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We don’t do it that way. Use probtrackx2 flags --xfm=${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz and --invxfm=${StudyFolder}/${Subject}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to bring seeds from standard space into structural
space and the results from structural space into standard space.
Peace,
Matt.
From: <Archer>, Derek B <[email protected]>
Date: Monday, May 18, 2015 at 2:22 PM To: Matt Glasser <[email protected]>, "[email protected]" <[email protected]> Subject: RE: [HCP-Users] Minimal Preprocessing Pipelines Hi Matt, So to get the diffusion data into the standard space, which files are relevant under the MNINonLinear folder? Sorry for the confusion. Derek From: Glasser, Matthew [mailto:[email protected]]
You also need to download the structural data. Peace, Matt. From: <Archer>, Derek B <[email protected]> Hi Matt, I’m looking at the preprocessed data that I downloaded from ConnectomeDB, and I am not seeing the “MNINonLinear” folder. Under the subject folder, there are the following folders: .xdlm release-notes T1w Do I need to download from elsewhere to get the nonlinear alignment?
Derek From: Glasser, Matthew [mailto:[email protected]]
Probably need to specify your probtrackx2 command lines, but both rigid alignment to MNI space and nonlinear alignment are available in the ${StudyFolder}/${Subject}/T1w and ${StudyFolder}/${Subject}/MNINonLinear
locations respectively. Peace, Matt. From: <Archer>, Derek B <[email protected]> Hello, For the diffusion data, are both FLIRT and FNIRT completed in the minimal preprocessing script? I am doing tractography on relatively small tracts, and there seems to be high variability in the placement of the
substantia nigra, putamen, and other regions. Thanks, Derek Archer _______________________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
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- [HCP-Users] Minimal Preprocessing Pipelines Archer,Derek B
- Re: [HCP-Users] Minimal Preprocessing Pipelines Glasser, Matthew
- Re: [HCP-Users] Minimal Preprocessing Pipelines Archer,Derek B
- Re: [HCP-Users] Minimal Preprocessing Pipeli... Glasser, Matthew
- Re: [HCP-Users] Minimal Preprocessing Pi... Archer,Derek B
- Re: [HCP-Users] Minimal Preprocessi... Glasser, Matthew
