Re: [HCP-Users] Projecting Label into White Matter

[Glasser, Matthew]

Good to hear you have something working. Peace, Matt. From: John Plass <johncpl...@gmail.com> Date: Friday, February 13, 2015 at 5:06 PM To: Matt Glasser <glass...@wusm.wustl.edu> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Projecting Label into White Matter With some experimentation, I found that mri_label2vol tends to create worse volumes than recon-all's aparc2aseg regardless of the surface you use. I ended up getting good results by making a binarized mask from the segmented volume in the T1w folder, dilating it, and multiplying by a binarized WM mask to constrain the dilation to WM. John On Fri, Feb 13, 2015 at 3:36 PM, John Plass <johncpl...@gmail.com> wrote: Hi Matt, Thanks for your help. Unfortunately, our analysis requires that we use other software that only accepts volumetric masks. Basically, I'd just like to mimic as closely as possible what was done in the pre-proccessing pipeline to create the segmented .nii.gz volumes in each subject's T1w folder, but selecting for a specific label of interest and projecting into the white matter 1 mm. mri_label2vol assumes that the labels derived from the annot files are defined for the ?h.white surface, but I wanted to see if this is actually the case. Should I use, e.g., ?h.white.hires instead? John On Fri, Feb 13, 2015 at 2:31 PM, Glasser, Matthew <glass...@wusm.wustl.edu> wrote: We recommend you run tractography directly from the surfaces using probtrackx2.  You can use these surfaces if you want your other volume (i.e. non-cortical) ROIs in native subject space: ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.${Hemisphere}.white.32k_fs_LR.surf.gii Or these if you want them in MNI space: ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.white.32k_fs_LR.surf.gii We recommend you stop tracking at the pial surface to avoid crossing sulci and that you use waystop masks in the subcortical greymatter to avoid connections going to sub cortex and then looping back around to cortex (which creates false positives). Peace, Matt. From: John Plass <johncpl...@gmail.com> Date: Friday, February 13, 2015 at 2:10 PM To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> Subject: [HCP-Users] Projecting Label into White Matter Hello, I have a few questions about using HCP structural data to create waypoints/masks for tractography. In the past, we've created masks of the white matter adjacent to a label of interest with Freesurfer's mri_label2vol, using the "proj" argument to project from the label into the adjacent white matter. I'd like do this with the HCP data, but its a bit unclear to me what would be the proper files to use: 1. I believe this command uses the ?h.white surface by default. The extended preprocessed structural data contains multiple white matter surfaces (?h.white, ?h.white.hires, lh.white.deformed lh.white.prehires). I am not sure which to use. Which surface were the labels defined on? 2. What is the best .mgz file to use as a template volume? T1.hires.norm.mgz appears to be a good match for the T1 nii.gz file, but I'd like to be sure I'm using the best file. Any help would be greatly appreciated! John Plass _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users   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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.   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 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users