Hi Guang,
to register two volumes of the same person (6 degree of freedom:
translation, rotation) you can use
mri_robust_register --mov 002.mgz --dst 001.mgz --lta 2to1.lta --warp
2to1.mgz
This will register 002.mgz to 001.mgz output the transform 2to1.lta and
the source mapped to the target as
> Hi Nick,
>
> I can't get the script to work but that might be due to my inexperience
> with matlab. I copied the script into my matlab directory, and tried to
> run
> dice_labels
> (/autofs/space/phrenic_007/users/jon/hires_amy/Round_1/HRDEV150/whole_amygdala.label,
> /autofs/space/phrenic_007
Jon,
Do the matlab scripts work for you? The approach you are taking with
the existing tools is the one I was considering myself but decided it
was too roundabout and probably wouldn't work for you anyway (because
mri_compute_seg_overlap looks for particular label ids corresponding to
subcortical
Hi Nick,
I was actually able to convert the label files into volumes using
mri_label2vol and then use the mri_segstats to get the total number of
pixels from each volume file. But the mri_compute_seg_overlap didn't
work as easily. I tried running the following but the results were all
zero, wh
here's a sample command string for the old fixer:
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 nicktp1 rh
and the new one:
mris_topo_fixer -mgz -warnings -seed 1234 nicktp1 rh
where 'nicktp1' is a subject name.
Nick
On Thu, 2009-08-20 at 09:23 -0400, Bruce Fischl wrote:
>
Jon,
None of the existing utilities will calculate the Dice of two labels (at
least not in a straightforward manner). However, its easy to do in
matlab.
Attached is a script to do this. Copy it to your
$FREESURFER_HOME/matlab directory.
Usage is:
dice_labels('label1.label','label2.label')
or
Hi Holly,
Can you please try to launch it on the fsaverage subject that you have
downloaded with the distribution? Just to see if you get the same
error, because I don't seem to get an error neither with fsaverage nor
with the average subject I just created.
Marie
On 20 août 09, at 15:
you can use fslregister or spmregister instead
doug
Guang Zeng wrote:
> Hi, there,
>
> Sorry, I asked the same question yesterday, but I think I didn't
> explain it clear.
> I have the two scans (001.mgz and 002.mgz) of the same subject,
> 001.mgz is used as the input of recon-all -autorec
Hi,
I need to compute the reliability of two manually traced ROIs and I was
told to use the command mri_compute_seg_overlap. However, it seems
this command needs its input to be in .mgz format, but the ROIs have
been saved as .label files in Freeview. A simple renaming function
does not work,
Hi, there,
Sorry, I asked the same question yesterday, but I think I didn't explain it
clear.
I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used
as the input of recon-all -autorecon1, and I only run -autorecon1.
now I have a brainmask.mgz using 001.mgz, I wan
Hello, Dr. Greve,
I used the vol2vol command with the previously acquired reg.dat,
It looks ok now. Thanks!
Guang
> Date: Wed, 19 Aug 2009 16:59:11 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] tkregsite
We are trying to compute a pial_lgi surface for an average brain.
When we run mris_compute_lgi, we get this error at the mris_fill
stage:
conforming output volume
setting resolution for intermediate calculations to 1.
reading surface from lh.pial...
reading group avg surface area 1015
Hi, Greve,
Thanks a lot! It works. But I got another question now,
I used mri_convert to convert a NIFTI file 002.nii to MGZ file 002.mgz. I also
want to register 002.nii
using the brainmask as the reference volume. Here, 002.nii is a 180x256x256
volume.
My command line is
bbregister --s
I can't remember. Nick?
On Thu, 20 Aug 2009, Falk Lüsebrink wrote:
Thanks, I'll try to do that.
Are the commands for mris_topo_fixer the same as of mris_fix_topology? I
haven't seen a help for that one.
Regards,
Falk
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mai
Thanks, I'll try to do that.
Are the commands for mris_topo_fixer the same as of mris_fix_topology? I
haven't seen a help for that one.
Regards,
Falk
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
you can use mri_surf2surf to map them all the fsaverage, then
mris_convert to convert each one to asciii.
cheers
Bruce
On Thu, 20 Aug 2009, Feng-Xian
Yan wrote:
> Hi,
>
> But I want to obtain the asc file or other files containing the same
> vertices and with the cortical thickness value and t
yes. The only time I've seen this error is when the surface file didn't
finish writing. You can load the defects with something like:
tksurfer -orig orig.nofix $subject $hemi inflated.nofix
then load the curvature file $hemi.defect_labels. You should be able to
use save point/goto point in tks
it looks like it failed trying to write the (new) file:
aseg.auto_noCCseg.label_intensities.txt
is the disk full? Do you have write access the this file?
cheers,
Bruce
On Thu, 20 Aug
2009,
Hui Zheng wrote:
> Hi freesurfer,
>
> We need some technical support here. The dataset was processed succ
Hi,
But I want to obtain the asc file or other files containing the same
vertices and with the cortical thickness value and their coordinates in the
file.
Could some ways to obtain?
Thank you in advance!
Feng-Xian
2009/8/20 Doug Greve
>
> Yes, this is what our group analysis tools d
Hi Bruce,
No, there are some hundreds of GB left.
Is the other topology fixer you meant before mris_topo_fixer?
Thanks in advance,
Falk
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Thursda
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