Using version 4.5.0, I get this error message with mri_vol2surf:
INFO: Source volume detected as selxavg format
number of frames is incorrect (0,1)
This error does not happen with version 3.0.5, and it only happens for input
volumes with particular file names.
This fails:
mri_vol2surf \
--s
Hi Ayaz,
A few questions first:
what FS version? How far are the TP apart? Same Scanner and same
software version on the scanner? Is the volume increase significant? How
much percent increase?
Generally: there can always be individual cases with volume increase,
e.g. due to motion in the scanner
Hi Martin,
We have processed groups of controls(40) and patients(15)for two time
points using longitudinal processing. In few controls and even patients we
saw increase in cortical volume. Ideally there should be no change in
cortical volume or we might expect cortical loss specially in the
patien
Great, thank you for your rapid response,
Marie
On 18 oct. 10, at 17:19, Martin Reuter wrote:
> Hi everyone,
>
> it is ok to run 5.0 cross sectionally and use that data for 5.1 base
> and
> long. We will try hard to make this work, even if new cross sectional
> files are needed (they will then
It is only going to sample it at the gray/white
Marco Loggia, PhD wrote:
> Thanks for the correction, Doug.
>
> So, if I understand correctly, with the current settings I should be
> sampling very close to the white surface (i.e., between the white and 10%
> along the normal between white and pia
Thanks for the correction, Doug.
So, if I understand correctly, with the current settings I should be
sampling very close to the white surface (i.e., between the white and 10%
along the normal between white and pial). But how would a delta of '1' be
interpreted in this case, as it is larger than
The problem was in the way I documented the flag for mris_preproc. It
should be mris_preproc "--projfrac-max Min Max Delta" instead of "Min
Delta Max". I've updated the documentation, and that will be live on the
next stable and/or dev update. But you can use the version that is
there, just cha
Hi everyone,
it is ok to run 5.0 cross sectionally and use that data for 5.1 base and
long. We will try hard to make this work, even if new cross sectional
files are needed (they will then be created in the base or long
stream).
However, these are reasons, why it might make sense to wait with the
Can you let me know when you have processed a set with the new tools?
It's going to be a lot easier for me to instruct you on how to do those
things.
doug
f.le...@donders.ru.nl wrote:
> Dear Doug,
>
> Thanks a lot for the reply, that really helps. I see that the new function is
> more integrat
I'll leave that for Martin also
On Mon, 18 Oct 2010, Derin Cobia wrote:
So if I understand correctly, you would not recommend getting a jump start on
cross-sectional processing and editing under 5.0, rerunning everything under
5.1 once it comes out, then run (for the first time) longitudinal u
0.5.mgh and max.mgh do not exist in that directory.
doug
Marco Loggia wrote:
> Dear all,
>
> Is it possible that the --projfrac-max has a bug (at least when used with
> mris_preproc)?
>
> I sampled the same volume using --projfrac 0.5 and --projfrac-max (see
> below) and, when I overimposed the t
Hi Marco, I'm copying the list on this because this is a good question
about an aspect that is not well documented.
The answer to the question has to do with the sign of the test. By
default, mri_glmfit produces p-values that are for unsigned tests. The
p-value for a signed test if half that of
Hi Jing, I'm reposting to the group in case someone else has any
suggestions. I've answered some of your questions below
1) all of our outputs are "conformed" meaning that they are resampled to
1mm3 256^3. To convert back to native anatomical space search for
"native" on our wiki.
2) Don't know
is it possible for you to update to v5.0? v5 fixes the mris_volmask
library problems.
n.
On Mon, 2010-10-18 at 10:12 +0200, Jordi Casals wrote:
> Hello everybody.
>
>
> There is a few days I try to run a recon-all process with one subject
> and there is some problem that can't let the proces
So if I understand correctly, you would not recommend getting a jump start on
cross-sectional processing and editing under 5.0, rerunning everything under
5.1 once it comes out, then run (for the first time) longitudinal under 5.1?
Are there going to be some incompatibilities with 5.1, where it
Try adding "-odt float" to the mri_convert command-line.
doug
Luis Lafer-Sousa wrote:
> We have anatomical NHP data that we unpack and preprocess using
> freesurfer and fsl (using Sebastian's scripts). An end product is a
> skull stripped brain in .mgz format, that I then convert to .nii using
What does it say in transforms/talairach_avi.log?
--
On Thu, 14 Oct 2010, Maria Luisa Mandelli wrote:
> Hi!
>
> I get this error running recon_all
>
>
> Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm
> transforms/talairach.auto.xfm
> ERROR: mpr2mni305 failed, see transforms/talairac
I'll leave that for Martin
Bruce
On Mon, 18 Oct 2010, Pedro Paulo de Magalhães
Oliveira Junior wrote:
Hi Bruce,
What's the ETA for 5.1?
thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter &
Hi Bruce,
What's the ETA for 5.1?
thanks
-
Pedro Paulo de Magalhães Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://www.netfilter.com.br/mobile
On Mon, Oct 18,
Hi Marie,
wait for 5.1. Martin has made some significant improvements.
cheers
Bruce
On Mon, 18 Oct
2010, Marie Schaer wrote:
> Hi,
>
> I am planing to process a longitudinal dataset with 3 timepoints. Is
> it worthy to begin already the cross-sectional processing with version
> 5.0 and then wai
Hello everybody.
There is a few days I try to run a recon-all process with one subject and
there is some problem that can't let the process finish correctly. The
command I want to run is the next one:
*recon-all -autorecon2-wm -force -i
/nfs/arpon/PROJCT/DEPR/orig/DICOM/T13D/GMI_544/GMI_544_0002
Hi,
I am planing to process a longitudinal dataset with 3 timepoints. Is
it worthy to begin already the cross-sectional processing with version
5.0 and then wait version 5.1 to continue from the template part. Or
would you advice me to wait the release of version 5.1 for the entire
process
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