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antspy can read anything ITK can read. to convert to ants image types, you might be able to read the .mat file into python somehow ( generally we have very limited knowledge about Matlab ) , convert to numpy then use from_numpy to get an ants image. generally, you should post such questions as an ANTsPy issue at the ANTsPy GitHub site. brian On Fri, Apr 24, 2020 at 9:01 AM Edite Figueiras areiasfi@users.sourceforge.net wrote: Hi, I am trying to use ANTSPy and I would like to know what is the best...

cc radius is voxels brian On Tue, Apr 14, 2020 at 4:39 PM Philip Cook cookpa@users.sourceforge.net wrote: Question for @ntustison https://sourceforge.net/u/ntustison/ - how does the metric radius handle anisotropic voxels? I know the shrink factors use the smallest of the three dimensions. Does CC[fixed, moving, 1, 4] work the same way? I kind of think it would have to, but I've not checked the code. Coregistering clinical scans with thick slices https://sourceforge.net/p/advants/discussion/840260/thread/5cf8330a1c/?limit=25#e0bf...

the convergence estimator needs something like 10 samples to estimate it (smooth) slope. thus inf ends after 10 iterations. this parameter is specified on the command line. performance is not particularly impacted by it. brian On Sun, Mar 8, 2020 at 6:22 PM Maximilian Hoffmann hoffmmax@users.sourceforge.net wrote: Unfortunately I forgot, as I was trying multiple things, but it happens fairly often: i.e. here Default paths used:RAW_DIR = /fast/groups/ag_judkewitz/scratch/xraw/PROC_DIR = /fast/groups/ag_judkewitz/scratch/xprocessed/RES_DIR...

LPS conversion is -1, -1, 1 RAS vs LPS ITK https://www.google.com/search?client=safari&rls=en&ei=oF5WXuqeGemFytMPl6C7gAk&q=RAS+vs+LPS+ITK&oq=RAS+vs+LPS+ITK&gs_l=psy-ab.3..33i160l3.1907.2376..2637...0.3..0.119.376.3j1......0....1..gws-wiz.......0i71j33i299j33i22i29i30.dVOVavVs-6k&ved=0ahUKEwjq7oyrlu_nAhXpgnIEHRfQDpAQ4dUDCAo&uact=5 On Wed, Feb 26, 2020 at 5:04 AM Tommaso Di Noto tommydino93@users.sourceforge.net wrote: Thanks a lot @philip https://sourceforge.net/u/philip/ and @ntustison https://sourceforge.net/u/ntustison/!...

help( ants.transform_index_to_physical_point ) help( ants.transform_physical_point_to_index ) brian On Tue, Feb 25, 2020 at 11:28 AM Ida Sand sandida@users.sourceforge.net wrote: Thanks for your answer, Brian. By using the apply_transforms_to_point - function I'm back again to the problem of the relation between point and pixel. I don't find any information about what a point in ANTsPY is in the documentation. Is there a way to convert a given pixel-coordinate into a point? My ANTsImage has dimensions...

maybe help( ants.apply_transforms_to_points ) help( ants.apply_transforms_to_point ) brian On Tue, Feb 25, 2020 at 8:28 AM Ida Sand sandida@users.sourceforge.net wrote: Hi, thank your for your answer. I will ask at GitHub repo next time :-) apply_transforms gives out the warped image, but I want to specify a given pixel in the fixed image and find the corresponding one in the moving image. How can I do that? Ida Points vs pixel in ANTs https://sourceforge.net/p/advants/discussion/840261/thread/0eb948e7cb/?limit=25#ccda...

the size of the template will be determined by the initial image. you can control the initial image via -z which will then influence the template size, resolution and anatomical orientation. brian On Tue, Jan 21, 2020 at 7:00 AM Simon Jones simonjones0@users.sourceforge.net wrote: I am not clear how AverageImages function decides what the output voxel dimensions of the output image are. If I have a bunch of images of differing voxel dimensions then It always seems to be the same as one of them. But...

are those inputs 4D? if so - probably won't work correctly. brian On Mon, Nov 18, 2019 at 6:02 PM Thomas DeRamus hermeckerogg@users.sourceforge.net wrote: Hi all. I'm trying to build a subject-specific template for some pediatric timeseries data. antsMultivariateTemplateConstruction2.sh -d 4 -j 6 -k 1 -n 0 -r 1 -t SyN -c 5 -o MY sub-M87192301_Session1_task-restopen_bold.nii.gz sub-M87192301_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restclosed_bold.nii.gz sub-M68290751_Session1_task-restopen_bold.nii.gz...