Hello Taylor, 

Thank you for your response. 

Within my /data/datafile/training directory, I have 00001.txt, 00002.txt, 00003.txt ... 00010.txt ( which includes all of the component labels for each sample and a last line that follows the [1, 5, 8, ...] format.) 

The hidden files within that directory show only the .Rlog error files. No .csv files are present. Do I need to write a script to convert these .txt files into .csv or have I configured my data incorrectly? 

Thank you, 

Yujie D.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Taylor Hanayik <[log in to unmask]>
Sent: Friday, June 28, 2019 3:58 AM
To: [log in to unmask]
Subject: Re: [FSL] FSL FIX - No .RData Produced
 
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Hi Yujie, 

You have an “NA” in place of the filename that’s trying to be read in:

/data/datafile/training/NA

Can you check the directory: /data/datafile/training/ and confirm that there are csv files listed?


Cheers,

Taylor Hanayik


Taylor Hanayik PhD
Analysis Research Software Engineer
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]





On 27 Jun 2019, at 21:38, Yujie <[log in to unmask]> wrote:

Hello,

I am having some difficulty creating a training set for FSL Fix. I have gone through the README, but cannot seem to find a way to get an .RDATA file.

Specifically, after running:

fix -t <training> <melodic.ica> ...

I am given the following errors:

Image Exception : #22 :: ERROR: Could not open image melodic.ica/reg/highres
terminate called after throwing an instance of 'RBD_Common::BaseException'
/apps/fix/fix_0b_apply_fast: line 21: 267955 Aborted (core dumped)

The above error occurs for both fast and flirt processes within FSL FIX.

Furthermore, I am given an output directory called "training." Within this "training" directory, I have the samplename.txt files that show all of the hand labeled components. The hidden files reveal that at the end of each .Rlog for each sample, I receive the following error:

Error in file(fie, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/data/datafile/training/NA' : No such file or directory
Execution halted.

What am I missing here? I have prepared all of the hand_labels_noise.txt files for each <melodic.ica>. Is there any way to trouble shoot this to obtain a training data set?

Thank you,

Yujie

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