Hi Lizanne,
Please, see below:
On 11 January 2016 at 23:44, Schweren, Lizanne <[log in to unmask]> wrote:
> Dear experts,
>
> I'm attempting to run a longitudinal analysis of hippocampal shape changes
> in PALM, where the baseline scan is entered as a per-voxel regressor. For
> input, I specify a 4D nifti file of hippocampus shape at follow-up
> (calculated from the concatenated .bvars using first_utils). For the
> per-voxel regressor, I specify a similar 4D nifti file but now at baseline.
> In my design.mat file I specify 8 EV's (not including the baseline
> per-voxel regressor). My contrast file has 8 contrasts, one for each EV in
> the design file.
>
> palm -i
> {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-r-hipp-scaled.nii
> ...
> -m
> {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-r-hipp-scaled-mask.nii
> ...
> -evperdat
> {path}/Desktop/r-hipp-vertex/regression-scaled/pvr-match-r-hipp-scaled.nii
> 9 1 ...
> -o {path}/Desktop/r-hipp-vertex/regression-scaled/palm ...
> -d
> {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-design.mat
> ...
> -t
> {path}/Desktop/r-hipp-vertex/regression-scaled/regression-match-tcontrast.con
> ...
> -demean -T -C 2.3 -n 1000
>
> My first question is: how do I specify the extra per-voxel regressor in my
> design and contrast files?
>
> If e.g. I should add an extra column in the design.mat file, what should
> this column consist of? I've tried changing numWaves/numContrast/matrices
> to 9 instead of 8 in many different combinations, but PALM keeps giving me
> the reshape-error.
>
The design would contain dummy EVs, that later are replaced by the
voxelwise data. So, you add for your current design, that has 8 EVs, a 9th
EV containing any number (it can be all zeroes, all ones, or even repeat an
already existing EV). This 9th EV will internally be replaced by the
voxelwise data.
The contrast in the same way: it considers that the design has 9 EVs, and
if the respective EV is marked as zero in the contrast, it will be treated
as nuisance, otherwise it is considered part of the effect of interest to
be tested.
>
> My second question is: can I specify a new mask for the baseline-scans
> after the -evperdat line?
>
Each mask pairs up with an input, so no mask specific for the baseline
scans. But maybe the same could be accomplished in different ways. What
exactly would you like to do with the extra mask?
>
> I've attached my design and contrast files (at this point with just the 8
> other predictors). The design file is a .txt file because my email server
> won't send it as .mat . Thank you very much for your help!
>
Looks good, only need to add the extra EV to the design and contrast.
Note that -evperdat is very slow to run.
Cheers,
Anderson
>
> All my best,
> Lizanne
>
>
>
>
