Hi Christian,
It works perfectly now, thank you very much for all your help!
Best,
John
--------------------
John Broulidakis
Developmental Brain-Behaviour Laboratory
University of Southampton
On 20/04/2014 22:06, "Christian F. Beckmann" <[log in to unmask]>
wrote:
>Hi,
>
>Ad 1: I suspect that you used the (standard) 4mm resampling resolution?
>If so then all the results are in MNI152 space, albeit in 4mm isotropic
>voxel size. If you want to show these in the space of the 2mm MNI152
>space you’ll need to resample using flirt.
>
>Ad2: neither ICA nor DR really loo at FOV or anything else, they just
>work with whatever is provided. You should certainly check that all
>registrations worked. ICA and Dr then will provided results in the
>lowest-common-denominator space, ie.. in the space where all subjects
>have data.
>
>hth
>Christian
>
>
>
>On 20 Apr 2014, at 19:58, Broulidakis M.J. <[log in to unmask]> wrote:
>
>> 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
>>>
>
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