Got it.
Thanks Louis!
2012-03-27
Chunhui Chen
_
State Key Laboratory of Cognitive Neuroscience and Learning
Beijing Normal University
Beijing, China 100875
发件人： Louis Nicholas Vinke
发送时间： 2012-03-26 23:27:09
收件人： chenchunhuichina
抄送： freesurfer
主题： Re: Re: [Freesurfe
I think we must be careful about including noisy large scale measurements as
global nuisance covariates in the General Linear Model (GLM). The
GLM assumes that the independent variables are measured almost without
error (eg. see
http://en.wikipedia.org/wiki/Errors-in-variables_models). For ins
not that I know of, sorry
On Mon, 26 Mar 2012, Jonathan A Winawer wrote:
> Are there any tools associated with freesurfer to aid in segmentation of the
> dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight
> sinus, etc) from a T1-weighted anatomical scan?
>
> Many thanks,
>
Are there any tools associated with freesurfer to aid in segmentation of the
dural sinuses (e.g., superior sagittal sinus, transverse sinus, straight sinus,
etc) from a T1-weighted anatomical scan?
Many thanks,
Jon
***
Jonathan Winawer
Stanford University
Depar
Thank you Doug and Satra,
I ran the same pipeline on another machine after I post the question and it
went through with no problem...
On the machine which the pipeline failed, I have
freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0. And on the machine that
the pipeline went through, I have
free
hi Qingyang,
you can simply copy and paste the command line into the shell.
cheers,
satra
On Mon, Mar 26, 2012 at 3:12 PM, Douglas N Greve
wrote:
> Can you run it outside of the pipeline to assure that it is not a
> pipeline issue?
> doug
>
> On 03/18/2012 08:54 AM, Qingyang Li wrote:
> > Hi
OK
T1 space is the space acquired from the machine, original anatomical space
regards
JG
On 03/26/2012 2:25 PM, Bruce Fischl wrote:
> can you post to the list so others can answer? And can you clarify
> what you mean by "T1" space?
>
> On Mon, 26 Mar 2012, Johnson wrote:
>
>> Hi
>> well, I had to
Can you run it outside of the pipeline to assure that it is not a
pipeline issue?
doug
On 03/18/2012 08:54 AM, Qingyang Li wrote:
> Hi all,
> I am new to the freesurfer world.
> I was running a pipeline where I met an error. Here is the command I
> run and the error message:
>
> Command:
>
Hi Johnson
what T1 did you register to? Most of the ones we generate (T1.mgz,
brainmask.mgz, ...) are in a common coordinate system and you shouldn't
have to transform from one to another.
cheers
Bruce
On Mon, 26 Mar 2012, Johnson wrote:
> Hi
> Let me re-phrase my question:
> I already did re
Try this
cd $SUBJECTS_DIR/subject
mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown
--volmask --o mri/wmparc.a2009s.mgz --a2009s --ctxseg aparc.a2009s+aseg.mgz
mri_segstats --seg mri/wmparc.a2009s.mgz --sum
stats/wmparc.a2009s.stats --pv mri/norm.mgz --excludeid 0
--brain-vol-
Actually, (1) should be more accurate, because bbregister uses the surface
reconstruction obtained from the T1 to optimize the contrast across the
gray/white boundary in the registered DWI.
However if you want to convert to the 1mm, 256^3 voxel size that was used
as input to freesurfer, see mr
Hi Jeff and all,
For normalization (i.e., divide the measurement under study by some
global measurement), I would not argue favourably, as this procedure can
bias the results in the opposite direction if a global effect is present.
Instead, include it as a covariate is not as harmful. My sugges
Hi
Let me re-phrase my question:
I already did registration from DWI to T1, this step is OK.
Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not
the aparc+aseg-in-rawavg file). I know I have two choices:
1) do registration using bbregister
2) since Freesurfer during processing ha
If you want to register your DWI to T1, you should register to
mri/brain.mgz. You can do this with bbregister, or with any affine
registration tool of your choice.
On Mon, 26 Mar 2012, Johnson wrote:
> Hi
> I found it in a 256x256x256 space while the T1 we use is in different space,
> I found
Hi
I found it in a 256x256x256 space while the T1 we use is in different
space, I found this page on the registration step:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
I wish to know how this script work?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz
--r
Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 used as
input to freesurfer.
a.y
On Mon, 26 Mar 2012, Johnson wrote:
> Hi FS expert
> I need to know the transformation matrix itself since I will do the
> transformation in matlab.
> I successfully transformed white matter fibers
Dear All,
Did someone already figured out a solution for this problem?
I get exactly the same error every time I run recon_all
There seems to be no answer on the mailing list yet
Thank you
Kind regards
Gregor
Hi Avi,
do you have any advise for Dana?
thanks
Bruce
On Tue, 30
You don't need to do that registration. Instead, use --identity xDS with
mri_surf2vol.
doug
Seok Lew wrote:
> Hi,
>
> After freesurfer reconstruction, I tried to project surface normal
> vectors on the ribbon. I used the following scripts, but the
> projected vectors were out of the ribbon whe
Hi Chunhui,
The wm-anat-snr missing step is misleading. That file gets created when
QAtools generates the SNR/WM measures using the wm-anat-snr command. It
is not part of the recon-all stream. If you specify the default status
log file included with the scripts you should not get that error
hi doug,
here is the error, it told me there was a problem in an if statement
somewhere.
if you use smooth = 2.0 instead of 2 you will get the error.
cheers,
satra
---
[snip]
fslmerge -t /mindhive/gablab/users/keshavan/scripts/BrainImagingPipeline
s/utils/test/fmunwarp/temp/ph.nii.gz /mindhive
what does it do? What is the terminal output?
Satrajit Ghosh wrote:
> epidewarp.fsl does not take non-integer smoothing kernel sizes.
>
> cheers,
>
> satra
>
>
>
> ___
> Freesurfer
which MNI coordinate system? We don't know anything about surfstat. Can
you tell us what you want to do without using the surfstat commands?
doug
xiaoning wu wrote:
> Hi all,
>
> Recently I have a problem about coordinate of freesurfer. I have
> reprocessed the MRI data to get the cortical thick
Zurcher Nicole wrote:
>
> Hi everyone,
>
> I have two questions regarding FreeSurfer and FSL interoperation and
> it would be great if someone could help.
>
> 1) When displaying subject-level FSL FEAT data onto the FS volume
> using the command
> "tkmedit blobby orig.mgz lh.white -overlay
>
ZhiLiangLong wrote:
Hi all:
I'm performing the group analysis on my own data using command line on
FS5.1.0 and i'm a little confused about the Clusterwise Correction for
Multiple Comparisions. the command is as follows:
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \
--sim mc-z 1 4 mc-z
Hi ZhiLiangLong, what you have set up probably does not make sense. By
using gender as a covariate (male=1 and female=2), you are saying that
you expect females to be twice as thick as males.
doug
ZhiLiangLong wrote:
Hi, FS experts:
I'm scanning freesurfer pages about FSGD files here:
http:
It might be failing on the aseg, so try it with --no-aseg
doug
Bruce Fischl wrote:
> Hi Sonya
>
> did you run out of RAM? How much is on your machine?
>
> cheers
> Bruce
>
> On Fri, 23 Mar 2012, sonya kaur wrote:
>
>
>> Dear all,I'm getting an error with the make_average_subject command on
>> f
You'll have to re-run the preprocessing (or change all the .nii files).
doug
Kiley Seymour wrote:
> Dear Doug,
>
> Thanks for your earlier reply. I have installed fsl on my machine, and
> have progressed a little further through the retinotopy analysis.
> However, I now have the following error.
Dear Doug,
Thanks for your earlier reply. I have installed fsl on my machine, and have
progressed a little further through the retinotopy analysis. However, I now
have the following error.
ERROR: TR mismatch between analysis and data
analysis TR = 2, data TR = 0
I used
mri_convert f.nii f.ni
Hi all:
A few days ago, i have asked about some questions about Correction for
Multiple Comparison. But i'm still confused about it. The version of FS is
5.1.0. when i performed Correction for Multiple Comparison using command line
with 'mris_glmfit-sim', it usually took many hours to complet
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