External Email - Use Caution
Hi,
there are some easy to use Matlab/Python functions to read/write native
Freesurfer files (.annot, surfaces etc.) available. Anyone knows something
similar for C++ (VTK)?
Thank you.
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Freesurfer mailing
can you send the entire output?
On Mon, 1 Jul 2019, Nillo, Ryan Michael R
wrote:
Hi Bruce,
We wanted to map values from a previous analysis to a representation of the
brain with the sulci
filled — something that resembles the output lh.pial-outer-smoothed from the
recon-all -localGI. I
tried
That is the problem. It is not a cortical surface (ie, white or pial); isn't
this LGI surface just a surface shrink wrapped around cortex? Not sure how to
map that across subject.
On 7/1/2019 2:53 PM, Nillo, Ryan Michael R wrote:
Pial-outer-smoothed was a surface created from recon-all -localGI.
Pial-outer-smoothed was a surface created from recon-all -localGI.
Ryan Michael Nillo
Staff Research Associate I
University of California San Francisco
Department of Radiology and Biomedical Imaging
> On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D.
> wrote:
>
> how was pial-outer-smoothe
how was pial-outer-smoothed create?
On 7/1/2019 2:33 PM, Nillo, Ryan Michael R wrote:
Hi Doug,
lh.test.nii was created with:
mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1
--regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o
./lh.test.nii
Where lh.
Hi Doug,
lh.test.nii was created with:
mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1
--regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o
./lh.test.nii
Where lh.probability.nii is a probability mask created from about 63 subjects.
Thanks in advanc
Who did you create lh.test.nii?
On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote:
Hi Bruce,
We wanted to map values from a previous analysis to a representation of the
brain with the sulci filled — something that resembles the output
lh.pial-outer-smoothed from the recon-all -localGI. I tried u
Hi Bruce,
We wanted to map values from a previous analysis to a representation of the
brain with the sulci filled — something that resembles the output
lh.pial-outer-smoothed from the recon-all -localGI. I tried using
mri_surf2surf, but I get the error:
ERROR: dimension inconsistency in sourc
Hi Ryan
I'm not sure why you would have a surface with 73K vertices on fsaverage.
Why not use one of the ico representations (40K or 160K vertices)? In any
case, mri_surf2surf should do the trick, although you will probably need to
create a new subject with a set of 73K vertex surfaces
cheer
Hello Freesurfer users/developers,
I have surface with ~73,400 vertices generated from the Freesurfer version 6
fsaverage brain, left hemisphere. I have a surface map that was created by
mapping a volume to the fsaverage white surface. Is there a way to map the
surface map to the new surface wi
Hi Sofia,
Would it be possible to send us the volume and one of the surface files
you loaded?
Best,
Ruopeng
On 07/24/2018 12:08 PM, Sofia Rodriguez Penuela wrote:
External Email - Use Caution
Dear Freesurfer team,
After loading a volume in Freeview, we try to load surfaces, but
Hi Romella
usually the left/right split is defined by the aseg, so try fixing it and
rerunning the surface generation and see if it resolves your problem
cheers
Bruce
On Fri,
22 Dec 2017, Romella Durrani wrote:
> Hi,
> I'm having problems with the surfaces along the midline for one scan. I hav
Yes the aseg.mgz has many issues towards the anterior regions, specifically on
the right side. Would this be fixed by manually editing the putamen aseg, etc.?
And would this then subsequently resolve the surface issues?
> On Dec 31, 2017, at 3:06 PM, Douglas Greve wrote:
>
> Did you check the
Did you check the aseg.mgz? It looks like the anterior portions of right
putamen, caudate, ventricle were not labeled properly.
On 12/22/17 1:29 PM, Romella Durrani wrote:
Hi,
I'm having problems with the surfaces along the midline for one scan.
I have attached pictures of the brainmask with
use fscalc, eg,
fscalc file1.mgh sum file2.mgh -o file1+file2.mgh
run fscalc without any options to get the list of operations
On 07/10/2017 03:28 PM, Van Der Deijl, Rosanne wrote:
> Dear Freesurfer team,
>
> Is it possible to add/subtract/compute the average of freesurfer
> surface .mgh files
do you actually mean the average of the (xyz) surface locations or do you
mean the average/difference of scalar fields over the surface?
On Mon, 10 Jul 2017, Van Der Deijl, Rosanne wrote:
> Dear Freesurfer team,
>
> Is it possible to add/subtract/compute the average of freesurfer surface
> .mgh
Dear Freesurfer team,
Is it possible to add/subtract/compute the average of freesurfer surface .mgh
files? And how would I do this?
Thank you in advance.
Kind regards,
Rose
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https://mail.nmr.m
Hi Sean
none of these things are easy to do. Unless you have a compelling reason
you are better off letting recon-all do it's thing. Otherwise you will
send lots more person time fixing things that it would have gotten right
if you had let it
cheers
Bruce
On Fri, 2 Dec 2016, Hatton, Sean wro
Hello,
We are just interested in generating the white and pial surfaces without
segmentation.
1. Are there additional switches for running mris_make_surfaces without aseg
(for -white section) or apar.annot (for -pial section)?
2. We would like to control intensity values - can we specify tissu
thanks Dr. Fischl,
Would there be a reason as to why recon-all crashed when doing the
conformation then? I got the following error in my terminal:
Original Data has (0.5, 0.5, 0.5) mm size and (394, 466, 378) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data
Hi Trisanna
you can use the -cm flag, but typically what we do is let recon-all
"conform" the data to 1mm, then do a post-hoc surface deformation with
the original highres data using mris_make_surfaces
cheers
Bruce
On Wed, 25 May 2016, Trisanna Sprung-Much wrote:
> Hi there
>
> My initial ema
Hi there
My initial email didn't seem to have sent and so I am re-sending it:
I would like to know if it is possible to create surfaces from a scan that
is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which
is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if th
Hello,
I would like to conduct a surface-based analysis with resting-state data
using SPM's CONN toolbox v14.0. Is there a way to combine the three
preprocessed freesurfer files (lh, rh, mni305) into one file? CONN seems to
only accept one file, or files that have exactly the same dimensions.
Th
Hi Freesurfer experts,
I am trying to perform whole brain tractography using FSL's Probtrackx2 with
Freesurfer white surfaces as seed and pial surfaces as targets. To obtain a
whole brain connectivity graph I need the streamlines between the hemispheres.
This means that I need to remove the par
t; temporary file? Error message:
> > “mkdir: /usr/local/fsl/data/standard/tmp.fslregister.9446: Permission
> > denied”
> >
> >
> > Message: 17
> > Date: Mon, 07 Oct 2013 11:01:23 -0400
> > From: Douglas N Greve > <mailto:gr...@nmr.mgh.
> denied”
>
>
> Message: 17
> Date: Mon, 07 Oct 2013 11:01:23 -0400
> From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?
> 116(14)
> To: freesurfer@nmr.mgh.harvard.edu <mailto:f
e: 17
Date: Mon, 07 Oct 2013 11:01:23 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?
116(14)
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5252ccc3.5070...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowe
32 -0400
> From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] FSL masks applied to Freesurfer surfaces?
> To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Message-ID: <524eeb0c.8050...@nmr.mgh.harvard.edu
&
reesurfer] FSL masks applied to Freesurfer surfaces?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <524eeb0c.8050...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Do you want to transfer them to fsaverage space or to the individual
anatomical space?
dou
Do you want to transfer them to fsaverage space or to the individual
anatomical space?
doug
On 10/04/2013 01:42 AM, Ruth Carper wrote:
> Hi,
> I'd like to take some masks that I have in MNI standard space in FSL
> and map them to Freesurfer surface space. The goal is to extract
> measures of
Hi,
I'd like to take some masks that I have in MNI standard space in FSL and map
them to Freesurfer surface space. The goal is to extract measures of average
cortical thickness (or area or etc) for those regions for each subject. Is
there a standard way to do this?
Dear all,
I think my issue is quite related to this one (if not duplicated,
sorry in that case):
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027622.html
As Shani, I used bbregister to coregister diffusion images to anatomical:
> bbregister --s OE0_T1 --mov DTI_b0_brain.ni
Hi Nick,
I did one pass at supporting a "both" prefix for both hemis combined. Can
you make the output "both.pial.gii" and let's adopt that convention?
thanks
Bruce
On Fri, 9 Dec 2011, Nick Schmansky wrote:
> this should work:
>
> mris_convert --combinesurfs ./lh.pial ./rh.pial ./pial.gii
>
>
this should work:
mris_convert --combinesurfs ./lh.pial ./rh.pial ./pial.gii
notice the output name has ./ in it, to override an old freesurfer-ism
of appending a default hemi. also note that .gz is not necessary as
gzip is the freesurfer default for gifti.
however, freesurfers implementation d
hi all,
this command: mris_convert --combinesurfs lh.pial rh.pial pial.gii.gz
resulted in lh.pial.gii.gz (the help says it should generate pial.gii.gz).
a related question. once i have this gifti file how do i get
annotations+curvature info also into the file? (the gifti schema supports
this rig
x128 axial image which has 0.83^3 resolution. I
> am intrested in generating the cortical surfaces and overlay
> it on this image. Freesurfer first converts this image to
> 256^3 voxels and 1^3 resolution and then generates the
> surfaces. Thus if I wan
t; 256x256x128 axial image which has 0.83^3 resolution. I am intrested in
> generating the cortical surfaces and overlay it on this image.
> Freesurfer first converts this image to 256^3 voxels and 1^3
> resolution and then generates the surfaces. Thus if I want to
> intersect freesur
Hi Navid, what do you mean by "the original image space"? Ie, what
coordinates do you specifically want? Voxel? Scanner?
doug
Navid Shiee wrote:
> Dear Freesurfer team,
>
> I have a question regarding Freesurfer surfaces. I submitted this
> questions to the wiki but di
Dear Freesurfer team,
I have a question regarding Freesurfer surfaces. I submitted this questions
to the wiki but did not get any response and I was wondering if you can help
me on this issue.
I am doing some experiments with Freesurfer and would like to have surfaces
in the original image space
e you to voxel space in the conformed
> coordinates (not the raw input). Is this good enough?
> doug
>
> Steffen Bollmann wrote:
>
>> Dear freesurfer experts,
>>
>> I would like to display freesurfer surfaces in the voxelspace of the
>> original subject image us
The --vox2ras-tkr transform will take you to voxel space in the
conformed coordinates (not the raw input). Is this good enough?
doug
Steffen Bollmann wrote:
> Dear freesurfer experts,
>
> I would like to display freesurfer surfaces in the voxelspace of the
> original subject image
Dear freesurfer experts,
I would like to display freesurfer surfaces in the voxelspace of the
original subject image using matlab.
Which coordinate transformation do I have to apply to get the
vertex-coordinates to the RAS space and finally to the original
voxelspace of the subject? (i guess
Hi,
I just added a quick tutorial on how-to export FreeSurfer surfaces and use
it as a render object for Blender
http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel
If someone has other tutorials I think you can use this new section of User
Contributions:
http://surfer.nmr.mgh.harvard.edu
not sure, you'll have to ask the slicer folks
On Fri, 26 Jun 2009, Gregory
Dierksen wrote:
Hi,
I'm trying to convert a binary volume to a surface that can be viewed with
slicer3. I've used the following commands:
mri_tesselate microbleeds.mgz 1 lh.microbleeds
mris_smooth lh.microbleeds
Hi,
I'm trying to convert a binary volume to a surface that can be viewed
with slicer3. I've used the following commands:
mri_tesselate microbleeds.mgz 1 lh.microbleeds
mris_smooth lh.microbleeds -n 5 lh.microbleeds-smooth
When I attempt to ope the lh.microbleeds-smooth surface using slicer
Fantastic. Thanks for the speedy responses.
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
Nick Schmansky wrote:
Jim,
There is a way to insert special flags into the recon-all command stream
for a particular binary. See the section 'E
Jim,
There is a way to insert special flags into the recon-all command stream
for a particular binary. See the section 'EXPERT OPTIONS FILE' in
recon-all --help. So you would create a file called expert.opts
containing:
mris_make_surfaces -fix_mtl
and then add the string '-expert expert.opts'
yes, although the white matter volume that comes from mris_wm_volume is
affected by the aseg (since non-wm voxels that are interior to the
?h.white surface are removed from the volume calculation)
cheers,
Bruce
On Mon, 10 Dec
2007, Chris Watson wrote:
Hi,
So if the volumes are estimated fro
Hi,
So if the volumes are estimated from the surfaces and not aseg.mgz, does
this mean it is unnecessary to edit aseg.mgz? Or is it still necessary,
but only for the subcortical structures? Is it best to make pial
surface/wm.mgz edits and control points for grey and white matter, and
aseg.mgz
Hi Jim,
yes, I think that should be fine
Bruce
On Mon, 10 Dec 2007, James N. Porter wrote:
Hello Bruce-
From the wiki, I gather that I would rerun recon-all from -finalsurfs onward,
as that is the step that calls make_final_surfaces. In order to insert the
fix_mtl flag I'll have to run that
Hello Bruce-
From the wiki, I gather that I would rerun recon-all from -finalsurfs
onward, as that is the step that calls make_final_surfaces. In order to
insert the fix_mtl flag I'll have to run that section via a separate
command line outside of recon-all. Are there any other subsequent step
Hi Jim,
you can actually run mris_make_surfaces with -fix_mtl and it will inhibit
all deformations in these regions. I didn't enable that by default as I was
afraid it would mean missing a bit of entorhinal. In general it doesn't
really matter as the gray and white volumes computed from the su
Hello FreeSurfer Folks-
I've seen several threads in the archives discussing the expected
inaccuracies in the pial, white, and orig surfaces running through
subcortical structures. However, I've been unable to ascertain exactly
how much and what kind of inaccuracy is acceptable. It makes sense
Hi freesurfers,
I have a question. I deleted some of the optic nerve on a participant and
ran
source /usr/local/freesurfer/nmr-std-env
cd /space/doodles/3/users/dwakeman/pilot/again
setenv SUBJECTS_DIR `pwd`
recon-all -autorecon2-wm -autorecon3 -subjid p001 -mail dwakeman
When the surfaces were
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