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Hi Himanshu, The 6 contrasts specified in the file given with "-t" are fine. The 7th contrasts is the F-test, specified with the option "-f". You can safely remove it and base your conclusions solely on the 6 corrected t-tests. PALM should read the files generated with the command Glm (or with FEAT). Did you receive any error message? In any case, it reads .csv too, so your run was fine at the end. All the best, Anderson On 1 May 2017 at 01:06, Him anshu <[log in to unmask]> wrote: > Dear FSL experts, > > I would like to perform a one-factor three level; one way between subjects > ANOVA using PALM. My design consists of six contrasts, but the output of > the command below "palm -i dr_stage2_ic0000.nii -d design.csv -t design.mat > -m dr_stage2_ic0000_mask.nii -f design.fts -n 5000 -corrcon -o palm_" is > as follows. > > Computing p-values. > Saving p-values (uncorrected, and corrected within modality and within > contrast). > Saving file: palm__vox_ztstat_uncp_c1 > Saving file: palm__vox_ztstat_fwep_c1 > Saving file: palm__vox_ztstat_uncp_c2 > Saving file: palm__vox_ztstat_fwep_c2 > Saving file: palm__vox_ztstat_uncp_c3 > Saving file: palm__vox_ztstat_fwep_c3 > Saving file: palm__vox_ztstat_uncp_c4 > Saving file: palm__vox_ztstat_fwep_c4 > Saving file: palm__vox_ztstat_uncp_c5 > Saving file: palm__vox_ztstat_fwep_c5 > Saving file: palm__vox_ztstat_uncp_c6 > Saving file: palm__vox_ztstat_fwep_c6 > Saving file: palm__vox_zfstat_uncp_c7 > Saving file: palm__vox_zfstat_fwep_c7 > Saving p-values (corrected across contrasts). > Saving file: palm__vox_ztstat_cfwep_c1 > Saving file: palm__vox_ztstat_cfwep_c2 > Saving file: palm__vox_ztstat_cfwep_c3 > Saving file: palm__vox_ztstat_cfwep_c4 > Saving file: palm__vox_ztstat_cfwep_c5 > Saving file: palm__vox_ztstat_cfwep_c6 > Saving file: palm__vox_zfstat_cfwep_c7 > > > PFA design.csv, design.mat and design.fts attached and comment what is > this seventh contrast for? Kindly pardon if I committed a silly mistake in > designing the input files properly.. > > I was surprised when PALM did not took the design_glm.mat, design_glm.con > constructed using Glm (Please find these designs also attached) thus I have > used the current files (design.csv, design.mat and design.fts) > > Thanking you in anticipation > > Regards > Himanshu Joshi > > >