Nagesh Adluru

Got it, Nick! Thanks so much.

Hi Nick, Got it. Just to solidify my understanding the differences are due to the y-coordinate of the origin in the 6th decimal place, and that crosses the ITK image filtering tolerance of differences, right? InputImage Origin: [1.2131356e+02, 1.2470340e+02, -7.9173729e+01], InputImageMaskImage Origin: [1.2131356e+02, 1.2470338e+02, -7.9173729e+01] I will play around with the CopyImageHeaderInformation. Thanks so much for the prompt reply! Best, Nagesh

Dear ANTs Team, Happy New Year to you all! I noticed a bit of interesting behavior of N4BiasFieldCorrection with respect to volume origins that I would like to share and get any advice on how to proceed, since I would like to avoid messing with the origins. The command is N4BiasFieldCorrection -d 3 -i mean_bzero.nii -w mask.nii -o [corrected.nii,init_bias.nii] -s 4 -b [100,3] -c [1000,0.0] Both the mean_bzero.nii and mask.nii have same origins to several decimal places but differ slightly. mask.nii...

Thanks so much for fixing it so quickly, Nick. It works now. Yes I am also trying to use ANTsR for voxelwise statistical analysis but I am so used to bash for batch processing of the images. I love everything ANTsX has :)

Thanks for clarifying that, Nick but when I try with either 1 or 0 it is giving a segmentation fault (core dumped) error. I was not able to upload the Mask.nii and LogJac.nii to this thread easily before so I put them here: http://brainimaging.waisman.wisc.edu/~adluru/Mask.nii http://brainimaging.waisman.wisc.edu/~adluru/LogJac.nii Thanks for your help in resolving this!!

Dear Brian, Nick, et al, I am not able to figureout the correct usage of the ConvertImageSetToMatrix operation using ImageMath. I am trying to use it as follows, ImageMath 3 out.csv ConvertImageSetToMatrix row Mask.nii LogJac.nii but it is giving the following error, terminate called after throwing an instance of 'std::invalid_argument' what(): stoi Aborted (core dumped) Could you let me know how I am misusing the command? Thanks so much for your help! Nagesh

Got it Nick! Thanks.

Hi Nick, Brian, Is there a utility in ANTs package that can get the list of image values for a given multi-label ROI file? ImageMath has LabelStats that gives mean values per ROI but I wanted to get the full list of values per ROI. It has SetOrGetPixel but I don't an easy to get a list of pixel coordinates just using ANTS. I can switch to Matlab and do it but I would like to stick to ANTS and command line if possible. Is there such a utility? Please let me know! Thanks so much. Nagesh