Dear all,
I have been trying so far to export Freesurfer labels into a volume created
by SPM
I tried to coregister the anatomical data from Freesurfer and SPM and use
the registeration file to turn my label file into volume but the resulting
output just goes outside the brain.
Has anyone tried t
Hi,
I'm running longitudinal recon-all
(freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 14.04.4, with
three timepoints per subject. I get this warning about geometry (please see
below). All three images have been converted from dicom to .mgz using
mri_convert. From a previous question
Hello Freesurfer Experts,
I wanted to see if I am setting up qdec correctly. I am using cortical
thickness as my measure. When using the Qdec gui in Freesurfer 6.0 i
supplied the following files:
qdec.table.dat which contains the following:
Subject Group Gender Age Site Yrs_Education
For cat
Hi Lars,
this test is too sensitive in FS5.3 . We have changed that a while ago.
The mri_diff command should be
mri_diff --notallow-pix --notallow-geo
if that still shows a difference, something is different in the image
resolution and that could be a problem. Only differences in the
tra
Dear all,
Would you please help me on this one?
Thank you,
best wishes,
Barbara
Forwarded Message
Subject:hippo subfield segmentation new beta version (version 6)
Date: Wed, 20 Apr 2016 11:45:02 +0100
From: Barbara Kreilkamp
To: Freesurfer support list
Dea
Dear FS community,
I used mri_robust_register to register a volume to the fsaverage space,
and then tried to use the resulting .lta file to register another vol on
the same space as the original volume, to fsaverage, using mri_vol2vol.
The structure of the command I used is:
mri_vol2vol --mov --t
Play around more with my .label file, I realized that while it wouldn’t open in
tksurfer or freeview, it DID open in tkmedit. So, I ran
mri_label2label -- srclabel-- s fsaverage
-- trglabel ./ -- hemi lh-- paint 30 pial -- trgsurf
pial
and now it opens on tksurfer!
Best,
Stephan
Sorry for the follow up email, but I realized my mistake. When running the
mri_robust_register command even though I used the lta flag for the output
register file, I gave the extension .dat to the file. It seems like this
is what caused the problem.
Panos
> Dear FS community,
>
> I used mri_rob
Hi everyone,
I'm using mri_convert to reinforce TR information into the Nifti header in the
following manner:
mri_convert $FILE $FILE -tr $TR
Before the conversion, my file size is usually around 550MB but after the
conversion is doubles in size to ~1.1GB. In the Nifto file header I've noticed
Hi Afsana,
I think adding "-odt int" or "-odt short" to your mri_convert command will set
the data type of the output Nifti to int16, but I'm not sure if it conflicts
with the -tr flag. You can also convert to .nii.gz instead of just .nii which
will help keep the file size down.
Hope that help
On 04/21/2016 10:15 AM, Ajay Kurani wrote:
> Hi Freesurfer Experts,
>
> I have used freesurfer smoothed images
> (lh.thickness.fsaverage.fwhm15.gii) to perform a cortical thickness
> analysis. I used qdec with a surface-based morphometric analysis to
> compare two groups. As my discrete fixed
need more info, can't tell what you are trying to do. try sending some
command lines
On 04/22/2016 06:29 AM, Mohamed Abdelhack wrote:
> Dear all,
>
> I have been trying so far to export Freesurfer labels into a volume
> created by SPM
>
> I tried to coregister the anatomical data from Freesurfer
In general, qdec should be used to "play" with your data in an
interactive way. For many designs, you may need to run the command-line
stream. This is probably one of them. If you have continuous nuisance
variables, then you should run the analysis using DODS and test for an
interaction of the
can you send your fsgd file?
On 04/21/2016 03:57 AM, Sophie Maingault wrote:
> Dear FS experts,
> There is already a post about that but the concerned person never answered
> so there is no solution.
> I’m currently running per-vertex analyses with the --pvr flag of mri_glmfit
> command. I did
You can use
mri_convert aseg.mgz --erode-seg 1 aseg.e1.mgz
and visualze aseg.e1.mgz vs aesg.mgz
you can use aseg.e1.mgz as input to mri_segstats (and turn off the erode)
On 04/15/2016 11:08 AM, Elijah Mak wrote:
>
> Hi Doug,
>
> I have pasted the previous emails below. I have computed mri_segstats
Is your $FSLDIR environment variable set?
On 04/22/2016 02:09 PM, Mcnorgan, Christopher wrote:
> That doesn't seem to be the problem. Attached are the file listings for the
> /usr/bin directory for fsl* for the working and not working computers. The
> symlinks for fsl binaries on both computers
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