Hi Stephanie,
That's not quite right. Take a look at the registration practical (http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html) and the FNIRT / FLIRT documentation.
David
On Feb 11, 2013, at 2:07 PM, Stephanie <[log in to unmask]> wrote:
> Hi David,
>
> Would the following make sense?
> bet my_structural my_betted_structural
> fnirt -ref my_betted_structural -refmask MNI152_T1_2mm.nii -in
> data/sub1/run1/filtered_func_data.nii.gz -dof 12
>
> Do you have a recommendation on how to best output the data so that it
> can be run in melodic?
>
> Thank you,
> Stephanie
>
>
> On Mon, Feb 11, 2013 at 12:18 AM, David V. Smith
> <[log in to unmask]> wrote:
>> Not quite. You'll first want to normalize each input (e.g.,
>> /data/sub1/run1/filtered_func_data.ica/filtered_func_data.nii.gz) with FLIRT
>> or FNIRT. Then you'll make a list of the resulting files.
>>
>> David
>>
>>
>>
>>
>>
>> On Feb 10, 2013, at 11:20 PM, Stephanie wrote:
>>
>> I'm trying to run the following cmd on ICA data (already run through
>> Feat) to concatenate multiple runs across multiple subjects.
>> melodic -i list_of_funcs.txt -o output.ica -v --nobet --tr=2 --report
>> --guireport=./report.html -d 25 --mmthresh=0.5 --Ostats -a concat
>>
>> My question is on the list_of_funcs.txt. I understand that I should
>> list all the input files in an ascii text file (one input per line).
>> So would the following format make sense?
>> sub1/run1/filtered_func_data.ica
>> sub1/run2/filtered_func_data.ica
>> sub2/run1/filtered_func_data.ica
>> sub2/run2/filtered_func_data.ica
>>
>>
>> --------------------------------------------
>> David V. Smith, Ph.D.
>> Postdoctoral Fellow, Delgado Lab
>> Department of Psychology
>> Rutgers University
>> Newark, NJ 07102
>> --------------------------------------------
>>
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David V. Smith, Ph.D.
Postdoctoral Fellow, Delgado Lab
Department of Psychology
Rutgers University
Newark, NJ 07102
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