Hi Steve,
Thank you.
I looked into my course materials again, but I am still confused on the exact order of using the commands.
Would this be the correct procedure:
1. First make a file with only the clusters: cluster -i <DR3_stage_corpstatfile> --thresh 0.95 (should I also enter --connectvitiy??)
2. Extract the values of this: fslmeants -i <DR3_stage_corpstatfile> -m <cluster_outputfile> -0 <new output>
But I am confused on how to separate the different clusters in the DR3stage file? Should I do that with fslmaths or fslstats?
Any help would be appreciated!
Thank you
Heidi
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Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
[log in to unmask]
www.maastrichtuniversity.nl
www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092
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________________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Stephen Smith [[log in to unmask]]
Verzonden: zaterdag 5 januari 2013 10:29
Aan: [log in to unmask]
Onderwerp: Re: [FSL] How to create clusters and extract values?
Hi - for this kind of thing there are various basic FSL commands that you might use - I recommend you work through the relevant parts of the FSL course practicals that are online, including the very first (basic intro) practical. Good luck!
Cheers, Steve.
On 4 Jan 2013, at 08:55, Jacobs H (NP) wrote:
Dear FSL developers,
Happy New Year!!
Currently, I am finalizing my resting state analyses. Looking at the results I saw group differences in several components, which make me happy of course.
Now I would like to create clusters from these results.
For example: I see a few voxels in the hippocampus and several voxels in the precuneus. How can I make two clusters from this? And how can I extract the values from these clusters for graphical purposes?
I also have a question on how to interpret a specific group difference:
In the dorsal visual stream component (Beckmann template), I found group differences in the inferior prefrontal gyrus, frontal pole, lateral temporal areas and in the hippocampus. How should I interpret this, as these areas are not part of this component?
Your help is greatly appreciated!!
All the best
Heidi
================================================
Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
[log in to unmask]<mailto:[log in to unmask]>
www.maastrichtuniversity.nl
www.heidijacobs.nl
Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092
================================================
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve
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