Can you confirm that /subjects/CI_01/mri/orig.mgz exists? Usually, your
SUBJECTS_DIR would not be directly in root, especially on a mac, but it
is not impossible.
On 10/14/2022 7:17 AM, Wandschneider, Britta wrote:
External Email - Use Caution
Hello,
I am trying to map tumour+oedem
External Email - Use Caution
Hello,
I am trying to map tumour+oedema lesion masks (generated with ITKSnap) to
subjects' freesurfer surface (in native space) using mri_vol2surf.
This is an example of the command I am using for a specific subject:
mri_vol2surf --mov CI_01_t+oedem
Pick a hemisphere (either lh or rh). Also, you should verify that your
volume overlays on fsaverage correctly with something like
tkmeditfv fsaverage orig.mgz -surfs -fminmax .01 1 -ov
rReslice_Combined_roi_meanRD.nii -reg
$FREESURFER_HOME/average/mni152.register.dat
On 7/11/2022 6:23 PM, R
External Email - Use Caution
Hello everyone,
I am trying to display my lesion map I created in Matlab on a cortical surface,
and am getting the following error:
developer@developer-VirtualBox:~$ mri_vol2surf --mov
rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject fsaver
Not ssure what is happening. CAn you send the full terminal output.
Also, remove the --out_type flag. No need to include --surfreg
sphere.reg (but should not hurt anything).
On 8/14/19 12:37 PM, Pratik Kashyap wrote:
>
> External Email - Use Caution
>
> mri_vol2surf --cortex --hemi lh --
External Email - Use Caution
mri_vol2surf --cortex --hemi lh --interp trilinear --o rest2.nii.gz
--out_type niigz --reg register.dat --projfrac-avg 0.500 --mov rest2.nii
--surfreg sphere.reg --trgsubject fsaverage
A source volume path must be supplied
Hey,
I'm running the abo
External Email - Use Caution
Hello FS users,
I am having a problem with mri_vol2surf. I want to project subcortical voxels
onto the cortical surface. I found out that I can do this with the mri_vol2surf
command. I am following the example given on the documentation, but I am
ge
External Email - Use Caution
Dear Doug Greve,
Sorry, issue solved!
I had used a wrong path directory in the commandline... it’s now working
perfectly well.
Thanks for your help,
Sincerely,
Loïc Daumail
Le mer. 17 avr. 2019 à 17:25, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.e
can you send the full terminal output of the mri_surf2vol command?
On 4/17/19 5:59 AM, Loïc Daumail wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I am currently trying to use mri_vol2surf on my bold data. I typed
> this commandline :
> "
> mri_vol2surf --mov
>
External Email - Use Caution
Dear Freesurfer experts,
I am currently trying to use mri_vol2surf on my bold data. I typed this
commandline :
"
mri_vol2surf --mov
${dir1}/${subject}/${subject}${scan}_space-MNI152NLin2009cAsym_desc-smoothAROMAnonaggr_bold.nii.gz
\
--mni152reg \
-
>
> > > > joseph
> > > >
> > > > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado
> > mailto:ladof...@gmail.com>
> > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>
> > >
<mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>
> <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>>> wrote:
> > >
> > > yes, I have the /Applications/freesurfer/lib/gcc
> > > directory.(actu
; Thanks so much
> > >
> > > joseph
> > >
> > > On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado > <mailto:ladof...@gmail.com>
> > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>>> wrote:
> > &g
>
> > yes, I have the /Applications/freesurfer/lib/gcc
> > directory.(actually, ‘had’ as I reinstalled 5.3) I installed 6.0
> > on top of 5.3 without uninstalling 5.3 first, so it was not a clean
> > install. I will try a
gt; On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado > <mailto:ladof...@gmail.com>> wrote:
> >
> > yes, I have the /Applications/freesurfer/lib/gcc
> > directory.(actually, ‘had’ as I reinstalled 5.3) I installed 6.0
> > on top of 5.3 without uninstal
without uninstalling 5.3 first, so it was not a clean
> install. I will try a clean re-install with the tar file with the
> steps you suggest. Thanks.
>
> Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST)
> From: zkauf...@nmr.mgh.harvard.edu <mailto:zkauf...@nmr.mgh.harva
EST)
> From: zkauf...@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_vol2surf error in FS6
> To: "Freesurfer support list"
> Cc: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> <62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
> Content-Type: text/p
Mar 2017 22:22:01 -0500 (EST)
From: zkauf...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf error in FS6
To: "Freesurfer support list"
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>
Content-Type: te
Hello Fred,
Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of
curiosity, did freesurfer 5.3 exist on your system before installed 6.0?
That error shouldnt happen if FS6 is cleanly installed and definitely
shouldnt happen of SIPS is disabled.
I suppose as a last resort could
Dear FreeSurfer Experts,
I just installed FS6 and encountered the following error, which I can
replicate by just entering “mri_vol2surf” on the command line:
/Users/fred 3> mri_vol2surf
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applicati
Hi Freesurfers,
I am trying to use projfrac 1 to threshold my newly created cortical label to
include the entire cortical ribbon since only a small number of voxels are
being included in my manual tracings. My input code is:
mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nift
Hi Doug,
Yes indeed there is such a file (converted from mgz for DTIStudio). Thanks for
your explanation.
Don
> Date: Tue, 19 Oct 2010 11:40:47 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: dhagle...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfe
Hi Don, is there a file called DTI5_corr_resDTI_DT_minb1000_FA.dat? If
so, it thinks that that file is a file created by selxavg and it tries
to load it in. Doubtless it is not a selxavg file, and so that is
failing in an unpredictable way. This file is not used anymore, so I'll
have mri_vol2su
Using version 4.5.0, I get this error message with mri_vol2surf:
INFO: Source volume detected as selxavg format
number of frames is incorrect (0,1)
This error does not happen with version 3.0.5, and it only happens for input
volumes with particular file names.
This fails:
mri_vol2surf \
--s
Unfortunately, when the NIFTI standard was set up, they copied a
shortcoming from ANALYZE, namely that each dimension is encoded by a
short int, meaning that a dimension cannot have more than 32k elements.
This is a problem when you have surfaces with 100k+ nodes. One
work-around is to break up
Hi,
I'm trying to paint functional data onto a cortical "midgray" surface.
The surface was generated using mris_expand to expand the WM surface to
50% of the pial surface.
The data I want to paint onto this surface is in a 96 x 96 x 17 x 512
dimension NIFTI file generated using the feat comma
Dear all,
I am trying to overlay group-averaged data (FSL) on an averaged anatomical
brain (Freesurfer).
I did the following,
mri_vol2surf --src AVG.gfeat/cope1.feat/thresh_zstat1.img --src_type analyze
--srcreg register.dat --hemi lh --projfrac 0.5 --out
AVG.gfeat/cope1.feat/thresh_zstat1-lh.w -
27 matches
Mail list logo
