[Freesurfer] dilating labels within a parcellation

Hi all, Is there a tool to surface-dilate all the labels contained within an annotation file simultaneously, while preserving the non-overlapping nature of the labels? I saw there is a development version of mri_label2label that works for individual label files separately, but that gets me into

Re: [Freesurfer] generating new FREESURFER directory from linear transform

will not be the same as applying it to the outputs) sorry Bruce On Fri, 4 Sep 2015, David Grayson wrote: > > Hi all, > >   > > I would like to take a single subject’s freesurfer directory and apply > a single linear transform (I already have the .dat file I would like

[Freesurfer] generating new FREESURFER directory from linear transform

Hi all, I would like to take a single subject's freesurfer directory and apply a single linear transform (I already have the .dat file I would like to use) to all of the recon-all output (volumes, surfaces, label files, etc). Essentially I would like to apply the transform and make a new freesu

Re: [Freesurfer] warping segmentations onto unprocessed brain

hen use it as > initialization for mri_nl_align. I would think you are better off doing the > surface recons and using cvs though. It's only computer time > > cheers > Bruce > > On Wed, 25 Feb 2015, David Grayson wrote: > > > Hey Bruce, > > Thanks for res

Re: [Freesurfer] warping segmentations onto unprocessed brain

? I would think bbregister > and mri_vol2vol would do the trick > Cheers > Bruce > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson > wrote: > > > > Hi freesurfers, > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > free

[Freesurfer] warping segmentations onto unprocessed brain

Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I

Re: [Freesurfer] applying manual freesurfer edits to warped brain image

: text/plain; charset="us-ascii" > > What format is the distortion field stored in? If you can get it into .m3z > I believe we have tools to do what you want > > > > > On Nov 2, 2014, at 9:37 PM, David Grayson > wrote: > > > > Hi freesurfer experts,

[Freesurfer] applying manual freesurfer edits to warped brain image

Hi freesurfer experts, I have two T1 images from the same subject acquired at the same time point. One of the images is distortion corrected using a calibration phantom, put through the full freesurfer pipeline and then extensively manually edited. The uncorrected image has had zero processing. Wh

[Freesurfer] overlapping labels

Hi freesurfers, Can a .annot file include labels with overlapping vertices? If not, then when using mris_label2annot, how does freesurfer decide which label to assign the vertices to? Thanks, David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harva

[Freesurfer] method for detecting neighboring labels?

Is there a way to output a list of all the labels within a given annotation file which share a border with another specified label? Thank you very much, David ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

[Freesurfer] last index missing when using mri_label2vol

Hi, I am noticing that when I use ‘mri_label2vol --annot’ it is not creating the final label from the color table file. I tried using the --thresh 1 option, but that didn't work either. i.e... mri_label2vol --annot lh.custom.annot --temp ../mri/orig.mgz --o custom_lh.nii.gz --subject FREESURF

Re: [Freesurfer] weird relabeling with mri_convert

--annot option, but then that gives me the parcellations in the gray matter, whereas I want them on the WM/GM boundary. Any ideas? Thanks if you’re still reading! David From: David Grayson Sent: Tuesday, February 21, 2012 7:04 PM To: 'Bruce Fischl' Cc: freesurfer@nmr.mgh.harvard.edu S

Re: [Freesurfer] weird relabeling with mri_convert

anything else I can try? Thank you, David From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, February 21, 2012 12:58 AM To: David Grayson Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] weird relabeling with mri_convert Try -odt short to stop it from changing the

[Freesurfer] weird relabeling with mri_convert

Hi freesurfer folks, I am using mri_convert to reorient my custom cortical parcellation (a nifti file generated from an annotation file), and I have run into some unexpected blips with some seemingly errant reindexing. Here is the command I am using: mri_convert -rl FREESURFER/mri/orig/001.mgz

[Freesurfer] applying new cortical parcellations

Hi Freesurfer experts, I would like to apply a novel cortical parcellation from an average surface (http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011) to subjects that I have previously ran through recon-all. I have found a number of tools that seem related to this – can any

Re: [Freesurfer] converting "annotation values" to "label codes"

That's perfect, Doug. Thank you so much! David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, November 03, 2011 2:22 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] converting "annotati

[Freesurfer] converting "annotation values" to "label codes"

Hi, I have converted a custom-made annotation file to a volume, and now I am trying to find a table with the labels and their corresponding label codes (index values which are created when the annotation file is converted to a volume). I only have the “annotation values” or color codes for each

Re: [Freesurfer] propagating labels to gray matter

hough. Is this important? Thanks, David -Original Message- From: Douglas Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 7:40 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter Hi Dav

Re: [Freesurfer] propagating labels to gray matter

once I have the surface labels, is there a way to re-propagate them back into the gray matter? Thanks again, David -Original Message- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Monday, October 31, 2011 2:38 PM To: David Grayson Cc: 'freesurfer@nmr.mgh.harv

Re: [Freesurfer] propagating labels to gray matter

: David Grayson Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] propagating labels to gray matter what was your label2vol command line? doug David Grayson wrote: > > Hi freesurfer experts, > > > > I currently have a set of cortical labels that are the re

[Freesurfer] propagating labels to gray matter

this requires a method to ‘propagate’ these labels through the gray matter. I have so far been unsuccessful – ‘mri_label2vol’ seems to only give me that pial or white surfaces, as opposed to the gray matter bodies. Does anyone know how to accomplish this? Thank you very much, David Grayson

[Freesurfer] Beginner question

Hey folks, I am totally new to freesurfer, so please forgive me… I am trying to open up an atlas in freesurfer that is in 4dfp.ifh format (or nii, if you like). Can anyone tell me how? Otherwise, I could try to reconstruct it straight from the T1 anatomical run, but when I try the following co