Fixelcfestats error

#1

Hi all,

I have a silly question.

I run the commands below:

set working_data=$HOME/COBRE_2/Fixel_Based_Analysis/
set log_fc_files=$HOME/COBRE_2/Fixel_Based_Analysis/log_fc_files
set file="awk 'FNR==$SGE_TASK_ID' ${log_fc_files}"
set subj_name=${file:t}
fixelcfestats ${working_data}/log_fc_files ${working_data}/output_analysis_fixel_mask.msf ${working_data}/input_design_matrix ${working_data}/output_contrast_matrix ${working_data}/output_tracks_2_million_sift.tck ${subj_name}

the log_fc_files textfile looks like this
A00024546.mif.gz_output_log_fc.msf
A00024568.mif.gz_output_log_fc.msf
A00024663.mif.gz_output_log_fc.msf
A00024684.mif.gz_output_log_fc.msf

I know the naming is messy. I was a bit lazy scripting this properly. I am sorry :innocent:

design matrix looks like this
1 0
1 0
1 0
1 0

contrast file looks like this
-1 1

and my error is the following
fixelcfestats: [ERROR] input fixel image not found: /home/k1465455/COBRE_2/Fixel_Based_Analysis/A00000456.mif.gz_output_log_fc.msf

In the next file the characters preceding the filename do not appear. Does this mean that somehow they are hidden?
If so, are there any suggestions about text editors that show hidden characters?

Cheers,
Vasiliki

#2

Hi all,

I just wanted to let you know that my issue is now fixed with the help of jdtournier. The issue seemed to be the character encoding and we had to convert the file from UTF-8 to ASCII format using

less log_fc_files
iconv -f utf-8 -t ascii//TRANSLIT < log_fc_files > log_fc_files_fixed

Cheers,
Vasiliki

Fixelcfestats: error in number of input files