David,
Thank you so much for the help below!
For future reference, would resampling to 2 mm avoid having to do this step? Or what would work here to avoid this step?
Cheers back at ya,
Varina
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of David V. Smith [[log in to unmask]]
Sent: Monday, April 30, 2012 9:28 PM
To: [log in to unmask]
Subject: Re: [FSL] Group Melodic transform matrix
Ah, ok -- you probably resampled to 4mm during your group ICA. The easiest thing to do would be to overlay the results onto the bg_image.nii.gz in your *.gica folder. Alternatively, you could take the standard brain you used during registration and then downsample it to the appropriate resolution with flirt:
flirt -ref MNI152_T1_2mm_brain -in MNI152_T1_2mm_brain -out MNI152_T1_4mm_brain -applyisoxfm 4
Cheers,
David
On Apr 30, 2012, at 5:37 PM, Wolf, Varina Louise wrote:
> Yes, fslview says "dimension is not compatible" between stat image and standard MNI152_T1_brain (the standard used in Melodic registration step). Fslinfo says stat image dim 1,2,3,4 is 45,54,45,1 - respectively. I tried and extra flirt between the stat and MNI image, but this did not work, and the stat image looks like it is from a bigger head on top of the standard. Strangely, the IC_stat images from Melodic and registration look perfect to me, no junk outside brain.
>
> Help!
> -Varina
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of David V. Smith
> Sent: Monday, April 30, 2012 3:59 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Group Melodic transform matrix
>
> Hi Varina,
>
> The dr_stage3_ic# files are already in standard space (or whatever you chose as the reference image in the group ICA). Are you getting an error when you overlay those stat maps onto the MNI image?
>
> Cheers,
> David
>
>
>
>
> On Apr 30, 2012, at 4:49 PM, Varina Wolf wrote:
>
>> Hello Experts,
>>
>> In order to overlay the stat images (after Concat ICA, dual regression with randomise) onto an MNI image, I think that I need to transform the stat matrix such that it has the same dimensions as the standard.
>>
>> I am familar with the single subject transform matrix example_func2standard.mat, but not sure where to find the transform matrix for this group data.
>>
>> I believe then the next step would be:
>>
>> flirt -in dr_stage3_ic#_tfce_corrp_tstat1.nii -ref MNI_2mm_brain.nii -out stattostandard -init TRANSFORMMATRIX -applyxfm
>>
>> Thanks for your teaching,
>> Varina
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