?
> On Nov 2, 2018, at 3:02 PM, Jayasekera, Dinal
> <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>> wrote:
>
> Dear Michael and Matt,
>
> I reconfigured R, updated sICA+FIX and FSL but I still continue to get the
> previous error:
>
> No valid labelling file specified
> Could not find a supported file with prefix
> "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean"
> Could not find a supported file with prefix
> "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean_vn"
>
>
> Do you have any other suggestions?
>
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> From: Jayasekera, Dinal
> Sent: Thursday, November 1, 2018 8:35:28 PM
> To: Glasser, Matthew; Harms, Michael;
> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
> Cc: NEUROSCIENCE tim
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Oh yes definitely not. I also upgraded my R packages.
>
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> From: Glasser, Matthew
> Sent: Thursday, November 1, 2018 8:33:58 PM
> To: Jayasekera, Dinal; Harms, Michael;
> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
> Cc: NEUROSCIENCE tim
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> That doesn’t discount Mike’s advice on needing to sort out R packages.
>
> Matt.
>
> From: "Jayasekera, Dinal"
> <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>
> Date: Thursday, November 1, 2018 at 8:32 PM
> To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Harms,
> Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>,
> "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
> Cc: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Matt,
>
> I will update my version of sICA+FIX as well and upgrade to FSL 6.0 and let
> you know how things change.
>
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
>
> From: Glasser, Matthew
> Sent: Thursday, November 1, 2018 6:56:26 PM
> To: Harms, Michael; Jayasekera, Dinal;
> hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
> Cc: NEUROSCIENCE tim
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Hi Dinal,
>
> Also make sure you have the absolutely latest version of sICA+FIX, as there
> were recent changes and upgrade to FSL 6.0. Finally, we are testing some
> updates to hcp_multi_run_fix that you will need to be using for your project,
> and we can let you know when that is available. For your project you will be
> cleaning all of the fMRI runs at the same time with multi-run fix.
>
> Matt.
>
> From:
> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
> on behalf of "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
> Date: Thursday, November 1, 2018 at 4:18 PM
> To: "Jayasekera, Dinal"
> <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>,
> "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
>
> Hi,
> Have you configured your R installation correctly, per the FSL FIX Wiki page?
>
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide
FIX/UserGuide - FslWiki - University of
Oxford<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide>
fsl.fmrib.ox.ac.uk<http://fsl.fmrib.ox.ac.uk>
Downloading and Installing FIX. Requirements: FSL. MATLAB (though see notes in
Introduction page), with official toolboxes: Statistics ; Signal Processing
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> -----------------------------------------------------------
> Associate Professor of Psychiatry
> Washington University School of Medicine
> Department of Psychiatry, Box
> 8134<https://maps.google.com/?q=8134+%0D%0A+660+South+Euclid+Ave&entry=gmail&source=g>
> 660 South Euclid
> Ave<https://maps.google.com/?q=8134+%0D%0A+660+South+Euclid+Ave&entry=gmail&source=g>.
> Tel: 314-747-6173
> St. Louis, MO 63110 Email:
> mha...@wustl.edu<mailto:mha...@wustl.edu>
>
> From:
> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
> on behalf of "Jayasekera, Dinal"
> <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>
> Date: Thursday, November 1, 2018 at 4:10 PM
> To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
> <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
> Subject: [HCP-Users] Debugging IcaFIxProcessingBatch.sh
>
> Dear HCP community,
>
> I am currently running the IcaFixProcessingBatch script on the data
> processing using the minimal functional pipelines. However, for each of my
> resting state conditions, I get the following error:
>
> /home/Desktop/Applications/fix1.066/fix: 252:
> /home/Desktop/Applications/fix1.066/fix: R: not found
> No valid labelling file specified
> Could not find a supported file with prefix
> "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean"
>
> Has anyone had any experience with a similar issue? Is this error indicative
> of a missing step from before?
>
> Kind regards,
> Dinal Jayasekera
>
> PhD Candidate | InSITE Fellow
> Ammar Hawasli Lab
> Department of Biomedical Engineering | Washington University in St. Louis
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you are
> not the intended recipient, be advised that any unauthorized use, disclosure,
> copying or the taking of any action in reliance on the contents of this
> information is strictly prohibited. If you have received this email in error,
> please immediately notify the sender via telephone or return mail.
> _______________________________________________
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> _______________________________________________
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> HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
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________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
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http://lists.humanconnectome.org/mailman/listinfo/hcp-users
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> library(party)
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo
Attaching package: 'zoo'
The following objects are masked from 'package:base':
as.Date, as.Date.numeric
Loading required package: sandwich
> library(e1071)
> library(kernlab)
Attaching package: 'kernlab'
The following object is masked from 'package:modeltools':
prior
> library(class)
> library(ROCR)
Loading required package: gplots
Attaching package: 'gplots'
The following object is masked from 'package:stats':
lowess
> library(randomForest)
randomForest 4.6-12
Type rfNews() to see new features/changes/bug fixes.
> library(MASS)
>
> # R CMD BATCH "--no-restore --args ${FIXDIR}/ ${MELOUT}/ Standard 0.1" ${FIXDIR}/fix_2_PREDICT.R ${MELOUT}/fix/logR_Standard_0.1.txt
>
> if (T) {
+ args <- commandArgs(TRUE)
+ path.to.fix <- args[[1]]
+ print(path.to.fix)
+ melodic.path <- args[[2]]
+ print(melodic.path)
+ weight.file.name <- args[[3]]
+ print(weight.file.name)
+ bin.thresh <- args[[4]]
+ print(bin.thresh)
+ #
+ #which.fix <- args[[5]]
+ #print(which.fix)
+ } else {
+ rm(list = ls())
+ path.to.fix <- "/Users/reza/Documents/Academic/FIX/fix1.02"
+ melodic.path <- "/Users/reza/Documents/Academic/FIX/raw_data/EXAMPLEL/20100509_151441IM-0015-140s015a001.ica"
+ weight.file.name <- "/Users/reza/Documents/Academic/FIX/raw_data/EXAMPLEL/TRAIN.RData"
+ bin.thresh <- 20
+ }
[1] "/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066"
[1] "rfMRI_REST1_PA_hp2000.ica"
[1] "/home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData"
[1] "10"
>
>
>
>
>
> if(substr(path.to.fix, nchar(path.to.fix), nchar(path.to.fix))!="/")
+ path.to.fix <- paste(path.to.fix, "/", sep = "")
> if(substr(melodic.path, nchar(melodic.path), nchar(melodic.path))!="/")
+ melodic.path <- paste(melodic.path, "/", sep = "")
> bin.thresh <- as.numeric(bin.thresh)
>
> load(weight.file.name)
> test.data <- read.csv(paste(melodic.path, "fix/features.csv", sep = ""), header = F)
> # drop the undesired features
> test.data <- test.data[, init.keep.list[-length(init.keep.list)]]
> # drop the zero-var features
> if (length(also.excl)) test.data <- test.data[, -also.excl]
> # make the feature numeric (i.e., not categorical, etc.)
> for(i in c(1:dim(test.data)[2])) test.data[,i] <- as.numeric(test.data[,i])
> names(test.data) <- test.features.names
>
>
> test.data.1 <- test.data # full
> test.data.2 <- test.data.1[, selected.features] # sub
> test.data.3 <- test.data.1[, test.features.types!=2] # temporal
> test.data.4 <- test.data.1[, test.features.types!=1] # spatial
> test.data.5 <- test.data.1[, (test.features.types!=2) & selected.features] # sub temporal
> test.data.6 <- test.data.1[, (test.features.types!=1) & selected.features] # sub spatial
>
> train.data.1 <- hcp.data # full
> train.data.2 <- hcp.data.sub # sub
> train.data.3 <- hcp.data.temporal # temporal
> train.data.4 <- hcp.data.spatial # spatial
> train.data.5 <- hcp.data.sub.temporal # sub temporal
> train.data.6 <- hcp.data.sub.spatial # sub spatial
>
>
> for(indx in c(1:6)) {
+ # SVM
+ eval(parse(text = paste("svm.rbf.prd",indx," <- attributes(predict(svm.rbf",indx,", test.data.",indx,", probability=T))$probabilities[,2]", sep = "")))
+ eval(parse(text = paste("svm.lin.prd",indx," <- attributes(predict(svm.lin",indx,", test.data.",indx,", probability=T))$probabilities[,2]", sep = "")))
+ eval(parse(text = paste("svm.pol.prd",indx," <- attributes(predict(svm.pol",indx,", test.data.",indx,", probability=T))$probabilities[,2]", sep = "")))
+
+ # Tree
+ eval(parse(text = paste("ctree", indx, " = ctree", indx, "@update()", sep = "")))
+ eval(parse(text = paste("ctree.prd.test",indx," <- treeresponse(ctree",indx,", newdata = test.data.",indx,")", sep = "")))
+ eval(parse(text = paste("ctree.prob.test",indx," <- c(1:length(ctree.prd.test",indx,"))", sep = "")))
+ eval(parse(text = paste("for(i in c(1:length(ctree.prob.test",indx,"))){ctree.prob.test",indx,"[i] <- ctree.prd.test",indx,"[[i]][2]}", sep = "")))
+
+ # KNN
+ eval(parse(text = paste("tmp <- knn(train.data.",indx,"[,-dim(train.data.",indx,")[2]], test.data.",indx,", train.data.",indx,"[,dim(train.data.",indx,")[2]], k = k.knn, prob = T)", sep = "")))
+ eval(parse(text = paste("knn.test",indx," <- attributes(tmp)", sep = "")))
+ eval(parse(text = paste("knn.test",indx,"$prob[tmp==0] <- 1-knn.test",indx,"$prob[tmp==0]", sep = "")))
+ }
>
> df.test.tmp <- data.frame(knn6 = knn.test6$prob,
+ tre6 = ctree.prob.test6,
+ rbf6 = svm.rbf.prd6,
+ lin6 = svm.lin.prd6,
+ pol6 = svm.pol.prd6,
+ knn5 = knn.test5$prob,
+ tre5 = ctree.prob.test5,
+ rbf5 = svm.rbf.prd5,
+ lin5 = svm.lin.prd5,
+ pol5 = svm.pol.prd5,
+ knn4 = knn.test4$prob,
+ tre4 = ctree.prob.test4,
+ rbf4 = svm.rbf.prd4,
+ lin4 = svm.lin.prd4,
+ pol4 = svm.pol.prd4,
+ knn3 = knn.test3$prob,
+ tre3 = ctree.prob.test3,
+ rbf3 = svm.rbf.prd3,
+ lin3 = svm.lin.prd3,
+ pol3 = svm.pol.prd3,
+ knn2 = knn.test2$prob,
+ tre2 = ctree.prob.test2,
+ rbf2 = svm.rbf.prd2,
+ lin2 = svm.lin.prd2,
+ pol2 = svm.pol.prd2,
+ knn1 = knn.test1$prob,
+ tre1 = ctree.prob.test1,
+ rbf1 = svm.rbf.prd1,
+ lin1 = svm.lin.prd1,
+ pol1 = svm.pol.prd1
+ )
>
>
> if(F) { # TREE, which.fix=='T'
+ fusion.tree.prd.testp <- simplify2array(treeresponse(fusion.tree, newdata = df.test.tmp))[2,]
+ }
>
> if(T) { # RF, which.fix=='F'
+ fusion.tree.prd.testp <- predict(fusion.tree, newdata = df.test.tmp, type="prob")[,2]
+ }
>
> if(F) { # SVM, RBF, which.fix=='R'
+ fusion.tree.prd.testp <- attributes(predict(fusion.tree, newdata = df.test.tmp, probability=T))$probabilities
+ fusion.tree.prd.testp <- fusion.tree.prd.testp[,which(colnames(fusion.tree.prd.testp)=='1')]
+ }
>
> if(F) { # SVM, LIN, which.fix=='L'
+ fusion.tree.prd.testp <- attributes(predict(fusion.tree, newdata = df.test.tmp, probability=T))$probabilities
+ fusion.tree.prd.testp <- fusion.tree.prd.testp[,which(colnames(fusion.tree.prd.testp)=='1')]
+ }
>
>
> bin.thresh <- bin.thresh/100
> weight.file.name.bits <- strsplit(weight.file.name, "/")[[1]]
> weight.file.name.bits <- weight.file.name.bits[length(weight.file.name.bits)]
> weight.file.name.bits <- substr(weight.file.name.bits, 1, nchar(weight.file.name.bits)-6)
> sink(paste(melodic.path, "fix4melview_", weight.file.name.bits, "_thr", bin.thresh*100, ".txt", sep = ""))
> cat("filtered_func_data.ica")
> cat("\n")
> end.string <- "["
> anynoise <- 0
> for(i in c(1:length(fusion.tree.prd.testp))){
+ if(fusion.tree.prd.testp[i]< bin.thresh){
+ cat(paste(i, ", ", "Unclassified Noise", ", ", "True", sep = ""))
+ cat("\n")
+ end.string <- paste(end.string, i, ", ", sep = "")
+ anynoise <- 1
+ }else if(fusion.tree.prd.testp[i]>.5){
+ cat(paste(i, ", ", "Signal", ", ", "False", sep = ""))
+ cat("\n")
+ }else{
+ cat(paste(i, ", ", "Unknown", ", ", "False", sep = ""))
+ cat("\n")
+ }
+ }
> if (anynoise>0) {
+ end.string <- substr(end.string, 1, nchar(end.string)-2)
+ }
> end.string <- paste(end.string, "]\n", sep = "")
> cat(end.string)
> sink()
>
>
> proc.time()
user system elapsed
23.504 6.784 21.491
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
TR =
0.8000
{Undefined function or variable 'gifti'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 46)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
}
>>
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
rfMRI_REST1_PA_hp2000.ica/
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End of Matlab Script
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
rfMRI_REST1_PA_hp2000.ica/
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End of Matlab Script
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
rfMRI_REST1_PA_hp2000.ica/
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End of Matlab Script
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
rfMRI_REST1_PA_hp2000.ica/
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End of Matlab Script
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
rfMRI_REST1_PA_hp2000.ica/
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End of Matlab Script
< M A T L A B (R) >
Copyright 1984-2018 The MathWorks, Inc.
R2018b (9.5.0.944444) 64-bit (glnxa64)
August 28, 2018
For online documentation, see https://www.mathworks.com/support
For product information, visit www.mathworks.com.
rfMRI_REST1_PA_hp2000.ica/
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End of Matlab Script
--------------------------------------------------------------------------------
std::terminate() detected at Mon Nov 12 15:14:47 2018 -0600
--------------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled - No sandbox or build area path
Crash Mode : continue (default)
Default Encoding : US-ASCII
Deployed : false
Desktop Environment : Unity
GNU C Library : 2.19 stable
Graphics Driver : Unknown software
MATLAB Architecture : glnxa64
MATLAB Entitlement ID : 2345557
MATLAB Root : /usr/local/MATLAB/R2018b
MATLAB Version : 9.5.0.944444 (R2018b)
OpenGL : software
Operating System : Ubuntu 14.04.5 LTS
Process ID : 82001
Processor ID : x86 Family 6 Model 85 Stepping 4, GenuineIntel
Session Key : 3e1dd74b-df87-4b60-88b9-3d8f730c3e4e
Static TLS mitigation : Enabled: Full
Window System : No active display
Fault Count: 1
Abnormal termination
Register State (captured):
RAX = 0000000000000000 RBX = 00007fde219651f8
RCX = 0000000000000000 RDX = 00007fde21948bf8
RSP = 00007fddfb3550a0 RBP = 00007fddfb355460
RSI = 00007fde2170d5a5 RDI = 00007fddfb3550b0
R8 = 00007fde21955168 R9 = 00007fde245ea740
R10 = 0000000000000000 R11 = 0000000000000000
R12 = 00007fde21955168 R13 = 00007fddfb355820
R14 = 00007fddfb355d10 R15 = 00007fddfb355ce0
RIP = 00007fde2167049e EFL = 0000000000000000
CS = 0000 FS = 0000 GS = 0000
Stack Trace (captured):
[ 0] 0x00007fde216682d3
bin/glnxa64/libmwfl.so+00762579
[ 1] 0x00007fde216684cc
bin/glnxa64/libmwfl.so+00763084
_ZN10foundation4core4diag15stacktrace_base7captureEm+00000028
[ 2] 0x00007fde2166ac1c
bin/glnxa64/libmwfl.so+00773148
[ 3] 0x00007fde12179e5a
bin/glnxa64/libmwmcr.so+01093210
[ 4] 0x00007fde1217c47b
bin/glnxa64/libmwmcr.so+01102971
[ 5] 0x00007fde1217c77a
bin/glnxa64/libmwmcr.so+01103738
[ 6] 0x00007fde1217cd4d
bin/glnxa64/libmwmcr.so+01105229
[ 7] 0x00007fde1217dd07
bin/glnxa64/libmwmcr.so+01109255
[ 8] 0x00007fde243053a6
/usr/local/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00582566
[ 9] 0x00007fde243043d9
/usr/local/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00578521
[ 10] 0x00007fde24304d2d
/usr/local/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00580909
__gxx_personality_v0+00000717
[ 11] 0x00007fde2406ff03
/usr/local/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00065283
[ 12] 0x00007fde2407026b
/usr/local/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00066155
_Unwind_RaiseException+00000251
[ 13] 0x00007fde243055fb
/usr/local/MATLAB/R2018b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00583163
__cxa_throw+00000091
[ 14] 0x00007fde15554532
/usr/local/MATLAB/R2018b/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoFoundation.so.48+00902450
_ZN4Poco10MemoryPool7releaseEPv+00000162
[ 15] 0x00007fde15b4423f
/usr/local/MATLAB/R2018b/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00639551
_ZN4Poco3Net19HTTPHeaderStreamBufD2Ev+00000031
[ 16] 0x00007fde15b44633
/usr/local/MATLAB/R2018b/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00640563
_ZN4Poco3Net21HTTPHeaderInputStreamD1Ev+00000067
[ 17] 0x00007fde15b37fa7
/usr/local/MATLAB/R2018b/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00589735
_ZN4Poco3Net17HTTPClientSession15receiveResponseERNS0_12HTTPResponseE+00000199
[ 18] 0x00007fde00e50db7
bin/glnxa64/libmwflhttpclient.so+00134583
[ 19] 0x00007fde00e4b108
bin/glnxa64/libmwflhttpclient.so+00110856
[ 20] 0x00007fde00e454ad
bin/glnxa64/libmwflhttpclient.so+00087213
_ZNK10foundation10httpclient16WebServiceClient23doWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiS9_+00000061
[ 21] 0x00007fde00e46739
bin/glnxa64/libmwflhttpclient.so+00091961
_ZNK10foundation10httpclient16WebServiceClient25makeWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiiS9_+00000121
[ 22] 0x00007fde0137c22f
bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00516655
[ 23] 0x00007fde01380448
bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00533576
[ 24] 0x00007fde01368da0
bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00437664
[ 25] 0x00007fde013dd3aa
bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00914346
[ 26] 0x00007fde0136eeaa
bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00462506
[ 27] 0x00007fde2222ce75
bin/glnxa64/libmwms.so+02625141
[ 28] 0x00007fde0136eb06
bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00461574
[ 29] 0x00007fde23461c0d
/usr/local/MATLAB/R2018b/bin/glnxa64/libmwboost_thread.so.1.65.1+00080909
[ 30] 0x00007fde224d4184
/lib/x86_64-linux-gnu/libpthread.so.0+00033156
[ 31] 0x00007fde23d9503d
/lib/x86_64-linux-gnu/libc.so.6+01040445 clone+00000109
[ 32] 0x0000000000000000
<unknown-module>+00000000
** This crash report has been saved to disk as
/home/functionalspinelab/matlab_crash_dump.82001-1 **
MATLAB is exiting because of fatal error
Killed
