If you upload it, we will take a look. Seems likely it is a topology fixing
problem
Cheers
Bruce
On Mar 12, 2012, at 5:38 AM, Martijn Steenwijk
wrote:
> Dear all,
>
> I've been correcting a recon with controlpoints and correction of the skull
> strip. Although the result is a lot better, s
Although the white surface finds its place based on intensity, it's starting
point is the wm.mgz. So if there are no voxels in the wm.mgz in the area you
mention, drawing in some voxels combined with the intensity changes that come
from the control points may help.
Allison
On Mar 12, 2012, at 6
Hi Mingxia,
If you are on Linux, you can use the convert command:
convert -fill white -opaque black
--Thomas
On Tue, Mar 13, 2012 at 6:11 AM, Satrajit Ghosh wrote:
> depending on what you are doing you could use PySurfer.
>
> cheers,
>
> satra
>
> On Mon, Mar 12, 2012 at 6:04 PM, Bruce Fisch
@ Louis, no I didn't correct the WM mask yet. But since it's a step clearly
'behind' correcting the skull strip and adding control points, and it takes
a lot of work to accurately draw the WM mask, I would prefer to automate
things as much as possible...
@Alan, thanks for your suggestion - althoug
depending on what you are doing you could use PySurfer.
cheers,
satra
On Mon, Mar 12, 2012 at 6:04 PM, Bruce Fischl wrote:
> no, sorry
> On Mon, 12 Mar 2012, zhang mingxia wrote:
>
> Hi dear freesurfer experts,
>> I am making pictures for publication. The images saving from Tksurfer
>> are bla
no, sorry
On Mon, 12 Mar 2012, zhang mingxia wrote:
Hi dear freesurfer experts,
I am making pictures for publication. The images saving from Tksurfer
are black backgrounds. Is there any way to save the image with white
background?
Thank you very much
Mingxia Zhang
___
How did you create the manual ROIs? How is the label2vol command
failing? Usually good to send the terminal output of a failing command too.
doug
Tina Jeon wrote:
> I want both the surface and volume. Sorry about the confusion. The command
> line is:
>
> mri_label2vol --label ./3t2234/label/15yr
Hi dear freesurfer experts,
I am making pictures for publication. The images saving from Tksurfer
are black backgrounds. Is there any way to save the image with white
background?
Thank you very much
Mingxia Zhang
___
Freesurfer mailing list
Freesurfer@
I want both the surface and volume. Sorry about the confusion. The command line
is:
mri_label2vol --label ./3t2234/label/15yr_lh_A1C_fs.label --temp
./3t2234/mri/brainmask.mgz --regheader 3t2234 --projfracmax 0 1 .1 --subject
3t2234 --hemi lh --o ./3t2234/label/15yr_lh_A1C_fs.mgz
I am using a
Hi Tina, I think I'm missing something. If you want a volume, why are
you converting it to the surface? Also, make sure to send command-lines
of commands that are failing.
doug
Tina Jeon wrote:
> Good to know, however I would like to display the volume, not the surface so
> that I can check to
Good to know, however I would like to display the volume, not the surface so
that I can check to see if the label is covering the entire cortex, not just a
small delegation of voxels around the pial surface. Is there a way I can
visualize a volume file using tkmedit?
I know mri_label2vol can con
Hi Juke, it will create a csd directory with csd files in them. This
will tell you how many iterations it's done. Note that if you have a
multi-core machine and want to use a couple of cores to do this
simulation, you can run mri_glmfit-sim with the --bg option.
doug
Juke Cha wrote:
> Hi all,
>
tkmedit only displays volumes. Use tksurfer for surfaces, something like
tksurfer 3t2234 lh inflated -overlay ./3t2234/label/15yr_lh_A1C_new2.mgh
doug
Tina Jeon wrote:
> Using tkmedit
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Monday, March 12,
Hi all,
I'm running a simulation to get corrected p values. I set the iteration as
5000 times and it's a group analysis of ~40 subjects.
Now the simulation has been going for three days on 2.8 Hz i7 CPUs and not
done yet. Simulation on 100 iterations completed pretty quick so assumed a
couple of d
Using tkmedit
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, March 12, 2012 1:01 PM
To: Tina Jeon
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf
how are you trying to display it?
On Mon, 12 Mar 2012, Tin
how are you trying to display it?
On Mon, 12 Mar 2012, Tina Jeon wrote:
> I am still getting the same display error with using an mgh file.
>
> mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out
> ./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1
I am still getting the same display error with using an mgh file.
mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out
./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1
--hemi lh
Any suggestions?
Thank you,
Tina Jeon
Graduate Student
Advanced
Hi Surfers,
I have done some Longitudinal Processing on a bunch of subjects and
although the pial and white surfaces are looking good after the
Longitudinal Processing, the aseg segmentation for each subject is
often looking much worse.
I have a link to a sample screen grab to show you what I me
In this case, the input file would be the sig.mgh file that you want to
extract clusters from. For this, you would not use a csd file (which is
created by the simulation, unless you want to exclude clusters based on
their p-values instead of size). You would set the --thmin to set the
voxel-wis
Hello, everyone,
I have question about fcfast. we have several bold numbers and run fcfast
at the same time. For example,
fcfast -id 070324_4TT00201 -mpr 3 -bold 15,16 -roi
/ncf/tools/mtt24/seeds/N12Trio_avg152T1_reg6mm_40_-18_48.nii.gz
I don't know if the final correlation (Z) images are mean v
Hi Martijn:
In our lab, we basically add a greater density of control points - almost 1
CP for every 2 voxels. This way the corrected pial looks closer to what's
expected.
best,
Alan
BIDMC
On Mon, Mar 12, 2012 at 5:38 AM, Martijn Steenwijk <
martijnsteenw...@gmail.com> wrote:
> Dear all,
>
>
Hi Martijn,
What does the wm.mgz look like in that area? Have you tried making any
white matter edits?
-Louis
On Mon, 12 Mar 2012, Martijn Steenwijk wrote:
> Dear all,
>
> I've been correcting a recon with controlpoints and correction of the skull
> strip. Although the result is a lot better, s
Hi John,
Could you send us the terminal output containing the error you receive
when running dt_recon?
-Louis
On Fri, 9 Mar 2012, John Fredy wrote:
Hello all, I am trying to process siemen dti data from a skyra model in the
dt_recon software. But the software fails in the conversion from Dico
Hi Charlotte
have you visually inspected them? I would be more concerned about the # of
voxels in wm which is way too low, but it looks like you eroded the wm
mask, so maybe it's ok. Take a look at the surfaces over the data in
tkmedit and see if it appears accurate in subjects like #8. The WM
Hello Freesurfer experts,
I'm trying to extract the data from the tutorial dataset
"buckner_data-tutorial_subjs.tar.gz" by typing this command "tar -xvzf
buckner_data-tutorial_subjs.tar.gz" and after it finished, I got this error
message:
tar: buckner_data/tutorial_subjs/130: Cannot create sym
Dear Freesurfer users,
I run FS on my 670 subjects. All the scans were acquired on a 1.5T Philips scan.
I noticed that my values in the WM are near 100-110 but not exactly 110. I
think it is a problem! Is it link to the 1.5T? How can I fix it?
I joined my log file of QA tools: could you help me
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