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Hi Shana,

It seems that the input data (given with the option "-i", i.e.,
myelin_R.func), after being read, is being identified as if it had just 1
vertex, as opposed to 163842.

The average area is fine, but if you'd like to be super sure, just remove
it from the command line, i.e., supply just "-s <surface>". The error will
persist.

Try confirming that the input data ("-i") is really correct. If it is, and
the error continues to happen, then please put the files in some file
sharing server and send me the link off-list. I'll try to have a look then.

All the best,

Anderson


On Thu, 28 Jun 2018 at 07:59, Shana Adise <[log in to unmask]> wrote:

>
> Hello all,
>
>
> I apologize if this question has already been answered or if the answer is
> obvious. I am trying to run PALM for my surface based analyses. I have
> closely followed steps in Example 10  (
> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/Examples#Example_10:_Using_CIFTI_files).
> I have also read the message threads (
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;e2ea47fb.1606 and
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1705&L=fsl&P=R69851&1=fsl&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4).
> However, I am running into a problem where the surface and input data do
> not match in size.
>
>
>
> Error using palm_takeargs (line 1688)
>
> Surface file does not match the input data:
>
> - Surface file 1 has 163842 vertices and 327680 faces
> (midthickness_average_R.surf.gii)
>
> - Input data file 1 has 1 points (myelin_R.func.gii)
>
>
> Error in palm_core (line 33)
>
> [opts,plm] = palm_takeargs(varargin{:});
>
>
> Error in palm (line 81)
>
> palm_core(varargin{:});
>
>
>
> **Using wb_command -file-information I see that the myelin and area files
> do not have 327680 number of triangles and maps
>
> midthickness_average_R.surf.gii
>
> # of vertices: 163842
>
> # of triangles: 327680
>
>
> myelin_R.func.gii
>
> # of vertices: 163842
>
> # of maps: 130
>
>
> R_area.func.gii
>
> # of vertices: 163842
>
> # of maps: 1
>
>
>
> I am assuming that I must have missed a step when creating the
> midthickness_average_R.surf.gii (labeled as option -s
> L_midthickness.surf.gii in the example 10):
>
>
>
> Example of palm script (#10): palm -i data_L.func.gii -d design.mat -t
> design.con -o results_L_cort -T -tfce2D -s L_midthickness.surf.gii
> L_area.func.gii -logp [...]
>
>
>
>
> The steps that I took to create the input files are below:
>
>
> #make a group myelin map:
>
> wb_command -cifti-merge myelin_average.dscalar.nii \
>
> -cifti subj1Pre.MyelinMap.164k_fs_LR.dscalar.nii \
>
> -cifti subj2Pre.MyelinMap.164k_fs_LR.dscalar.nii \
>
>
> #separate the myelin maps into L and R hemispheres:
>
> wb_command -cifti-separate myelin_average.dscalar.nii COLUMN -metric
> CORTEX_LEFT myelin_L.func.gii -metric CORTEX_RIGHT myelin_R.func.gii
>
>
>
> #for both hemispheres, do the following to create area maps:
>
>
> #uncompress
>
>
> wb_command -gifti-convert BASE64_BINARY myelin_R.func.gii myelin_R.func.gii
>
>
>
> for subj in $(cat subject_list.txt);
>
> do
>
> wb_command -surface-vertex-areas
> ${subj}.R.midthickness.164k_fs_LR.surf.gii
> ${subj}.R.thickness.164k_fs_LR.shape.gii;
>
> done
>
>
> R_MERGELIST=""
>
> for subj in $(cat subject_list.txt) ;
>
> do
>
> R_MERGELIST="${R_MERGELIST} -metric
> ${subj}.R.thickness.164k_fs_LR.shape.gii"
>
> done
>
> wb_command -metric-merge R_midthick_va.func.gii ${R_MERGELIST}
>
>
>
> #reduce:
>
> wb_command -metric-reduce R_midthick_va.func.gii MEAN R_area.func.gii
>
>
>
> #create an average surface map
>
> wb_command -surface-average midthickness_average_R.surf.gii \
>
> -surf subj1.R.midthickness.164k_fs_LR.surf.gii \
>
> -surf subj2.R.midthickness.164k_fs_LR.surf.gii \
>
>
>
>
> #PALM script
>
>
> palm -i myelin_R.func.gii \
>
> -s midthickness_average_R.surf.gii R_area.func.gii \
>
> -d design_myelin.mat \
>
> -t OneSample_v0.con \
>
> -n 10 \
>
> -T \
>
> -tfce2D \
>
> -savemetrics \
>
> -saveglm \
>
> -saveparametric \
>
> -transposedata \
>
> -o myelin_cortical_R_130 \
>
> -corrcon \
>
> -ise \
>
>
>
>
> Thank you for your help,
>
> Shana
>
>
>
>
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