Hi Natalia,
I had the same issue in some cases. This is happens if you native data is not
perfectly isotropic and seems to be related to a rounding error. The only the
solution I found is to fix the resolution of your data prior to mri_nu_correct
manually.
Check your voxel size with mri_info.
Hello,
I am trying to run a paired analysis (a two time-point longitudinal
analysis) on some subjects which have been longitudinally pre-processed for
me on another computer. The computer I am now working on is originally a
Windows computer, but is now running Linux on a partition (CentOS Release
Hi,
Is there an official thought on using freesurfer on cases were there is
volume loss after old stroke, or surgery, or trauma? I have a number of
cases were the results in general look reasonable for the remaining brain
tissue, and was was wondering if it is valid to use that data for analyses?
Hi Salil
in the end of the look valid there's not much more you can do. It would be
on a case-by-case basis depending on the details of the lesion/surgery
cheers
Bruce
On Tue, 10 Feb 2015, Salil Soman wrote:
> Hi,
> Is there an official thought on using freesurfer on cases were there is
> volu
When loading a lookup table in freeview on the Mac with version 5.3 the program
freezes. I saw a similar issue was reported previously. Is there an fix or
patch for this? I tried modifying the FreeSurferColorLUT.txt, but that doesn’t
change the default colors. If there is no patch for this,
Hi Falk,
glad to hear that I am not the only one, and thanks!
Actually I cropped the image with mri_convert --cropsize to a size wich has one
voxel less in every dimension, and it worked.
Not sure, but maybe cropping is better if one wants to avoid interpolation
(which, in turn, can introduce
Hi Ronald,
No the issue is still there. I will let you as soon as it is fixed. The
default LUT is FreeSurferColorLUT.txt. But it is hard-coded into the binary.
Best,
Ruopeng
On 02/10/2015 12:03 PM, Ronald Pierson wrote:
> When loading a lookup table in freeview on the Mac with version 5.3 the
Hi,
I am wondering is there a way in freesurfer to map manually labeled IBSR
MRI .img/.hdr volume files to freesurfer surface file (e.g. lh.pial/rh.pial
etc.) keeping the original labels?
Thanks,
Razib
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You should ask the sys admin to create a directory for you on the shared
drive. If only root can write to it, that defeats the purpose of a
shared drive...
On 02/10/2015 08:21 AM, Kate Riggall wrote:
Hello,
I am trying to run a paired analysis (a two time-point longitudinal
analysis) on some
Hi Razib
yes, I think mri_label2label will do this if you have reconstructed the
surfaces.
cheers
Bruce
On Tue, 10 Feb 2015, Muhammad Razib wrote:
Hi,
I am wondering is there a way in freesurfer to map manually labeled IBSR MRI
.img/.hdr volume files to freesurfer surface file (e.g. lh.pial/
Any help and direction you can provide with this error would be appreciated.
The full log is attached.
I was running with -openmp 5 on a machine with 6 cores and 8 Mbytes of RAM.
0033: dt=73.984000, rms=0.641 (0.133%), neg=0, invalid=96777
0034: dt=73.984000, rms=0.640 (0.104%), neg=0, invalid=967
If the labels are a segmentation volume, then you'll need to run
mri_vol2surf with --interp nearest.
doug
On 2/10/15 6:39 PM, Bruce Fischl wrote:
Hi Razib
yes, I think mri_label2label will do this if you have reconstructed
the surfaces.
cheers
Bruce
On Tue, 10 Feb 2015, Muhammad Razib wr
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