Yue Yang

I changed to absolute paths but still got a segmentation fault. inputs.csv: /home/yueyang/test/ants_template_example/Cmuti/connectom_Ci_0_A.nii.gz,/home/yueyang/test/ants_template_example/Cmuti/connectom_Ci_2_A.nii.gz /home/yueyang/test/ants_template_example/Cmuti/connectom_Ci_0_B.nii.gz,/home/yueyang/test/ants_template_example/Cmuti/connectom_Ci_2_B.nii.gz /home/yueyang/test/ants_template_example/Cmuti/connectom_Ci_0_C.nii.gz,/home/yueyang/test/ants_template_example/Cmuti/connectom_Ci_2_C.nii.gz...

I ran antsRegistrationSyNQuick.sh. The command is as below: antsRegistrationSyNQuick.sh -d 3 -o ${PWD}/onecommand_result/MY -f K_Ci_0_prisma.nii.gz -m MYtemplate0_p.nii.gz -f K_Ci_2_prisma.nii.gz -m MYtemplate1_p.nii.gz -f K_Ci_4_prisma.nii.gz -m MYtemplate2_p.nii.gz -f K_Ci_6_prisma.nii.gz -m MYtemplate3_p.nii.gz -f K_Ci_8_prisma.nii.gz -m MYtemplate4_p.nii.gz I only got one registration image for the first modality. How can I get all the five registration images?

I used antsRegistration and antsRegistrationSyNQuick.sh to map the five templates to five moving image seperately, but the results were not good. Since the five templates were constructed by calling antsMultivariateTemplateConstruction2.sh, I am wondering if I could do multi-channel registration and map the five images in one registration call. I want to keep the connection between five modalities during the registration. But I am confused about how to do so. Do you have any suggestions? :(

I ran antsMultivariateTemplateConstruction2.sh and constructed 5 templates for five modalities: Ci0, Ci2, Ci4, Ci6. Ci8. Now I want to map the five templates to five moving images, K_Ci0, K_Ci2, K_Ci4, K_Ci6, K_Ci8. I want to map K_Ci0, K_Ci2, K_Ci4, K_Ci6 and K_Ci8 together in one antsRegistration command, what should I call in antsRegistration command?

So if I want to warp a counterpart image OASIS-TRT-20-Slice121Laplacian.nii.gz to the template, should I use template0.nii.gz as the fixed image? Is it right if I call as below? Command: $ antsApplyTransforms -d 2 -i counterpartImageOASIS-TRT-20-Slice121Laplacian.nii.gz -r MYtemplate0.nii.gz -o ImageAWarpedToTemplate.nii.gz -n Linear -t MYtemplate0Warp.nii.gz -t MYtemplate0GenericAffine.mat Or should I use the command as below? Command: $ antsApplyTransforms -d 2 -i counterpartImageOASIS-TRT-20-Slice121Laplacian.nii.gz...

I ran the 2-D example but only got affine file ("0GenericAffine.mat") and two warp files ("1Warp.nii.gz" and "1InverseWarp.nii.gz") for OASIS-TRT-20-Slice121.nii.gz, not for OASIS-TRT-20-Slice121Laplacian.nii.gz. Here is my command and output files: yueyang@ISIP-IW4200-4G-2:~/test/ants_template_example/OASIS2$ ./my-antsMultivariateTemplateConstruction2.sh -d 2 -o ${PWD}/result2/MY -i 4 -g 0.2 -j 2 -c 0 -k 2 -w 1x1 -f 8x4x2x1 -s 3x2x1x0 -q 100x70x50x10 -n 1 -r 1 -l 1 -m CC[2] -t BSplineSyN[0.1,26,0]...

I ran antsMultivariateTemplateConstruction2.sh and constructed templates for connectom_Ci_0, connectom_Ci_2, connectom_Ci_4, connectom_Ci_6, connectom_Ci_8. And I want to apply the tarnsform to prisma_Ci_0, prisma_Ci_2, prisma_Ci_4, prisma_Ci_6, prisma_Ci_8. I want to use antsApplyTransforms to apply the wrap but I am confused about the -t parameter. The antsMultivariateTemplateConstruction2.sh command only creates GenericAffine.mat file for the first modality and I get the GenericAffine.mat file...

I changed the output back but it still didn't work. Here is my command and result. yueyang@user-SYS-7048GR-TR:~/test/ants_template_example/OASIS2$ antsMultivariateTemplateConstruction2.sh -d 2 -o TemplateMultivariateBSplineSyN/T_ -i 4 -g 0.2 -j 2 -c 0 -k 2 -w 1x1 -f 8x4x2x1 -s 3x2x1x0 -q 100x70x50x10 -n 1 -r 1 -l 1 -m CC[2] -t SyN antsinputs.csv Multivariate template construction using the following 2-tuples: /home/yueyang/test/ants_template_example/OASIS2/OASIS-TRT-20-10Slice121.nii.gz /home/yueyang/test/ants_template_example/OASIS2/OASIS-TRT-20-10Slice121Laplacian.nii.gz...