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FSL  June 2018

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Subject:

problem with FIX

From:

Eleni <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 5 Jun 2018 17:25:29 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (198 lines)

Dear Experts, 

I have previously ran FIX successfully using the Matlab configuration and necessary R packages. Now, after reinstallation on a new computer, I am getting the dreaded “No valid labelling file specified” error. I also receive the errors below. 

I have searched the forum for the error I’m receiving from the logMatlab text file (“Assignment has more non-singleton rhs dimensions than non-singleton subscripts”) but have not come across a thread with a similar issue (although I did come across many who also didn’t have “valid labelling file specified” but for different reasons that I’ve now checked on my end). 

Any help would be greatly appreciated!

Very best, 
Eleni

=========================

Software details: 
Sierra 10.12.6, Matlab R2017a, and I downgraded R to 3.3.3 and installed the following packages:
  kerlab 0.9-24
  ROCR 1.0-7
  class 7.3-14
  party 1.2-4
  e1071 1.6-8
  randomForest 4.6-12
I previously had the most up-to-date version of R with all necessary packages (current versions) and FIX didn’t work, so I downgraded since I read the earlier version was recommended for FIX.

==========================

Command: 
/Users/Eleni/Documents/FSL/fix1.06/fix SubID.ica /Users/Eleni/Documents/FSL /fix1.06/training_files/Standard.RData 20

==========================

Error from terminal:
/Users/Eleni/Documents/FSL/fix1.06/fix SubID.ica/ /Users/Eleni/Documents/FSL/fix1.06/training_files/Standard.RData 20
FIX Feature extraction for Melodic output directory: SubID.ica/
 create edge masks
 run FAST
 registration of standard space masks
 extract features
FIX Classifying components in Melodic directory: SubID.ica/ using training file: /Users/Eleni/Documents/FSL/fix1.06/training_files/Standard.RData and threshold 20
FIX features not already generated, so creating them now.
FIX Feature extraction for Melodic output directory: SubID.ica/
 create edge masks
 run FAST
 registration of standard space masks
 extract features
No valid labelling file specified

==========================

Note: “/.fix.log” did not generate

==========================

Error from logMatlab.txt:
			< M A T L A B (R) >
                  Copyright 1984-2017 The MathWorks, Inc.
                   R2017a (9.2.0.556344) 64-bit (maci64)
                               March 27, 2017

 
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
 
SubID.ica/
    29     1

Error Time: 06/05/2018 11:01:26
Assignment has more non-singleton rhs dimensions than non-singleton subscripts
 

                            < M A T L A B (R) >
                  Copyright 1984-2017 The MathWorks, Inc.
                   R2017a (9.2.0.556344) 64-bit (maci64)
                               March 27, 2017

 
For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.
 
SubID.ica/
    29     1

Error Time: 06/05/2018 11:05:04
Assignment has more non-singleton rhs dimensions than non-singleton subscripts


==========================


Error from .fix_2b_predict.log:

 R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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.

  Natural language support but running in an English locale

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] "/Users/Eleni/Documents/FSL/fix1.06"
[1] "SubID.ica/"
[1] "/Users/Eleni/Documents/FSL/fix1.06/training_files/Standard.RData"
[1] "20"
> 
> 
> 
> 
> 
> 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)
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'SubID.ica/fix/features.csv': No such file or directory
Execution halted

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