Hi, I am looking for a tool of FreeSurfer. In fact, the tool is supposed to
take in input 2 surfaces ( hemispheres) of subjects, registrate the surfaces
and display the difference between the 2surfaces ( like 'euclidian distance').
What I want is exactly that output
Hi,
I saw in the documentation that since the version 5.2.0 of Freesurferw ecan
open and write .gii file. I have a surface in .gii and I would like open it on
FS. The fact is that, I didn't find a way to do that in the documentation.
Does anyone know a way?
Thanks.
Hi everyone,
I would just say you thank you for the help you give to Freesurfer users. I use
Freesurfer for my school project and I ended yesterday. I didn't know anything
about Linux before and before segmentation software of cortical surface. I
don't think I would did an so great job
Hi, I'm a new user of Freesurfer.
1) I would like to extract only the cortex cerebrum . So I think I don't need
the complete subcortical segmentation ( 20-40 hours). Do you know a way to
segment only cortex or only ( cortex+ pial ( left/rigt hemispher)?2) I already
try the complete
Hi, I have 8 folders of 26 slice odf dicom. Yesterday, I launched the
conversion to .mgz with the command recon-all -i
path-to-first-structural [-i path-to-second-structural] -s
subjid . All my folders are created but in the Orig folder I don't fige files
.mgz.
I think that the processing time
give recon-all a folder as input. It must be an image file.
If you have multiple files, you need multiple -i flags.
doug
On 03/07/2013 03:48 PM, Valtina Pouegue wrote:
Hi,
Here it is
[esther@IP132-207-67-224 ~]$ recon-all -i
/home/esther/Freesurfer/freesurfer/subjects/Patient13B -s
in the series, the software
will find the other slices and create the .mgz.
On Mar 7, 2013, at 9:02 PM, Valtina Pouegue pval...@hotmail.com wrote:
Oh yes. It's my mistake. But should I give the adress of the first file of my
set for having the result in .mgz. Thanks.
Date: Thu, 7 Mar 2013 16
...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Time
Does that file exist? What was your command to create the mgz file?
On 03/08/2013 12:12 PM, Valtina Pouegue wrote:
Hi,
I convert my files and i get news folders
recon-all to get a volume, you can just run
mri_convert, eg
mri_convert /path/to/dicomfile out.mgz
tkmedit -f out.mgz
doug
On 03/08/2013 12:54 PM, Valtina Pouegue wrote:
If i'm right, the command: recon-all -s 13A -all execute the whole
segmentation ( between 20-40 hours).
So , if I
not need to run recon-all to get a volume, you can just run
mri_convert, eg
mri_convert /path/to/dicomfile out.mgz
tkmedit -f out.mgz
doug
On 03/08/2013 12:54 PM, Valtina Pouegue wrote:
If i'm right, the command: recon-all -s 13A -all execute the whole
segmentation ( between 20-40
to write to that directory (or the
disk is full)
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
VP,I try FreeView,, tits really nice!
I dont really know what going on, i try mri-convert with another subject
aand i get this:
[esther@IP132-207-67-224
...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu;
gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Time
what are you trying to do? If run a recon, your first command should have a
-all at the end of it
cheers
Bruce
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
I don't think
Hi Freesurfers,
I would like to extract the whole pial surface of a brain volume. I already
done the segmentation and i have ( rh.pial and lh.pial surfaces). Does it
exist a way to get the whole pial surface without separation?
Thanks.
VP
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz. But I
think I shoul first convert mnc to nii then nii to mgz. , so I try the command
mri_convert and I have this error; -[esther@m3012-04 ~]$
mri_convert $SUBJECTS_DIR/Patient1/fichierMnc.mnc
Bruce
On Fri, 15 Mar 2013, Valtina Pouegue wrote:
Hi,
I have a problem of conversion. I would like to convert mnc file to mgz.
But I think I shoul first convert mnc to nii then
nii to mgz. ,
so I try the command mri_convert and I have this error;
-
[esther@m3012
] mri_convert problem
can you run ls -l and mri_info on it?
On Fri, 15 Mar 2013, Valtina Pouegue
wrote:
I get this error-
esther@m3012-04 ~]$ mri_info
$SUBJECTS_DIR/AA/t1_icbm_normal_1mm_pn3_rf20.mnc
mincRead(): can't find file/home/esther/Freesufer/freesurfer/subjects/AA/t
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to
get measurements with FreeSurfer. SO, I convert my rile ( readdfs --
write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I
tried to get measurements with the command
I could see the created surface in MAtlab ( 'read_surf,) but I could't open
the file in Freesurfer with tksurfer
VP
From: pval...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: Brainsuite -- FreeSurfer
Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with
?
Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't open
the file in Freesurfer with tksurfer
VP
it depends on what measures you want
Bruce
On Wed, 20 Mar 2013, Valtina Pouegue
wrote:
Hi Bruces,
It's because i'm doing a comparison between brainsuite and freesrufer. So , I
would like to export results of
segmentation with Brainsuite and make measurements with FreeSurfer. In Fact
Hi,
Is it possible to get the algorithm of mris_anatomicacl_Stats. Just ot know
which files it uses to compute metrics ...
Thanks.
VP___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
I have a volume in mnc and nii format. I would like to extract the outer
surface from those volumes to be able to use in Freesurfer. I tried
'mri_vol2surf' but I didn't have the registration file. So I try make_register
to create a registration file and the system give me an error as it
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