Dear FSL experts,
I'm newcomer in imaging and FSL. Actually, I bogged down with an FSL Melodic ICA analysis and do not know, how to carry on.
I have one group (subject 1 to 12) with two sessions (before (“pre”) and after (“post”) treatment). I run MELODIC with my whole group data, including subjects before and after treatment in the concat-ICA mode. I got 134 components, with 32 “true” networks after visual inspection.
As next step I wanted to perform a paired t-test. As described on the fsl homepage (Single-Group Paired Difference (Paired T-Test)), I calculated the difference between the resulting components for subject 1 to 12 separately:
fslmaths 001_post/filtered_func_data.nii.gz -sub 001_pre/filtered_func_data.nii.gz sub1_diff
fslmaths 002_post/filtered_func_data.nii.gz -sub 002_pre/ filtered_func_data.nii.gz sub2_diff
etc…
and subsequently used “fslmerge” to create a single 4D volume:
fslmerge -t 4Dvolume sub1_diff sub2_diff sub3_diff sub4_diff sub5_diff sub6_diff sub7_diff sub8_diff sub9_diff sub10_diff sub11_diff sub12_diff
Finally, I used the resulting “4Dvolume” to perform a one sample t-test:
randomise -i 4Dvolume.nii.gz -o 4DvolumeT -1 -v 5 -T
and used “fslmaths” to get the clusters and peak information from is the raw tstat image by masking the raw tstat image with the significant voxels from corrp:
fslmaths 4DvolumeT_tfce_corrp_tstat1 -thr 0.95 -bin -mul 4DvolumeT_tstat1 4DvolumeT_thresh_tstat1
As a final result I get one image with significant cluster across various networks, which I interpret as significant group differences “post versus pre across all networks”.
Now I have two questions
1) I am still not sure, if this is statistical the right way to perform a Melodic ICA paired t-test and would like to hear your view on this – maybe there is a more appropriate way to perform the analysis?
2) If I perform the paired t-test by substracting the two sessions for each person separately, do I have to substract the raw “filtered_func_data.nii.gz” images or do I have to perform first a dual regression analysis and then substract the “dr_stage2_subject[#SUB].nii.gz” images?
Thanks in advance.
Kind regards,
Christine
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