Hi Christian,

Thank you so much for your help! As you suggested I didn¹t input the
complete path and just started from the directory I was in when I booted
up melodic.
 

I have two more questions and I would be grateful if you or anyone could
give me a little more advice. Due to some errors during data collection a
lot of my resting state data has (to varying degrees) the vertex of the
brain missing.
 

I have completed group ICA and I am trying to view the file melodic_IC in
the standard space. However despite the functional data being registered
(I assume successfully) to the standard MNI 2mm brain as part of group ICA
I cannot seem to overlay the two (perhaps because of the missing data and
the two files not having the same base dimensions?) So my questions are,
1) is it possible to view the file melodic_IC in the standard space given
some of the functional data is missing? And 2) would having a small chunk
of functional data missing interfere with processes like duel regression?
(Fortunately, the areas missing do not encompass any of my regions of
interest).
 

Many thanks and once again happy Easter,
 

John  


--------------------

John Broulidakis	
Developmental Brain-Behaviour Laboratory
University of Southampton





On 19/04/2014 09:15, "Christian F. Beckmann" <[log in to unmask]>
wrote:

>Hi
>
>So ŒC/subj_011/SE9/rest¹  is the complete path to your input file? If so
>then I suggest pre-processing all data separately and running melodic
>from the command line insteadŠ then it¹s easier to figure out if the
>pre-processing or the melodic I/O is not happyŠ
>hth
>Christian
>
>
>On 17 Apr 2014, at 16:28, Broulidakis M.J. <[log in to unmask]> wrote:
>
>> Dear FSL experts,
>>  
>> I desperately need your help! I am trying to preform group ICA on
>>resting state data using Melodic and have been running into a serious
>>difficulty. While melodic seems to work fine for single subject analysis
>>or even group ICA on only a limited number of participants it is unable
>>to run my entire data set (n=73).
>>  
>> At the very start of the analysis the progress report appears to freeze
>>at:
>>  
>> /bin/cp /tmp/feat_5cCO9X.fsf design.fsf
>>  
>> mkdir .files;cp /Applications/fsl/doc/fsl.css .files;ln -s
>>/Applications/fsl/doc/images .files/images
>>  
>> Melodic progress report for the first subject generates this error
>>message:
>>  
>> /Applications/fsl/bin/fslmaths C/subj_011/SE9/rest
>>prefiltered_func_data -odt float
>> Cannot open volume C/subj_011/SE9/rest for reading!
>>  
>> FATAL ERROR ENCOUNTERED
>> Cannot open volume C/subj_011/SE9/rest for reading!
>>     while executing
>> "if { [ catch {
>>  
>> for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
>>     switch -- [ lindex $argv $argindex ] {
>>  
>>      -I {
>>          incr argin..."
>>     (file "/Applications/fsl/bin/feat" line 119)
>>  
>> I have no idea what it means by ³cannot open volume for reading²
>>because, as mentioned previously, the dataset (including subj_011) works
>>fine for many other types of analysis. If anyone else has had a similar
>>problem or may suspect what the matter is please let me know.
>>  
>> Thanks in advance and a happy Easter,
>>  
>> John
>>  
>> --------------------
>> 
>> John Broulidakis	
>> Developmental Brain-Behaviour Laboratory
>> University of Southampton
>