Hi
nope, you should be able to use the entire melodic_IC (4D file). You
need to make sure, though, that you;re running it against the correct
file. If all the pre-processing was done from the melodic gui in a
group analysis then the correct filtered_func_data is the one in the
reg_standard sub-directory. Check the file .filenames.txt to see which
files the group melodic run used as inputs and take these for the
first regression. The alternative to all of this is not perform the
first regression and only collect the subject-specific time courses
from all the tXX.txt files in the melodic report column-wise into a
single text file (which is a bit of a paint I'm afraid).
hth
Christian
On 14 Nov 2008, at 23:25, Christopher Bell wrote:
> Thanks for your help. The output for my first regression has
> finished now, but I am unable to open the file. I don't think it
> worked properly. I have done something similar to this before, but I
> used the timecourses from melodic_mix instead of melodic_IC.nii.gz
> Do I need to extract single volumes from melodic_IC.nii.gz for this
> to work? Thanks for your help.
>
> Chris Bell
>
>
> On Nov 14 2008, Christian F. Beckmann wrote:
>
>> Hi
>>
>> You can cut down on memory use if you also specify the correct
>> mask usign the -m option to fsl_glm.
>> Also, the second regression can actually be performed against the
>> filtered data in native space (if available) so that denoising can
>> then be carried out in native space
>> hth
>> Christian
>>
>>
>> On 14 Nov 2008, at 23:07, Christopher Bell wrote:
>>
>>> Christian,
>>>
>>> I tried this first regression step on a group dataset I had
>>> already run through melodic, against a subject's 4D
>>> filtered_func_data in global space 2x2x2 mm resolution, and was
>>> finding it quite memory intensive. It was using up to 7GB of
>>> memory to run this application, is this what you would expect?
>>>
>>> Chris
>>>
>>>
>>>
>>>
>>>
>>> On Nov 14 2008, Christian F. Beckmann wrote:
>>>
>>>> Hi Jim,
>>>>
>>>> For de-noising to work you need subject-specific spatial maps
>>>> and time courses. You can get them quite easily by regressing
>>>> the subject specific data sets against the melodic_IC file and
>>>> then re- regressing the same data set against the output from
>>>> the first regression:
>>>>
>>>> (i) fsl_glm -i filtered_func_X -d group_melodic_IC -o timecourses_X
>>>>
>>>> (ii) fsl_glm -i filtered_func_X -d timecourses_X -o maps_X
>>>>
>>>> After this you can simply follow the normal melodic instructions
>>>> and use timecourses_X and maps_X for each data set X
>>>>
>>>> hth
>>>> Christian
>>>>
>>>>
>>>>
>>>>
>>>> On 11 Nov 2008, at 20:18, James Porter wrote:
>>>>
>>>>> Hello-
>>>>>
>>>>> On the Melodic instructions page there are clear instructions
>>>>> on how to denoise a functional volume at the single-subject
>>>>> single- scan level. However, if one wants to denoise a group-
>>>>> wise data set after running tensor-ICA, is there an equivalent
>>>>> procedure?
>>>>>
>>>>> --
>>>>> ---------
>>>>> Jim Porter
>>>>> Graduate Student
>>>>> Clinical Science & Psychopathology Research
>>>>> University of Minnesota
>>>>
>>>>
>>>> _______________________________________________
>>>> Christian F. Beckmann, DPhil
>>>> Senior Lecturer, Clinical Neuroscience Department
>>>> Division of Neuroscience and Mental Health
>>>> Imperial College London, Hammersmith Campus
>>>> Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK
>>>> Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548
>>>> Email: [log in to unmask]
>>>> http://www.imperial.ac.uk/medicine/people/c.beckmann/
>>>>
>>>> Senior Research Fellow, FMRIB Centre
>>>> University of Oxford
>>>> JR Hospital - Oxford OX3 9DU
>>>> Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717
>>>> Email: [log in to unmask]
>>>> http://www.fmrib.ox.ac.uk/~beckmann
>>>>
>>
>>
>> _______________________________________________
>> Christian F. Beckmann, DPhil
>> Senior Lecturer, Clinical Neuroscience Department
>> Division of Neuroscience and Mental Health
>> Imperial College London, Hammersmith Campus
>> Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK
>> Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548
>> Email: [log in to unmask]
>> http://www.imperial.ac.uk/medicine/people/c.beckmann/
>>
>> Senior Research Fellow, FMRIB Centre
>> University of Oxford
>> JR Hospital - Oxford OX3 9DU
>> Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717
>> Email: [log in to unmask]
>> http://www.fmrib.ox.ac.uk/~beckmann
>>
_______________________________________________
Christian F. Beckmann, DPhil
Senior Lecturer, Clinical Neuroscience Department
Division of Neuroscience and Mental Health
Imperial College London, Hammersmith Campus
Rm 419, Burlington Danes Bldg, Du Cane Road, London W12 0NN, UK
Tel.: +44 (0)20 7594 6685 --- Fax: +44 (0)20 7594 6548
Email: [log in to unmask]
http://www.imperial.ac.uk/medicine/people/c.beckmann/
Senior Research Fellow, FMRIB Centre
University of Oxford
JR Hospital - Oxford OX3 9DU
Tel.: +44 (0)1865 222551 --- Fax: +44 (0)1865 222717
Email: [log in to unmask]
http://www.fmrib.ox.ac.uk/~beckmann
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