400MB per subject, sorry.
also i should have made clear that we will continue to support the
existing GPU CUDA code that runs on recon-all with the -use-gpu switch.
by support i mean keeping it running with each new nvidia cuda driver
release as best as we can.
Nick
>
> I think Nick meant to s
Dear FreeSurfers,
I want to convert cortical labels to volumetric masks, and I run the following
commands:
1. tkregister2 �Cmov sub/mri/rawavg.mgz �Cnoedit �Cs sub �Cregheader �Creg
./register.dat
2. mri_label2vol �Clabel ./lh.entorhinal.label �Ctemp sub/mri/rawavg.mgz
�Csubject sub �Chemi
On 04/25/2013 10:13 AM, limengsecret wrote:
> Dear FreeSurfers,
> I want to convert cortical labels to volumetric masks, and I run the
> following commands:
> 1. /tkregister2 –mov sub/mri/rawavg.mgz –noedit –s sub –regheader –reg
> ./register.dat/
> 2. /mri_label2vol –label ./lh.entorhinal.label
I have run mri_ms_fitparms (version 5.1.0) on phantom data from two
multiecho flash volumes (5 and 20 degrees with 8 echos: 1.67ms - 14.83ms in
1.88ms steps) at 7T utilizing a b1 map for correction.
How does mri_ms_fitparms know the field strength (I can't figure out where
the information is when
See attached image for reference. Large area has been incorrectly segmented
as WM, also WM surface has completely been skipped over. Planning to remove
segmentation in that area and run recon-all again, is this correct or
should something else be done to alleviate issue.
Worth noting this issue is
Dear expert,
I am doing source reconstruction with MEG.
First, I am corregistering my head surface mesh from the freesurfer
(obtained with mkheadsurf)
to the headshape of the subject obtained with the Polhemus tracking system.
So I already have one affine transformation (Aff_1)
The head surface
Hi Jonathon
that's pretty bad. Did the skull stripping fail? If you upload the subject
I'll take a look
Bruce
On Thu,
25 Apr 2013, Jonathan Holt wrote:
See attached image for reference. Large area has been incorrectly segmented
as WM, also WM surface has completely been skipped over. Plan
Hi Dan
how do you do the B1 correction? And why would we need to know the field
strength? The T1 is certainly a function of the field strength, but we
will just find the T1 for whatever strength field the input data was
acquired with.
And yes, we search in 5ms increments. You could certainly c
Hi Bruce,
Thanks for your response.
On Thu, Apr 25, 2013 at 1:45 PM, Bruce Fischl wrote:
> Hi Dan
>
> how do you do the B1 correction?
using -afi with a custom B1 map.
> And why would we need to know the field strength? The T1 is certainly a
> function of the field strength, but we will jus
hi Jose,
why don't you use MNE for this? MNE is designed to work smoothly with
FreeSurfer.
http://martinos.org/mne/
Cheers,
Alex
On Thu, Apr 25, 2013 at 7:35 PM, José Ángel Pineda
wrote:
> Dear expert,
>
> I am doing source reconstruction with MEG.
>
> First, I am corregistering my head surfac
Thansk Doug. I tried it but still doesn't work. Any other thoughts?
jeni
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The information in this e-mail is intended only for the p
Hi Jeni, what is your command line and terminal output? In general, just
saying that something does not work is not enough information to track
down the problem. Also, please include previous correspondence. We
answer a lot of emails here, and the easier you make it on us, the
faster we can sol
Hi,
I was wondering if the -autorecon2-pial flag has been superseded on the
newer release of Freesurfer, for it isn't being recognized?
Also, is the use of this flag equivalent to running recon-all with the
-autorecon-pial option?
Thanks,
Gabriel
___
Hi Doug,Sorry; didn't realize it wasn't included.So to state the original problem, I tried running mri_glmfit-sim with the following options (previous message included below):mri_glmfit-sim \--glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \--cwpvalthresh .999 \--no-sim GLMFIT/LH_1GroupAvg_Mod
what was your orignal mri_glmfit-sim command line?
On 04/25/2013 05:17 PM, Jeni Chen wrote:
> Hi Doug,
>
> Sorry; didn't realize it wasn't included.
>
> So to state the original problem, I tried running mri_glmfit-sim with
> the following options (previous message included below):
>
> mri_glmfit-
The original command line:
> mri_glmfit-sim \
> --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> --cwpvalthresh .999 \
> --no-sim
> GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS/csd/mc-z.abs.3.j001-1GroupAvg-Cor-thickness-Mod-VAS.csd
To which you suggested
> mri_glmfit-sim \
> --glmdir G
Sorry, I mean the first time that you ran it to create the csd files in
the first place
doug
On 04/25/2013 05:30 PM, Jeni Chen wrote:
> The original command line:
> > mri_glmfit-sim \
> > --glmdir GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS \
> > --cwpvalthresh .999 \
> > --no-sim
> > GLMFIT/
Hi Gabriel,
-autorecon-pial is equivalent to -autorecon2-pial, although in 5.2 there
are some additional stats steps, but basically the same.
You can always look at the flag definitions in the recon-all script to see
what exact steps a certain flag triggers.
emacs $FREESURFER_HOME/bin/recon-all
Hi Doug,
The very first command line was:
mri_glmfit-sim \
--glmdir
/Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS
\
--sim mc-z 5000 3 mc-z.abs.3 \
--cwpvalthresh .05 \
--sim-sign abs \
--overwrite
I was wondering
The csdbase is mc-z.abs.3
Try using that
doug
On 04/25/2013 05:55 PM, Jeni Chen wrote:
> Hi Doug,
>
> The very first command line was:
>
> mri_glmfit-sim \
> --glmdir
> /Volumes/RainvilleHD2/Imaging_Data/Thickness/MATHIEUP_IBS/FS_1stAnalysis/GLMFIT/LH_1GroupAvg_ModVAS_nuissanceAGE_DOSS
>
>
aha! That did the trick. Thanks!
My other question is, since the purpose of running mri_glmfit-sim at
--cwpvalthresh .999 is to see all the clusters, wouldn't it be the same if I
were simply to look at sig.mgh?
Jeni
> The csdbase is mc-z.abs.3
> Try using that
> doug
>
>
On 2013-04-25, at 5
that will show you all the vertices with uncorrected p-values. It will
not show you what the clusters are or what the p-value of the cluster is.
dopug
On 04/25/2013 06:02 PM, Jeni Chen wrote:
> aha! That did the trick. Thanks!
>
> My other question is, since the purpose of running mri_glmfit-sim a
Hi Doug,
Thanks for your reply.
The mask created is used to register with the normalized functional data and to
define the roi, so could I run the following command?
tkregister2 -mov sub/func.nii -noedit -s fsaverage -regheader -reg
./register.dat/
and the func.nii has been normalized (sub.nii)
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