If you know name of the package at the top of the dependency tree you can try:

 

install.packages("packagename", dependencies = TRUE)

 

Greetings,

Jacek Jońca-Jasiński

 

TTU_DblT_fl4C

 

Jacek Jońca-Jasiński, Ph.D.

 

Director

 

The Graduate School

Administration Bldg 328 / 40D  |  2625 Memorial Circle

Box 41030 | Lubbock, TX 79409-1030

T 806.834.3348 | F 806.742.4038

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Michel Thiebaut de Schotten
Sent: Thursday, July 3, 2014 3:29 AM
To: [log in to unmask]
Subject: Re: [FSL] FIX issue

 

I installed the required packages as indicated in the readme file, but FIX seems to require extra R packages that I'm installing now.

The issue is that I have to relaunch FIX every time in order to know which package is missing... I've been doing that repetitively since yesterday. Is there a faster way to do this?

 

Cheers,

Michel



Sent from my iPhone


On 3 Jul 2014, at 09:05, Andreas Bartsch <[log in to unmask]> wrote:

Have you installed the packages or did you just do the base R installation?

Cheers,

Andreas

 

Von: Michel Thiebaut <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Mittwoch, 2. Juli 2014 18:38
An: <[log in to unmask]>
Betreff: Re: [FSL] FIX issue

 

looks like it Matt yes :).

The report is giving these packages one by one (I have to relaunch fix everytime...) so I'll send the list of package I was missing at the end of the day for future reference.

 

Kind regards,

 

michel

 

On Wed, Jul 2, 2014 at 5:32 PM, Matt Glasser <[log in to unmask]> wrote:

Looks like you are both missing R packages?

 

Peace,

 

Matt.

 

From: Michel Thiebaut <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, July 2, 2014 at 11:14 AM
To: <[log in to unmask]>
Subject: Re: [FSL] FIX issue

 

Don't know if it helps but my .fix_2b_predict.log says:

 

 

R version 3.1.0 (2014-04-10) -- "Spring Dance"

Copyright (C) 2014 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin13.1.0 (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: zoo

Error: package ‘zoo’ could not be loaded

In addition: Warning message:

In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :

  there is no package called ‘zoo’

Execution halted

 

On Wed, Jul 2, 2014 at 5:03 PM, Ricarda Menke <[log in to unmask]> wrote:

Hi Ludo,

 

I'm experiencing a similar problem. I also didn't get a .fix file, but there is a .fix_2b_predict.log file that contains the following message (even though the coin.so seems to exist in the specified directory):

-----

cat .fix_2b_predict.log 

 

R version 3.1.0 (2014-04-10) -- "Spring Dance"

Copyright (C) 2014 The R Foundation for Statistical Computing

Platform: x86_64-redhat-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.

 

  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: survival

Loading required package: splines

Loading required package: grid

Loading required package: modeltools

Loading required package: stats4

Loading required package: coin

Loading required package: mvtnorm

Error in dyn.load(file, DLLpath = DLLpath, ...) : 

  unable to load shared object '/opt/fmrib/R/site-library/coin/libs/coin.so':

  libRblas.so: cannot open shared object file: No such file or directory

Error: package ‘coin’ could not be loaded

Execution halted

-----

 

Cheers,

Ricarda

 

 

 

On 2 Jul 2014, at 16:49, Michel Thiebaut <[log in to unmask]> wrote:



Dear Ludovica their is no .fix file in the folder unfortunately

(I tried open -a TextEdit .fix)

 

I also installed R with all the toolboxes required. I have no idea what to try next.

Thanks a lot for your help,

 

michel

 

On Wed, Jul 2, 2014 at 4:27 PM, Ludovica Griffanti <[log in to unmask]> wrote:

Hi Michel,

try to have a look at the file:    output.ica/.fix 

It should be a log file containing general errors in the whole fix pipeline.

I guess this time is a problem related to the classification part (done with R)

Hope that helps.

 

Best,

Ludovica

 

---

Dr Ludovica Griffanti, PhD

Analysis Postdoctoral Research Assistant
Oxford Centre for Functional MRI of the Brain (FMRIB)
Nuffield Department of Clinical Neurosciences, University of Oxford
John Radcliffe Hospital
Oxford, OX3 9DU, UK
email: [log in to unmask]

 

On 2 Jul 2014, at 12:41, Michel Thiebaut <[log in to unmask]> wrote:



Thanks a lot Ludovica,

I did correct Matlab setup and now the output.ica/fix/logMatlab.txt does not report any error.

 

but still fix doesn't work and report

 

Michels-MacBook-Air:testfix michelthiebautdeschotten$ /usr/local/fix1.06/fix  output.ica  /usr/local/fix1.06/training_files/Standard.RData  20 -m

FIX Feature extraction for Melodic output directory: output.ica

 create edge masks

 run FAST

 registration of standard space masks

 extract features

FIX Classifying components in Melodic directory: output.ica using training file: /usr/local/fix1.06/training_files/Standard.RData and threshold 20

No valid labelling file specified

 

Any other suggestion?

thanks a lot for your time,

 

kind regards,

 

michel

 

On Wed, Jul 2, 2014 at 9:44 AM, Ludovica Griffanti <[log in to unmask]> wrote:

Hi Michel,

the problem is during features extraction, which is done with MATLAB/Octave.

You can find more details about the error in the file: output.ica/fix/logMatlab.txt
You will probably have to check your Matlab/Octave setup following the instruction in the README file provided with the tool.

 

 

Best,

Ludovica

 

---

Dr Ludovica Griffanti, PhD

Analysis Postdoctoral Research Assistant
Oxford Centre for Functional MRI of the Brain (FMRIB)
Nuffield Department of Clinical Neurosciences, University of Oxford
John Radcliffe Hospital
Oxford, OX3 9DU, UK
email: [log in to unmask]

 

On 1 Jul 2014, at 19:37, Michel Thiebaut <[log in to unmask]> wrote:



Dear Experts,

 

I tried to launch FIX today following the instructions online but it did not produce the final filtered functional data.

 

This is the message the terminal gives

 

/usr/local/fix1.06/fix  output.ica /usr/local/fix1.06/training_files/Standard.RData  20 -m

 

FIX Feature extraction for Melodic output directory: output.ica

 create edge masks

 run FAST

 registration of standard space masks

 extract features

FIX Classifying components in Melodic directory: output.ica using training file: /usr/local/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: output.ica

 create edge masks

 run FAST

 registration of standard space masks

 extract features

No valid labelling file specified

 

I was wondering whether you could tell me what I did wrong.

Thanks a lot for your time.

Kind regards

 

michel