Hi all,
I was trying to create an average subject however received this error
message. I temporarily removed that subject however I was wondering
what a possible cause for this error is?
Applying LTAtransformInterp (resample_type 1)
writing to
/sdata/images/projects/EHRS/2/Freesurfer_EHRS/R
Dear FreeSurfer Experts,
What is the best way of creating surfaces approximating layer IV of the cortex
or the 'mid' surface (I.e. Surface between grey and white matter).
Thank you very much for your help.
Regards,
Christine
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Hi Doug and the list,
I think I still have a problem understanding what cesvar.nii contains. As a
sanity check, I tried to create 95% confidence intervals around my CES. I found
that in some voxels (or ROIs in my case) that had a p-value of less than 0.05,
my 95% confidence interval for my CES
Hi Christine
we use mris_expand for this. E.g. from the surf dir
mris_expand -thickness lh.white 0.5 lh.mid
cheers
Bruce
On Thu, 14 Feb 2013, Ecker, Christine wrote:
> Dear FreeSurfer Experts,
>
> What is the best way of creating surfaces approximating layer IV of the
> cortex or the 'mid' s
Hi Christine,
If you cd to the subject directory you can locate the ?h.white surface and
use mris_expand command to do this.
Hth,
Shantanu
On Thu, February 14, 2013 5:39 am, Ecker, Christine wrote:
> Dear FreeSurfer Experts,
>
> What is the best way of creating surfaces approximating layer IV of
sorry the files are in the surf directory
On Thu, February 14, 2013 9:53 am, Shantanu Ghosh wrote:
> Hi Christine,
> If you cd to the subject directory you can locate the ?h.white surface and
> use mris_expand command to do this.
> Hth,
> Shantanu
>
> On Thu, February 14, 2013 5:39 am, Ecker, Chr
Tudor,
Now that there is free space on the virtualbox ubuntu disk, are you able
to complete recon-all's on data that is located on your external disk? I
ask because although i'm not certain, i think nu_correct uses tmp space on
the ubuntu local drive, which if it was full would cause recon failur
Hi Luigi,
1 is the right way of calling it. 2 will have a negative effect in the
sense that it takes the same image twice and then creates the mid-space
at the same location, so 2 could be biased.
1 is creating an artifical mid-space and makes sure the image gets
mapped there.
Best, Martin
Dear All,
I have been trying to recon all a patient and unfortunately nothing is
happening after 24 hrs of processing so far .No error messages are
coming up either .This is the line it got stuck,CORRECTING DEFECT 10
vertices 67735 convex hull 9509
This is a rerun after my initial processi
Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached
doug
On 02/14/2013 11:22 AM, Varghese Chikku wrote:
> Dear All,
> I have been trying to recon all a patient and unfortunately nothing
> is happening after 24 hrs of processing so far .No error messages
> are coming up
You can compute the t = ces/sqrt(cesvar) and from that (and the DOF) you
can compute the p to see if it is consistent with pValue.
doug
ps. I don't know that your conf interval formula is correct. I don't
have a reason to think it is wrong, I just don't know, so you might want
to double check i
Dear All,
When I was checking the talairach transformation output, I noticed that some of
the white matter was not included inside the green line. Instead of drawing the
green line to include all of the white matter of the whole brain, it somehow
only includes the bottom half of the white matte
Hi,
I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon
processors. is it possible to run recon-all and trac-all on multiple cores.
Jon
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or if the skull is attached or the two hemis. The time it takes to
correct a defect is quadratic in the size of the (convex hull of) the
defect, so small ones are fast, and big ones take forever. Anything over
15K vertices or so usually means there is something dramatically wrong
with your data
yes, some of our binaries will make use of multiple cores, starting with
version 5.2. You need to specify how many to use on the recon-all command
line with -openmp N
On Thu, 14 Feb 2013, Jon Wieser wrote:
> Hi,
> I am runnning fressurfer on a Mac with 23.06 Ghz 6-core intel Xeon
> process
Hi Catherine
can you send us an image of what you are looking at?
thanks
Bruce
On Thu, 14 Feb 2013,
Rongxiang Tang wrote:
Dear All,
When I was checking the talairach transformation output, I noticed that some of
the white matter was not included inside
the green line. Instead of drawing th
Tudor,
In the default installation, there should be 2GB of free space on the
default disk, so somehow it got filled. Try deleting unnecessary stuff
(packages added during an upgrade I think mentioned doing, or subjects in
the freesurfer/subjects dir). Freeing just a few tens of MB should be
enou
probably not, although it's hard to say. If you upload the whole subject
dir I'll take a look. How does the aseg look?
On Thu, 14 Feb 2013, Rongxiang
Tang wrote:
Hi Bruce,
I checked the skullstrip stage using this command:
tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs
and both of th
Hi Catherine, if the skull strip is ok, then it might be that there were
some defects that messed things up. Try running defect-segto generate
segmentations of the defects. Look in the help for how to view the
segmentations.
doug
On 02/14/2013 03:36 PM, Rongxiang Tang wrote:
> Hi Bruce,
>
> I
Hi Bruce,
The aseg is also problematic for several slicesI uploaded the subject dir
on theMatinos center file drop...since the file is too big, I separated into
two parts.
Thanks,
Catherine
From: Bruce Fischl
To: Rongxiang Tang
Cc: "freesurfer@nmr.mgh
Thanks - it turned out that the zero voxels I put in my fake ROI volumes were
causing the cesvar voxels to be misaligned relative to the ces voxels. All
seems to be right for the moment.
-Clark
On Feb 14, 2013, at 12:47 PM, Douglas N Greve wrote:
> You can compute the t = ces/sqrt(cesvar) an
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