Dear FS expert：
Today i put two contrast in the file {subjects},and run the command line
recon-all -s mgz -all, several minutes later,the terminal tells error,it says:
[brain@localhost ~]$ recon-all -s mgz -all
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp:
转发邮件信息
发件人：传玺 shandongren2...@163.com
发送日期：2012-04-11 19:26:41
收件人：freesurfer freesurfer@nmr.mgh.harvard.edu
主题：[Freesurfer] consult
Dear FS expert：
Today i put two contrast in the file {subjects},and run the command line
recon-all -s mgz -all, several minutes
Hello
When I run recon-all with -cm switch, that generates error as follows:
/*
mri passed volume size is different from the one used to create M3D data
ERROR: mri_ca_register with non-zero status 0
*/
Without -cm switch, recon-all completes all processing without error.
Any help would be
HI all,
I ran longitudinal processing with
reco-all -base templateID -tp MRI_T1 -tp MRI_T2 -all
but in base-tps file of template ID I found the subject ID of MRI_T1 twice
instead of MRI_T1 and MRI_T2. I want to run recon-all -long which I am able
to do for MRI_T1 but could not do the same for
are your data really .46 mm in plane? It looks you are running out of
memory, but even if you weren't it's very hard to reconstruct data that is
that anisotropic (0.4688, 0.4688, 1.19996). You are better off getting 1mm
isotropic and using it, which these days with 3T and 32 channels is only
Hi Hiroyuki
what size is your original data?
Bruce
On Wed, 11 Apr 2012, Oya, Hiroyuki (UI
Health Care) wrote:
Hello
When I run recon-all with ?cm switch, that generates error as follows:
/*
mri passed volume size is different from the one used to create M3D data
ERROR:
Hi haochuanxi
please post to the list so that others can help! It looks to me like your
voxel size is (0.4688, 0.4688, 1.19996). Is that the case? If so, it's
going to be har to reconstruct good surfaces even if you find a machine
with enough memory. in plane means the resolution of your
Hi Sabin,
If the base-tps file contains a time point twice, that indicates that it has
been created by passing the same time point twice, probably a typo.
You need to remove the base and tp1.long and run again with the correct
parameters.
Best Martin
On Apr 11, 2012, at 9:31, Sabin Khadka
Dear FS expert：
Today I put two contrast in the file {subjects},and run the command line
recon-all -s mgz -all, several minutes later,the terminal tells error,it says:
[brain@localhost ~]$ recon-all -s mgz -all
Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
Current Stamp:
H i Nick,
Will the centos5 build of v5.1 work with centos6? I'm getting a new
workstation and want to know which version of centos is better to install.
On 04/10/2012 10:08 AM, Nick Schmansky wrote:
Wil,
Hi, the contents of that 'misc' directory is just a filedrop of sorts to
supply fixes to
Hi Wil:
The model we use for manual morphometry is the Wacom BAMBOO (pen) : Model
CTL-460.
best,
Alan
On Mon, Apr 9, 2012 at 12:22 PM, Irwin, William wir...@memory.ucsf.eduwrote:
Hi-
** **
I have been considering this option, and these comments pretty much make
it a given.
**
Hi everybody,
I have a question about FS longitudinal post-processing. Currently I
obtained some corrected results comparing a Control vs. an Experimental
group (pre-post).
What i would like to know is if there's a thinning in the control group or
a increase in the thickness of the experimental
Hi
Can someone tell me please in*_details_*what does this line do?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz
--regheader aseg.mgz
thanks
--
Johnson J. GadElkarim
Research Assistant, Department Of Psychiatry,
PhD Candidate, Department Of Electrical Computer Eng.,
Hi all,
Is there a longitudinal processing stream to compare local gyrification
index (lgi) across two time points.
-Sabin
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The
Hi Johnson
I believe it resamples the aseg to have the same geometry as the original
scan.
cheers
Bruce
On Wed, 11 Apr 2012, Johnson wrote:
Hi
Can someone tell me please in details what does this line do?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --reg
header
Hello FreeSurfers,
I ran the following command:
mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 1 1.3 mc-z.abs.13.jls
--sim-sign abs --overwrite
When it gets to the part to do mri_segstats, it throws this error:
0 1*** glibc detected *** mri_segstats: malloc(): memory corruption:
And it exactly does that, does it register them together or use a
pre-known transformation matrix
On 04/11/2012 3:46 PM, Bruce Fischl wrote:
Hi Johnson
I believe it resamples the aseg to have the same geometry as the
original scan.
cheers
Bruce
On Wed, 11 Apr 2012, Johnson wrote:
Hi
it registers them based on the header information, but since the aseg is
derived from the rawavg that should be exactly correct
On Wed, 11 Apr 2012, Johnson wrote:
And it exactly does that, does it register them together or use a pre-known
transformation matrix
On 04/11/2012 3:46 PM, Bruce
Yes, just extract the stats on each time point as done in a cross
sectional analysis (but instead on the ?.long.base directories) do a
paired t (or a t on the difference) to see if there is increase or
decrease.
If you look at one of the reported ROI's (e.g. caudate volume, or
pre-central
No,
should be very similar across time, or not?
But the surfaces will be more reliable after longitudinal processing,
can't you just run the lgi analysis on the tp?.long.base directories?
Best, Martin
On Wed, 2012-04-11 at 15:49 -0400, Sabin Khadka wrote:
Hi all,
Is there a longitudinal
great, so if I can read the header from the aseg file and the header
from the rawavg header file I would be able to transfer any point from
the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers them based on the header information, but
Yes, that is correct.
On 04/11/2012 06:54 PM, Johnson wrote:
great, so if I can read the header from the aseg file and the header
from the rawavg header file I would be able to transfer any point from
the aseg space to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl
yes
On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the
rawavg header file I would be able to transfer any point from the aseg space
to the rawavg space is that correct ?
On 04/11/2012 4:40 PM, Bruce Fischl wrote:
it registers
Hard to say. Can you send the full terminal output? You can just run it
like:
mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 1 1.3
mc-z.abs.13.jls --sim-sign abs --overwrite | glmfitsim.log
Then send me the log file.
doug
On 04/11/2012 05:14 PM, Jeff Sadino wrote:
Hello FreeSurfers,
I
there are two transformation matrices one in aseg and one in rawavg, how
do I use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes
On Wed, 11 Apr 2012, Johnson wrote:
great, so if I can read the header from the aseg file and the header from the
rawavg header file I would be able to
Hi all,
I have a question about controlling freeview from the command line.
I would like to overlay some z-score maps for individual subjects on the
fsaverage inflated surface. I would like to use the 'color wheel' color
scale setting and threshold the images between -1 and 1 standard deviations
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM, Johnson jgad...@uic.edu wrote:
there are two transformation matrices one in aseg and one in rawavg, how do I
use them ?
On 04/11/2012 6:12 PM, Bruce Fischl wrote:
yes
On Wed, 11 Apr 2012, Johnson wrote:
great, so
so to be clear about it, suppose T1 is the matrix in aseg and T2 is the
one in rawavg,
to transform from aseg to rawavg I will apply invert(T1)*T2
is that correct?
On 4/11/2012 8:12 PM, Bruce Fischl wrote:
Invert one and compose it with the other
On Apr 11, 2012, at 7:48 PM,
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