Liz,
to be precise, this is true for the standard FS stream.
The longitudinal stream is different, as in FS 4.4 the base actually
lives in two similar, but slightly different spaces, because the
template is created for T1 and recreated for the norm.mgz. The aseg is
in the space of the norm and th
Its in the native space of the TP (orig, nu, T1, norm, brainmask, aseg,
brain .. all in the same space).
-Martin
On Mon, 2009-08-03 at 16:40 -0400, Elizabeth Selgrade wrote:
> Hi Martin,
>
> Thanks for the quick response. I have a follow-up question: In what space
> do the segmentations take pl
Hi Liz,
the registrations are stored in
baseid/mri/transforms
look for files baseid_to_tpNid.lta
and the inverse tpNid_to_baseid.lta (which is the map you are looking
for). These should align all your TPs to the base space.
Best, Martin
On Mon, 2009-08-03 at 16:19 -0400, Elizabeth Selgrade wrot
Hello FreeSurfer Users,
I am using the longitudinal stream to look at four timepoints/subject, and
I'd like to transform all of my timepoints to the base scan's unbiased space
so that I can calculate ROI volume overlap. I have been using tkregister2
to calculate the transform from my scan.base.lo
I mean multiple subjects simultaneously on the same machine
On Mon, 3 Aug 2009, Nathan Dankner wrote:
Do you mean running multiple subjects simultaneously or more than one recon
on an individual subject? In either case, the answer is yes. I could try
running them individually to see if the pr
Do you mean running multiple subjects simultaneously or more than one recon
on an individual subject? In either case, the answer is yes. I could try
running them individually to see if the problem persists.
On 8/3/09 3:42 PM, "Bruce Fischl" wrote:
> yes, I just saw that. I thought it only hap
yes, I just saw that. I thought it only happened when the machine ran out
of memory. Are you running more than 1 recon at a time?
On Mon, 3 Aug 2009,
Nathan Dankner wrote:
I have 4 gigs of ram on here. This is the response that I got from Nick
Schmansky:
This is a known and long-standing pro
I have 4 gigs of ram on here. This is the response that I got from Nick
Schmansky:
This is a known and long-standing problem with mris_volmask. The fault
occurs deep within a library, VTK, of which we make use (null pointer in
vtkDataArrayTemplate::GetTuple). We're trying to find a fix or
worka
looks like it's failing in mris_volmask. How much RAM do you have on your
machine?
On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors
after autorecon2, and they have exclusively been segmentation faults. I¹m
running sta
I think you need to send more info about where it crashed
---
Pedro Paulo de M. Oliveira Junior
2009/8/3 Ritobrato Datta
> Hello All,
>
> I got this error when I ran recon-all -all. I changed machines and the same
> dataset went all the
Hi,
actually in the newer FS versions (don't know when it started), the
cortribbon is part of autorecon3. In those cases all that is necessary
is to rerun the final steps:
-cortribbon
-aparc2aseg
-wmparc
Martin
On Mon, 2009-08-03 at 14:18 -0400, Nathan Dankner wrote:
> Hello all,
>
> I’ve recen
Hello All,
I got this error when I ran recon-all -all. I changed machines and the same
dataset went all the way through without any errors. I ran another dataset with
the machine "taxi" and it ran fine.
Any suggestions will be helpful.
__
Nathan,
This is a known and long-standing problem with mris_volmask. The fault
occurs deep within a library, VTK, of which we make use (null pointer in
vtkDataArrayTemplate::GetTuple). We're trying to find a fix or
workaround to this really annoying problem.
The cheap workaround is to run the -
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