Dear Jeanette,
Thank you very much for your help.
However, I came across another error: the number of time points in the merged 4D file does not match my design matrix.
Probably this is because I used the Beckmann template in the dual regression (providing the components).
So, now I have 40 people x 10 components, which is different from my design matrix (having 2 groups of 20 people).
How should I proceed to get separate files for each component? And still be able to proceed to stage 3 from DR do the 2 sample t-test on the subtracted images (condition-condition2)?
Thank you very much!
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
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Aan:
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Onderwerp: Re: [FSL] Repost: question regarding pre and post comparison
Hi,
you need to first create a 4D image and use that as input into randomise fslmerge -t can be used for this purpose. See the the help for complete usage.
Cheers,
Jeanette
On Thu, Sep 27, 2012 at 3:36 PM, Jacobs H (NP) <
[log in to unmask]<mailto:
[log in to unmask]>> wrote:
Hi,
I managed to subtract all the pre and post files of all my subjects from stage 2 from DR (where I used the Beckmann template). Furthermore, I also made a .mat and .con file for an 2 group unpaired t-test of these files.
I now would like to run the statistics on these ' subtracted' images and then find out in which components there is a group difference for the condition1-2.
Should I use randomise for this? I tried it, but it won't work:
randomise -i A01_subtracted_DR2.nii.gz A02_subtracted_DR2.nii.gz A03_subtracted_DR2.nii.gz A04_subtracted_DR2.nii.gz A05_subtracted_DR2.nii.gz A06_subtracted_DR2.nii.gz A07_subtracted_DR2.nii.gz A08_subtracted_DR2.nii.gz A09_subtracted_DR2.nii.gz A10_subtracted_DR2.nii.gz A11_subtracted_DR2.nii.gz A12_subtracted_DR2.nii.gz A13_subtracted_DR2.nii.gz A14_subtracted_DR2.nii.gz A15_subtracted_DR2.nii.gz A16_subtracted_DR2.nii.gz A17_subtracted_DR2.nii.gz A18_subtracted_DR2.nii.gz A19_subtracted_DR2.nii.gz A20_subtracted_DR2.nii.gz J01_subtracted_DR2.nii.gz J02_subtracted_DR2.nii.gz J03_subtracted_DR2.nii.gz J04_subtracted_DR2.nii.gz J06_subtracted_DR2.nii.gz J07_subtracted_DR2.nii.gz J08_subtracted_DR2.nii.gz J09_subtracted_DR2.nii.gz J10_subtracted_DR2.nii.gz J11_subtracted_DR2.nii.gz J12_subtracted_DR2.nii.gz J13_subtracted_DR2.nii.gz J14_subtracted_DR2.nii.gz J15_subtracted_DR2.nii.gz J16_subtracted_DR2.nii.gz J17_subtracted_DR2.nii.gz J18_subtracted_DR2.nii.gz J19_subtracted_DR2.nii.gz J20_subtracted_DR2.nii.gz J21_subtracted_DR2.nii.gz -o Output_DR3_subtraction -d model_subtractedDR2.mat -t model_subtractedDR2.con -n 5000
Could you tell me what I am doing wrong and how I should proceed on this?
Thank you very much!
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
Van: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] namens Stephen Smith [[log in to unmask]<mailto:[log in to unmask]>]
Verzonden: donderdag 27 september 2012 10:22
Aan: [log in to unmask]<mailto:[log in to unmask]>
Onderwerp: Re: [FSL] Repost: question regarding pre and post comparison
HI - yes it's the stage 2 outputs you want.
Cheers.
On 27 Sep 2012, at 09:18, Jacobs H (NP) wrote:
Hi,
I got fslmaths working!
But should I use the dr_stage2_subject[#SUB].nii.gz from stage 2 dual regression? Thus: subtract the two measurements for each subject and feed this stage 3 DR (with the subtracted maps) for doing a 2 sample t-test?
Thanks
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]><mailto:[log in to unmask]<mailto:[log in to unmask]>>
________________________________________
Van: FSL - FMRIB's Software Library [[log in to unmask]<mailto:[log in to unmask]>] namens Jeanette Mumford [[log in to unmask]<mailto:[log in to unmask]>]
Verzonden: maandag 24 september 2012 16:35
Aan: [log in to unmask]<mailto:[log in to unmask]>
Onderwerp: Re: [FSL] Repost: question regarding pre and post comparison
Hi,
Yes, to test how the pre/post differences compare between your two groups, you would first subtract the pre/post within subject and then enter these differences into a 2-sample t-test.
Other within pre or within post difference between your groups would be run with separate two-sample t-tests.
Cheers,
Jeanette
On Mon, Sep 24, 2012 at 3:35 AM, Jacobs H (NP) <
[log in to unmask]<mailto:
[log in to unmask]><mailto:
[log in to unmask]<mailto:
[log in to unmask]>>> wrote:
Dear FSL team,
I am struggling a bit with the statistics for my resting state analyses.
I have two groups (each 20 subejcts) and a pre and post measurement. I already ran the ICA and now would like to do the dual regression.
In this regression I would like to investigate the main effect of group, condition (pre/post) and the interaction (group differences on the difference between post and pre).
Should I do a 2by2 anova with 4 EV's (group1 timepoint 1; group 1 timepoint 2; group 2 timepoint 1; group 2 timepoint 2).
And then create the following contrast file
main effect group: 1 1 -1 -1
main effect time 1 -1 1 -1
interaction: 1 -1 -1 1
However, I read somewhere that I should subtract both conditions for each individual and then compare the two group on this 'subtracted image'??
Is this correct?
Any advice would be greatly appreciated!!
Thanks!
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
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