Dear All,
This worked for me...
for x in SZ1 SZ2 SZ3
do
recon-all -i $x.nii -s $x -all -hippo-subfileds
done
Thanks for your valuable inputs...
From: Bruce Fischl
To: "Watson, Christopher"
Cc: Anupa AV ; KOOL ; Freesurfer
Sent: Saturday, September 7, 20
Hi,
I've noticed that occasionally when I manually edit recons, the white matter
surface will be drawn to include a portion of the volume where no white matter
pixels are present. Therefore, when I go to correct the incorrectly drawn
surface, there are no pixels to delete under the white matter
Hi everyone,
I was hoping that someone could clarify for me the role played by norm.mgz
in the command
mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz
from the -tessellate step of the -autrecon2 section on the page
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable.
My u
Hi Krista
1. it's hard to answer 1 as it depends on the magnitude of the error, how
accurate the fix would make the surfaces and what you are going to use the
surfaces for. Allison or Louis or someone can correct me but in general I
think we only edit a small % of the surface.
2. If the skull
You cannot. You will have to do the conjunction on the cluster sig
files, then extract a label from that.
On 09/09/2013 06:30 PM, Yang, Daniel wrote:
> Thanks so much! I used the cluster analysis, I will look for the .annot there.
>
> I am also performing a conjunction analysis. One question I h
Thanks so much! I used the cluster analysis, I will look for the .annot there.
I am also performing a conjunction analysis. One question I have is that can I
perform mri_concat on those label files? I wanted to obtain the thickness value
from the regions from the conjunction analysis.
Thanks!
Hi Siddharth,
if you plan to run the full longitudinal stream in 3), you need the
aseg.mgz files in each cross sectional directory. so 3 should not
complete unless the aseg.mgz is available in all timepoints in the cross
sectional runs (1). In fact we recommend to run the full recon-all -all
If you have run the correction for multiple comparisons, there should be
an annotation (.annot) file in the QDEC output directory (in the
contrast folder). You can convert that into labels using
mri_annotation2label. Otherwise use Gari's suggestion.
doug
On 09/09/2013 03:00 PM, Garikoitz Lerm
Hi Daniel,
you can use mri_surfcluster.
br,
Gari
On Mon, Sep 9, 2013 at 8:25 PM, Yang, Daniel wrote:
> Dear all,
>
> Is there a way to convert .mgh to .label? My .mgh is a ROI file from
> qdec-based group analysis and I don't want to draw the ROIs manually.
>
> Thanks!
> Daniel
> --
> Yun
Dear all,
Is there a way to convert .mgh to .label? My .mgh is a ROI file from qdec-based
group analysis and I don't want to draw the ROIs manually.
Thanks!
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
Just wanted to resend these questions to see if anyone has any answers.
Thanks!
I am doing cortical thickness and surface area analyses and had a few
questions regarding editing the borders.
1) Is it reasonable to edit every (big and small) error that I find?
Basically, how much a difference woul
Dear FreeSurfer community,
My recon-all commands have stopped working, when previously they (usually)
completed just fine. I am not sure at what level the problem is at.
I'm working off the Jalapeno cluster at FMRIB, where FreeSurfer is centrally
installed. I run a configuration script to get s
Hi all,
I was trying to run freesurfer longitudinal analysis for my subjects at 2 time
points and when I ran the pre_proc step it gave me an error that file
'lh/rh.thickness is missing'. Here is what I have done.
1) Run the Freesurfer till CA Normalize stage (till norm.mgz stage).
2)
Hi Damien
Doug can correct me if I'm wrong, but I don't think there is any easy way
to do this except to assume that the number of independent tests is equal
to the number of vertices, which is of course pretty conservative.
cheers
Bruce
On Mon, 9 Sep 2013, Damien
MARIE wrote:
Hello eve
Hi Martin
yes, there have been lots of changes. You should definitely get the most
recent version
cheers
Bruce
On Mon, 9 Sep 2013, Martin Kavec wrote:
> Hi Bruce,
>
> I thought to have a bit of fun with c++ instead of Matlab and would like to
> use ITK to open the
> wmparc.mgz. I have FreeSu
glad to hear it
Bruce
On Mon, 9 Sep 2013, Martijn Steenwijk wrote:
Hi Bruce, it seems to work flawlessly. Thanks!
On Sat, Sep 7, 2013 at 11:44 AM, Martijn Steenwijk
wrote:
Thanks for your quick reply. It seems that we have some other problems
now with the
machine, but 'll let
Hi Sean
I think using mris_expand with a negative number is the better way to do
this. Then use the resulting surface for the seed. It should prevent the
surface from passing through itself (which is what you are seeing)
cheers
Bruce
On Mon, 9
Sep 2013, Sean Hatton wrote:
> Hello FS Gurus,
>
I'd probably try GM plus a (DWI-sized) voxel or so into the WM.
On Mon, 9 Sep 2013, Sean Hatton wrote:
Great, I will give that a shot. In the seeding ROI should I combine the gm and
wm labels or is the GM sufficient to encapsulate, say, the superior temporal
gurus GM and WM?
Anastasia Yendi
Great, I will give that a shot. In the seeding ROI should I combine the gm and
wm labels or is the GM sufficient to encapsulate, say, the superior temporal
gurus GM and WM?
Anastasia Yendiki wrote:
Hi Sean - Do you mean that the streamlines go through non-brain voxels?
You could you a slightl
Hi Sean - Do you mean that the streamlines go through non-brain voxels?
You could you a slightly dilated version of the aparc+aseg as a mask. You
can use bbregister to map it to the subject's DWI space.
a.y
On Mon, 9 Sep 2013, Sean Hatton wrote:
Hello FS Gurus,
I would like to export FS l
Hi Bruce,
I thought to have a bit of fun with c++ instead of Matlab and would like to
use ITK to open the wmparc.mgz. I have FreeSurfer sources dating back to
December 2010including itkMGHImageIO. Have there been any important
changes, based on which I should rather get the most recent version of
Hi Doug,
That sounds good! Thanks so much!
Best,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 9/8/13 10:15 PM, "Douglas Greve"
mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Hi Daniel, there is no difference. Once you select
Hi Bruce, it seems to work flawlessly. Thanks!
On Sat, Sep 7, 2013 at 11:44 AM, Martijn Steenwijk <
martijnsteenw...@gmail.com> wrote:
> Thanks for your quick reply. It seems that we have some other problems now
> with the machine, but 'll let you know whether the new "mri_tessellate"
> works ;-
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