Activity for Matt
-
Matt posted a comment on discussion Open Discussion
No, I don't think so. By the way, on a side note, it seems that applying afni's 3dcopy can restore the sform matrix that we talked about.
-
Yes, I have the average image from the EPI. Thanks
-
Thanks Nick, I'm afraid I lost you there, would you please elaborate more? or point me to an example? Matt
-
Hi Nick, You are right. I did these two lines of motion correction for one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files pre-processed in FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt
-
Hi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files pre-processed in FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt
-
Hi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files preprocessed inFSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt
-
Hi Nick, You are right. I did these two lines of motion correction of one subject and although in fsleyes and ITK-SNAP (it only works on the first volume) the orientations are OK, but sform matrix is not showing. So, there is some effect here. If I skip the motion correction in ANTs, can we proceed to next step using the files FSL? P.S. Interestingly, the template that I created, seems to have not affected and all the matrices are ok. Thanks, Matt
-
Oh, I see... then this could cause a problem down the line. I want to run group ICA on the final registered EPI files. On the other hand, FSL's registration would not give the best outcome, so I like to use ANTs for registration. Any work around you might think of? Thanks!
-
Thanks Nick, I have already my EPI data motion corrected using FSL's tools. Since you mentioned these set of parameters might not be optimal on my dataset, I might skip the motion correction for now. In that case, what would be my next step? Matt
-
Hello, I have followed the script you mentioned, now I have all these files for each subject. Ready for next step. Thanks!
-
OK Nick, now I have this for all subjects.
-
No, just for one. for all, it is in progress...
-
Hi Nick, Thanks! this is how I ran this: antsRegistrationSyNQuick.sh -d 3 -f template0.nii.gz -m sbj_MPRAGE_brain.nii.gz -o sub_reg -n 1 it took ~5 mins to finish and it created these files: sub_reg0GenericAffine.mat sub_reg1InverseWarp.nii.gz sub_reg1Warp.nii.gz sub_regInverseWarped.nii.gz sub_regWarped.nii.gz Matt
-
Hello, Thanks for your help. I managed to create my template using antsMultivariateTemplateConstruction.sh from each subjects MPRAGE images! Since I am very new to ANTs, I appreciate your help again: my goal is to use these to do nonlinear registration of each subject 4D data (EPI image) to this newly created template. So, antsMultivariateTemplateConstruction.sh creates 4 files as the output template: template0.nii.gz (the output template) template0Affine.txt template0warp.nii.gz templatewarplog.txt...
-
Another question: what is the main differences between antsMultivariateTemplateConstruction.sh and antsMultivariateTemplateConstruction2.sh? I noticed that in the antsMultivariateTemplateConstruction.sh we do not have shrink factor or smoothing factor to be specified, while in the other, there are such options. also, max iteration is in different format: DDxDDxDDxDD or DDxDDxDD what is the order of these numbers? I mean, to what specs these three or four digits refer to? Thank you very much.
-
Another question: what is the main differences between antsMultivariateTemplateConstruction.sh or antsMultivariateTemplateConstruction2.sh? I noticed that in the antsMultivariateTemplateConstruction.sh we do not have shrink factor or smoothing factor to be specified, while in the other, there are such options. also, max iteration is in different format: DDxDDxDDxDD or DDxDDxDD what is the order of these numbers? I mean, to what specs these three or four digits refer to? Thank you very much.
-
Hello, I am getting this message while running antsMultivariateTemplateConstruction.sh or antsMultivariateTemplateConstruction2.sh: HDF5-DIAG: Error detected in HDF5... .#000: /home/avants/ANTsR/src/ANTS/ANTS-build/ITKv4/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5F.c line 794 in H5Fis_hdf5(): unable to open file major: Low-level I/O minor: Unable to initialize object .# 001: /home/avants/ANTsR/src/ANTS/ANTS-build/ITKv4/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5FD.c line 1086 in H5FD_open(): open failed...
-
Hi, I want to create a template from a set of MP-RAGE brain-extracted images to use as a standard space instead of MNI space for registration. I tried to use buildtemplateparallel_VBM.sh for this purpose, but it takes a lot of time which our computer cluster cannot support to run for more than 72-hours. Is there a way that I could run this in sperate stages, I mean being able to store the scripts results and then later resume the job from where it was terminated on the computer? Thanks.
1