Re: [Freesurfer] mri_surf2vol with inflated surfaces

I'm not sure what a ribbon for the inflated surface would look like. You can try mri_surfacemask to create a binary volume of everything inside the surface. On 10/14/2021 7:47 PM, Nicolas Munera Garzon wrote: External Email - Use Caution Greetings freesurfuer community, I've been

Re: [Freesurfer] mri_surf2vol method one

We have not used .w files in years. Try converting the .w file to .mgz using mri_surf2surf (or even better, don't save them as .w files) On 10/22/2020 4:03 PM, Yixin Ma wrote: External Email - Use Caution Hi Freesurfer experts, I'm trying to write the normals of the GM/WM meshes to

Re: [Freesurfer] mri_surf2vol -lost cluster

You can ask it to sample the maximum along the surface normal over a certain distance. Use --projdist-max. Run mri_vol2surf --help for more info On 9/27/2019 2:04 PM, Albrecht, Daniel S. wrote: Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the

Re: [Freesurfer] mri_surf2vol: has many more faces than vertices

Hi Stephanie the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white) cheers Bruce On Sun, 9 Dec 2018, Winkelbeiner, Stephanie A wrote: External Email - Use

Re: [Freesurfer] mri_surf2vol

Try using mri_label2vol with the ribbon.mgz file. That has a segmenentation of everything inside the white surface. On 08/10/2017 03:58 PM, Rockers, Elijah D. wrote: > I am attempting to create a volume from a surface. My ultimate goal is > to obtain a mask that includes everything "inside"

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Not sure if I followed. Does the look up table have the labels at all? > On May 15, 2017, at 7:46 PM, Bruce Fischl wrote: > > hmm, not sure. Ruopeng? > > On Mon, 15 May 2017, Lukas Pezenka wrote: > >> Thank you. The tip about Christophe's parcellation was very

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

hmm, not sure. Ruopeng? On Mon, 15 May 2017, Lukas Pezenka wrote: > Thank you. The tip about Christophe's parcellation was very helpful - I > can actually see the sulcal labels in freesurfer when loading > aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing > labels only"

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Thank you. The tip about Christophe's parcellation was very helpful - I can actually see the sulcal labels in freesurfer when loading aparc.a2009s+aparc volume. Oddly enough, when I check the "show existing labels only" box, none of them is displayed - I wonder why that is? I should, in any

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

no, they shouldn't be labeled as 0. You can create your own though, possibly using Christophe's parcellation instead of the aparc.annot (check in recon-all.cmd to see how to run it). Christophe's has sulci labeled separately so might be better for your purposes. Or you could create your own

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

You need to use a valid output format like mgh, mgz, nii, etc (eg, surf/lh.inflated.mgh). Also, you should not run vol2surf mapping to the inflated surface as this surface is mostly outside the head. Use the default white surface and then visualize on the inflated only On 05/12/2017 10:18 AM,

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Hi Bruce, not sure - from what I see, sulci are labelled as 0 in the wmparc, are they not? In my understanding, only gyri are actually labelled... I might as well get that totally wrong, though, so sorry if I do... Best regards, Lukas On 15.05.2017 15:53, Bruce Fischl wrote: > Hi Lukas > >

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Hi Lukas lh.sulc is not a surface - it's a scalar field over the surface. Have you looked at the wmparc? Does it not fill your needs? cheers Bruce On Mon, 15 May 2017, Lukas Pezenka wrote: > Hi all, > > here's my follow-up: I've now tried to use mris_fill on my lh.sulc. > However, I got the

Re: [Freesurfer] mri_surf2vol cannot recognize the type of surf/lh.inflated

Hi all, here's my follow-up: I've now tried to use mris_fill on my lh.sulc. However, I got the error message that "there are many more faces than vertices". Running recon-all on this dataset takes 30+ hours on my machine, hence I don't want to do it again unless it is absolutely necessary.

Re: [Freesurfer] mri_surf2vol

The overlay Control21/rest/fc.ramgseed.surf.rh/R_Amygdala/sig.nii.gz is in fsaverage space, so either change the subject to fsaverage, or use mri_surf2surf to map the overlay into Control21's space, then run mri_surf2vol On 05/13/2016 06:03 PM, std...@virgilio.it wrote: > Hi list, > > I'm

Re: [Freesurfer] mri_surf2vol {Disarmed}

nclude any voxel even if only a corner of it has some surface > in it. > > On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > > here it is. thanks, > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > From: gr...@nmr.mgh.harvard.edu > > > Date: Fr

Re: [Freesurfer] mri_surf2vol {Disarmed}

it is hard to tell from that view. Can you click on a point that appears to be outside the brain so we can see what it looks like around that point in all three views? On 01/15/2016 10:56 AM, Xiaomin Yue wrote: > Hi All, > > In fs5.3, I tried to generate a volume mask from the pial surface >

Re: [Freesurfer] mri_surf2vol {Disarmed}

d.edu > > From: gr...@nmr.mgh.harvard.edu > > Date: Fri, 15 Jan 2016 12:00:02 -0500 > > Subject: Re: [Freesurfer] mri_surf2vol {Disarmed} > > > > it is hard to tell from that view. Can you click on a point that > appears > > to be outside the brain so we can see what it looks lik

Re: [Freesurfer] mri_surf2vol {Disarmed}

your voxel size? It will include any voxel even if only a corner of it has some surface in it. On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > here it is. thanks, > > > > > To: freesurfer@nmr.mgh.harvard.edu > > From: gr...@nmr.mgh.harvard.edu > > Date: Fri, 15 Jan 2016 12:00:02 -0

Re: [Freesurfer] mri_surf2vol {Disarmed}

some surface > in it. > > On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > > here it is. thanks, > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > From: gr...@nmr.mgh.harvard.edu > > > Date: Fri, 15 Jan 2016 12:00:02 -0500 > &g

Re: [Freesurfer] mri_surf2vol {Disarmed}

t; > > here it is. thanks, > > > > > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > From: gr...@nmr.mgh.harvard.edu > > > > Date: Fri, 15 Jan 2016 12:00:02 -0500 > > > > Subject: Re: [Freesurfer] mri_surf2vol

Re: [Freesurfer] mri_surf2vol {Disarmed}

ven if only a corner of it has some surface > > in it. > > > > On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > > > here it is. thanks, > > > > > > > > > > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > From: gr...@nmr.mgh.harvard.edu > &g

Re: [Freesurfer] mri_surf2vol {Disarmed}

t; > That point is fairly close to the pial surface. What is your voxel size? > > It will include any voxel even if only a corner of it has some surface > > in it. > > > > On 01/15/2016 12:16 PM, Xiaomin Yue wrote: > > > here it is. thanks, > > > > >

Re: [Freesurfer] mri_surf2vol in fsaverage space

Convert the thickness maps to fsaverage using mri_surf2surf, then use mri_surf2vol doug On 12/03/2013 10:00 AM, Govindarajan, Koushik Athreya wrote: Dear Freesurfers, I am trying to export the cortical thickness maps in nifti format using the mri_surf2vol command. Is it possible

Re: [Freesurfer] mri_surf2vol in fsaverage space

] On Behalf Of Douglas N Greve Sent: Tuesday, December 03, 2013 9:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2vol in fsaverage space Convert the thickness maps to fsaverage using mri_surf2surf, then use mri_surf2vol doug On 12/03/2013 10:00 AM, Govindarajan, Koushik Athreya

Re: [Freesurfer] mri_surf2vol in fsaverage space

? Regards Koushik -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Tuesday, December 03, 2013 9:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2vol

Re: [Freesurfer] mri_surf2vol questions

: [Freesurfer] mri_surf2vol questions To get them both in one file, run mri_surf2vol to get the left hemisphere. When you run it a 2nd time for the right hemisphere add --merge vol.lh.nii. I think FSL has software to swap dimensions doug On 11/04/2013 09:53 AM, Govindarajan, Koushik Athreya wrote

Re: [Freesurfer] mri_surf2vol questions

To get them both in one file, run mri_surf2vol to get the left hemisphere. When you run it a 2nd time for the right hemisphere add --merge vol.lh.nii. I think FSL has software to swap dimensions doug On 11/04/2013 09:53 AM, Govindarajan, Koushik Athreya wrote: Hello Freesurfers,

Re: [Freesurfer] mri_surf2vol

Hi Douglas, Yes, I know that, I just put subjid in the email not to enter a long pathname and an actual subject id that is irrelevant to the email. Sorry about the confusion. Do you see any other problem with the command? Thank you, Peter On 09/16/2011 02:22 PM, Douglas N Greve wrote: subjid

Re: [Freesurfer] mri_surf2vol

Hi Douglas, I removed the --surf curv option from the command, but had exactly the same error output. Also, if curv is not a surface, how can I get the curvature values into a 3D volume? This is all I'm really interested in. Thank you once again, Peter On 09/16/2011 02:39 PM, Douglas N

Re: [Freesurfer] mri_surf2vol

Is that subject in your $SUBJECTS_DIR ? Peter Savadjiev wrote: Hi Douglas, I removed the --surf curv option from the command, but had exactly the same error output. Also, if curv is not a surface, how can I get the curvature values into a 3D volume? This is all I'm really interested in.

Re: [Freesurfer] mri_surf2vol

You are right, it turned out there was an issue with $SUBJECTS_DIR and when I fixed it, everything worked fine. Thank you very much for your help! Peter On 09/16/2011 03:22 PM, Douglas N Greve wrote: Is that subject in your $SUBJECTS_DIR ? Peter Savadjiev wrote: Hi Douglas, I removed the

Re: [Freesurfer] mri_surf2vol

For surfval, you need to give it a file name eg, lh.curv, lh.thickness. You'll also need a registration file (or indicate that it is a header registration with --regheader subjectname) doug Antonella Cappelletti wrote: Hi all, I don't understand what's wrong with this command line:

Re: [Freesurfer] mri_surf2vol

try using mris_fill. cheers Bruce On Tue, 13 Apr 2010, Jerald Zhao wrote: Hi all, I'm a new user of freesurfer. It's a simple question. I want to convert ?h.smoothwm and ?h.smoothwm.nofix to .mgz as binary volume (foreground/background = 1/0). So I found mri_surf2vol command, but the

RE: [Freesurfer] mri_surf2vol

but that doesn’t work with mri_convert _ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doug Greve Sent: mercredi, 15. août 2007 23:11 To: Leila BH Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_surf2vol Do you want a mask of just the ribbon or everything