When to use/ correct usage of: -ise -ee -corrmod -corrcon
Experimental design:
Tasked based fMRI was acquired pre and post treatment for all patients. Disease severity was also measured pre and post treatment to use as covariate of interest in analysis. All patients were preprocessed in FSL and for each contrast of interest the MNI registered COPE images of each individual were concatenated into a 4D.nii file
Pre scan vs study outcome/measure:
ie.
fslmerge -t Cope1_contrast_1_4D.nii
/SUBJECT_1_MR_01/Study.feat/reg_standard/stats/cope1.nii.gz
/SUBJECT_2_MR_01/Study.feat/reg_standard/stats/cope1.nii.gz
/SUBJECT_3_MR_01/Study.feat/reg_standard/stats/cope1.nii.gz
/SUBJECT_4_MR_01/Study.feat/reg_standard/stats/cope1.nii.gz
/SUBJECT_5_MR_01/Study.feat/reg_standard/stats/cope1.nii.gz
.
.
.
Cope1_contrast_1_4D.nii ---> (Reward Cue+)
Cope2_contrast_2_4D.nii ---> (Reward Cue-)
Cope3_contrast_3_4D.nii ---> (Non Reward Cue+)
Cope4_contrast_4_4D.nii ---> (Non Reward Cue-)
.
.
.
palm
-i /Cope1_contrast_1_4D.nii
-o /Contrast_1 /PreScan_vs_Outcome_Cope_1
-d /Design_1SampleTTest_PreScan_vs_ Outcome_AgeSexSite.mat
-t /Design_1SampleTTest_PreScan_vs_HRSD_Cov_AgeSexSite.con
-m /MNI152_T1_2mm_brain_mask.nii
-n 5000
-T
-C 3.1
-save1-p
1) Is the above palm script suitable to measure the activation with respect to each individual contrast and a covariate of interest or do I need to enter all contrasts into the palm command preceded by (-i) to correctly measure the statistical significance of each contrast or can each contrast be calculated separately and be statistically valid?
2) When would it be appropriate to use -ise, -ee, -corrmod, -corrcon? (I believe that I only have one modality which is fMRI data, but multiple contrasts that i want to compare with my covariates of interest would I then have to use -corrcon in the palm command?)
Please see bellow for .mat and .con file structures.
Thank you so much in advance for your help.
Kind regards,
Arsalan
----
/Design_1SampleTTest_PreScan_vs_HRSD_Cov_AgeSexSite.con
/ContrastName1 percent_improvement
/NumWaves 1
/NumContrasts 1
/PPheights 1.625641e+00
/RequiredEffect 1.915
/Matrix
1.000000e+00
----
Design_1SampleTTest_PreScan_vs_ Outcome_AgeSexSite.mat
]/NumWaves 1
/NumPoints 121
/PPheights 1.625641e+00
/Matrix
2.798318e-03
-6.127491e-02
-6.127491e-02
-1.781227e-01
2.113003e-01
3.185878e-01
-4.562273e-02
-1.434005e-01
-6.656227e-01
3.218773e-01
-4.072894e-01
1.899328e-01
-1.989561e-01
-4.182543e-01
-8.784496e-02
1.899328e-01
-3.656227e-01
2.593773e-01
-2.174746e-01
2.798318e-03
-1.550964e-01
.
.
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