Samantha Baldi

Hi Nick, Thanks for your reply. Here’s the folder I put together, let me know if you have problems with it or if you need any other file: https://drive.google.com/open?id=1DTgDFPSsVawDPqXQisgWlgRAt79vScbs Best, Sam From: Nick Tustison ntustison@users.sourceforge.net Reply-To: "[advants:discussion]" 840260@discussion.advants.p.re.sourceforge.net Date: Thursday, 23 May 2019 at 16:07 To: "[advants:discussion]" 840260@discussion.advants.p.re.sourceforge.net Subject: [advants:discussion] Re: Registration...

Dear ANTs experts, I am having troubles with registering the avgB0 to T1 image. Because some of the images are quite far off from each other, I am using an antsRegistrationSyN.sh call that includes an initial moving transform in the attempt of bringing them closer to one another: antsRegistrationSyN.sh -d 3 -f T1BrainExtractionBrain.nii.gz -m skullstripped_avgB0.nii.gz -o b0toT1 -i [T1BrainExtractionBrain.nii.gz,skullstripped_avgB0.nii.gz,1] Whereas for some subjects this yields a good result, for...

Yes… If I leave out the extraction mask it works From: Nick Tustison ntustison@users.sourceforge.net Reply-To: "[advants:discussion]" 840261@discussion.advants.p.re.sourceforge.net Date: Monday, 6 May 2019 at 13:15 To: "[advants:discussion]" 840261@discussion.advants.p.re.sourceforge.net Subject: [advants:discussion] Re: Problems with BrainExtraction on centos7 Just to be clear, everything works if you don't use a mask, correct? Problems with BrainExtraction on centos7 https://sourceforge.net/p/advants/discussion/840261/thread/0748b77e88/?limit=25#9fdf/7bd1...

Any news on this? I still have this problem :|

Dear ANTs experts, I am running into an error when trying to perform antsBrainExtraction.sh on a Linux machine (centos7). The weird thing is that I first tried out this pipeline on my MacOS High Sierra without running into any problem. Namely, what I did is the following: - Build a costum-based template using antsMultivariateTemplateConstruction.sh. I created the template based on 20 subjects of my total sample, and I then proceeded by using the created template as initial template (-z parameter)...

Dear ANTs experts, I am running into an error when trying to perform antsBrainExtraction.sh on a Linux machine (centos7). The weird thing is that I first tried out this pipeline on my MacOS High Sierra without running into any problem. Namely, what I did is the following: Build a costum-based template using antsMultivariateTemplateConstruction.sh. I created the template based on 20 subjects of my total sample, and I then proceeded by using the created template as initial template (-z parameter) in...

Thanks! One additional question. Based on your experience and expertise, when it comes to registering diffusion data to anatomical T1 data do you have an opinion on the best interpolation method to use? And additionally on what scalar image it is best to use (i.e. average of all b0 volumes vs. first b0 volume)? From: Nick Tustison ntustison@users.sourceforge.net Reply-To: "[advants:discussion]" 840261@discussion.advants.p.re.sourceforge.net Date: Monday, 8 April 2019 at 14:45 To: "[advants:discussion]"...

Dear ANTs experts, I have a general question about the output of antsRegistrationSyN. Let's say I want to register moving image A to fixed image B. I wonder if there is any difference, and eventually what difference, between the antsRegistrationSyN output file AtoB1Warped.nii.gz and the output of an antsApplyTransforms call with the same images A and B. My current pipeline always includes this extra step, however I wonder whether there is an addedd value compared to just using the Warped.nii.gz file...