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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