Hi Afton,
If the comparison is merely between groups (i.e., at between-subject), and never between conditions within subject, and assuming each row of the design represents one condition, and each block represents one subject, then you can permute blocks as a whole. So, you'd provide the EB file with the option -eb, and additionally, the option -whole, such that blocks are permuted in their entirely, while keeping the observations within block unaltered across permutations.
For the masks, since the inputs use diverse data formats, so need the masks be. Say the behavioral.csv file has 5 columns; you'd then create a mask indicating that you want to test all the five columns as they are ordered. So, the file would contain:
1,1,1,1,1
Say you save it as "beh_mask.csv". The call to PALM will be (already adding the EB option):
palm -i all-subj_cope1.nii -i behavioral.csv -m ROI_mask.nii -m beh_mask.csv -o /outputs -t design.con -d design.mat -n 1000 -T -corrcon -save1-p -eb EB.csv -whole
Make sure the order is right: each input provided with -i will match one of the masks provided with the -m in the order as entered. So if you enter the cope1.nii file first, the ROI_mask.nii needs to be also the first mask supplied.
Hope this helps!
All the best,
Anderson
On 9/21/23, 9:17 AM, "FSL - FMRIB's Software Library on behalf of Afton" <[log in to unmask] <mailto:[log in to unmask]> on behalf of [log in to unmask] <mailto:[log in to unmask]>> wrote:
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Dear FSL experts,
I have two questions regarding exchangeability blocks and ROI masks with FSL PALM.
I have a design where I defined block-wise differential contrasts of within-subject conditions at the subject-level. At the group level, I want to compare the activation of two separate groups in an ROI analysis using PALM that includes some behavioral data (.csv).
Question 1: I am unclear about exchangeability blocks and whether they would fit in my case. Considering that I am comparing two groups (not the condition blocks from the subject-level), would I need to specify exchangeability blocks? If so, how might this look?
Question 2: When I run PALM (via Matlab), I get an error regarding the size of the incompatible size of the behavioral.csv and ROI_mask.nii. I assume this is because the behavioral.csv has an input for each subject, whereas the ROI_mask is a single mask image. How can I specify an ROI analysis with PALM including both .nii and .csv inputs?
error message:
The size of the data does not match the size of the mask:
- Data file behavioral.csv
- Mask file ROI_mask.nii
command used:
palm -i all-subj_cope1.nii - behavioral.csv -m ROI_mask.nii -o /outputs -t design.con -d design.mat -n 1000 -T -corrcon -save1-p
Many thanks in advance!
Afton
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