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
? 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
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
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
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
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
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
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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
: 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,
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
: 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
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
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
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
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
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
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
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
--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
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
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
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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
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