CIFTI files (.dscalar.nii) vs design matrix [Error using palm_takeargs (line 2062)]

[JacMatu]

Hello,

I'm trying to set up my first PALM using CIFTI outputs from hcppipelines - I know that CIFTI support is limited here, but PALM was recommended to me by Mathew Glasser so I believe it's doable.

I'm trying a toy example of setting up a 2-sample T-Test with just 2 subjects per group (final will be 20/20).

1. I concatenated CIFTI files using wb_shortcuts -cifti-concatenate into one 4D input image using

output='<path/to/output.dscalar.nii>'

input1='<path/to/input1.dscalar.nii>'
input2='<path/to/input2.dscalar.nii>'
input3='<path/to/input3.dscalar.nii>'
input4='<path/to/input4dscalar.nii>'

wb_shortcuts -cifti-concatenate \
    $output \
    $input1 \
    $input2 \
    $input3 \
    $input4 

2. I created a design.mat and some basic contrasts to go with it and converted them with Text2Vest
   (design matrix preview)
   1 0
   1 0
   0 1
   0 1

Next, I wanted to run a basic palm but it seems that the data read from the 4D file is not read properly, as I get an error:

Running PALM (github using MATLAB 9.7.0.1190202 (R2019b) with the following options:
-i toyCIFTI4D.dscalar.nii
-d design.mat
-t [conBlind.con conSig.con]
-n 5000
-corrcon
-o opt.dir.stats
Reading input 1/1: toyCIFTI4D.dscalar.nii
Reading design matrix and contrasts.
Error using palm_takeargs (line 2062)
The number of rows in the design matrix does
not match the number of observations in the data.
- Rows in the matrix: 4
- Observations in the data: 298261
In file design.mat


Error in palm_core (line 33)
[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)
palm_core(varargin{:});

Is there any additional step that has to be taken to ensure proper inputs from CIFTI files? I assumed that for simple non-spatial stats analyses this should be ok, but I'm completely new to this environment and I'm not sure why palm / wb_command read 298261 observations from concatenating just 4 files

[andersonwinkler]

Hi Jacek,

I was working on it just yesterday. Could you try pulling from the repo again and let me know if the problem persists?

Thanks!

Anderson

[JacMatu]

Hi Anderson,

Yes, it worked! Thank you, I didn't notice recent commits!