You cannot simply concatenate the thickness files. Use mris_preproc, which will sample them to fsaverage space and then concatenate them

On 07/14/2017 12:49 PM, Dev vasu wrote:

Dear all,

I have 115 subjects , and I would like to perform average cortical thickness ,pial surface .

I have used mri_concat for this and i am getting dimension mismatch

*/" mri_concat k***/surf/lh.thickness --mean --o /media/vasudev/vkirsch4/Data_Driven/Thickness_Pial/lh_thickness/lh.thickness.fsaverage.mean.mgh

ninputs = 115 Checking inputs ERROR: dimension mismatch between k100/surf/lh.thickness and k102/surf/lh.thickness "/*

I have checked the dimensions of the subjects and following is the output , it seems there is a problem with dimensions of all the thickness files, could some one please let me know how i could perform group average thickness in this case ?

" mri_info k102/surf/lh.thickness Volume information for k102/surf/lh.thickness type: curv dimensions: 109303 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 109303.000 dof: 0 xstart: -54651.5, xend: 54651.5 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : ??? Primary Slice Direction: unknown

voxel to ras transform: -1.0000 0.0000 0.0000 54651.5000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000

voxel-to-ras determinant -1

ras to voxel transform: -1.0000 0.0000 0.0000 54651.5000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 "

mri_info k100/surf/lh.thickness Volume information for k100/surf/lh.thickness type: curv dimensions: 116434 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 116434.000 dof: 0 xstart: -58217.0, xend: 58217.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform not present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 Orientation : ??? Primary Slice Direction: unknown

voxel to ras transform: -1.0000 0.0000 0.0000 58217.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 "

Thanks, Vasudev

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