Module Detail Information

Name:First Utils
Type: Module
Short URL:
http://bit.ly/1B7Eecl
Description:This command can be used to fill meshes, as well as for running vertex analysis. To fill a mesh : Usage: first_utils --meshToVol -m mesh.vtk -i t1_image.nii.gz -l fill_value -o output_name --meshToVol : Set to fill mesh mode of operation. -i : Base image to which the mesh corresponds. -m : An ASCII vtk mesh. -o : Name of output volume. -l : Label with which to fill the mesh (boundary voxels will be assigned label+100). Labels 10 Left-Thalamus-Proper 40 11 Left-Caudate 30 12 Left-Putamen 40 13 Left-Pallidum 40 16 Brain-Stem /4th Ventricle 40 17 Left-Hippocampus 30 18 Left-Amygdala 50 26 Left-Accumbens-area 50 49 Right-Thalamus-Proper 40 50 Right-Caudate 30 51 Right-Putamen 40 52 Right-Pallidum 40 53 Right-Hippocampus 30 54 Right-Amygdala 50 58 Right-Accumbens-area 50 For vertex analysis: Run first_utils giving it the combined bvars file and the design matrix. For example: first_utils --vertexAnalysis --usebvars -i con_to_dis_L_Hipp.bvars -d con1_dis2.mat -o shape_analysis/con1_dis2_L_Hipp --useReconNative --useRigidAlign -v >& shape_analysis/con1_dis2_L_Hipp_output.txt Run randomise using the output 4D image (containing projections of the vertex displacements per subject) and the mask image, together with the design matrix and contrast files. For example: randomise -i con1_dis2_L_Hipp.nii.gz -m con1_dis2_L_Hipp_mask.nii.gz -o con1_dis2_L_Hipp_rand -d con1_dis2.mat -t con1_dis2.con -f con1_dis2.fts --fonly -D -F 3 Note that the option -F 3 is only one of several multiple-comparison-correction options available, and this is just an example, not a standard recommendation. Output of vertex analysis In the same way as in FSLVBM and TBSS, randomise is used to generate the statistics. The output of most interest is the probability that is corrected for multiple comparisons. This will contain corrp in the filename. The values within this file contain 1-p values, such that p=0.05 corresponds to a value of 0.95, and so displaying all values over 0.95 with FSLView will show the significant areas. For more information about how to view these results refer to the documentation for randomise, FSLVBM or TBSS.
Executable:
/first_utils
Input Parameters:
 - extra image in bvars
 - flirt matrices
 - Overlap
 - UseNorm
 - Surfaceout
 - Thresh
 - Use bvars
 - UseReconMNI
 - VertexAnalysis
 - UseReconNative
 - UseRigidAlign
 - ReconMeshFromBvars
 - ReadBvars
 - MeshToVol
 - SaveVertices
 - Verbose
 - Number of modes
 - SingleBoundaryCorr
 - DoMVGLM
 - ConcatBvars
 - Debug
 - Input filename
 - Normalization factors
 - Reference image
 - Stats
 - Mesh
 - Mesh Label
 - Center origin
 - Use PCA Filter
Output Parameters:
 - Output name
File size:30.1 KB
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