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