Hi Doug,
I just read from the .log files that the lh.thickness/area/pial/... files
in subject/xhemi/surf are copied from subject/surf at the end of the
command. Thus it seems that I can just copy lh.volume, too?
Thanks,
Cherry
On Mon, Apr 28, 2014 at 6:25 PM, Yizhou Ma wrote:
> Thanks D
he log file to me
>
> On 04/28/2014 04:14 PM, Yizhou Ma wrote:
> > Thanks Doug. I have ?h.volume in subject/surf but not in
> > subject/xhemi/surf. I followed this page
> > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a
> > problem with surfreg r
On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve
wrote:
>
>
> There should be a ?h.volume file. Are you sure there is not? You can
> specify -meas volume when you run mris_preproc
> doug
>
> On 04/27/2014 08:35 PM, Yizhou Ma wrote:
> > Dear freesurfer experts,
> >
Dear freesurfer experts,
I am working on a project on cortical asymmetry and I have analyzed
vertex-wise cortical thickness/surface area asymmetry. However, I noticed
that Freesurfer doesn't not seem to facilitate such analysis for gray
matter volume, as after running surfreg -xhemi there is no ?h
in my case due to the
difference in Freesurfer versions. What do you think I can do?
Thanks,
Cherry
On Thu, Apr 24, 2014 at 12:06 PM, Yizhou Ma wrote:
> Great. Thanks Doug.
>
>
> On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>&
Great. Thanks Doug.
On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve wrote:
>
> It is ok to run -qcache using 5.3.
>
>
> On 04/23/2014 10:54 PM, Yizhou Ma wrote:
> > Dear Freesurfer experts,
> >
> > I have processed my images and done analysis with cortical th
Dear Freesurfer experts,
I have processed my images and done analysis with cortical thickness using
FS510. Now that I want to do vertex-wise analysis with surface area and
volume, I learned that there is a bug in FS510 with this. (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August
ume using
> surface-based methods. The subcortical structures it uses the volume-based
> method. To compute total GM, you need both.
> doug
>
>
>
> On 9/16/13 9:11 PM, Yizhou Ma wrote:
>
> Dear Freesurfer experts,
>
> I'm doing ROI analysis on surface are
Dear Freesurfer experts,
I'm doing ROI analysis on surface area and gray matter volume using the
aparc.2009 parcellation. Now that I wanted to use corresponding whole brain
measures as covariates, I could not find whole brain gray matter volume
measures in the aparc.a2009s.stats file. However, I f
that if
we change the parameters for certain subjects, we would have to rerun all
of the other subjects with the same set of parameters, which may not be
desirable at the moment.
Thanks for all the help,
Cherry
On Wed, May 22, 2013 at 4:46 PM, Yizhou Ma wrote:
> Hi Michael,
>
> Thi
t of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: Yizhou Ma
> Date: Wednesday, May 22, 2013 2:30 PM
> To: Bruce Fischl
> Cc: freesurfer , Chris Watson <
> christopher.wat...@childrens.harvard.e
Ok. I'll give it a try. Thanks, Chris & Bruce!
On Wed, May 22, 2013 at 3:29 PM, Bruce Fischl wrote:
> Hi Cherry
>
> Chris is right. Putting control points in the WM will help the pial
> surface as well.
>
> cheers
> Bruce
>
> On Wed, 22 May 2013, Yizhou Ma w
points in the white matter, not around it.
>
> On 05/22/2013 03:04 PM, Yizhou Ma wrote:
>
> Dear FS experts,
>
> I have a subject where large portions of temporal lobe is not included
> in the pial surface. A member in my lab has suggested edits on
> brain.finalsurf
t; Finally, I want to point out that it may be better to smooth before
> >>> computing the LI because the LI computation is non-linear and it has
> >>> the
> >>> potential to divide by a noisy number. To do this, run without the
> >>> --paired-diff flag
Dear freesurfer experts,
I'm doing small volume correction for multiple comparison. However, when I
run "mri_glmfit-sim" with "--label mylabelfile", I got the error that
"--label unrecognizable". I use "mri_glmfit-sim --help" to see the help
information but there is no information regarding "--lab
In my study, I ran it both ways and it did not make a difference, but I
> think smoothing before LI is the safer bet.
>
> doug
>
>
> On 03/29/2013 12:33 PM, Ejoe Yizhou Ma wrote:
> > Hi freesurfer experts,
> >
> > I'm investigating lh-to-rh asymmetry and am follo
Hi freesurfer experts,
I'm investigating lh-to-rh asymmetry and am following instructions on this
page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi.
My question is, what does the "--xhemi" flag do in the "mris_preproc"
command? It seems to me that it calculates (lh-rh) value at each vertex for
lh-rh)/[(lh+rh)/2] rather than (lh-rh). Can I do that using mris_preproc
and how?
Thanks,
Cherry
On Thu, Mar 28, 2013 at 1:32 PM, Ejoe Yizhou Ma wrote:
> I see. Then I think I'd better just follow the instructions on the Xhemi
> page. Thanks!
>
>
> On Thu, Mar 28, 2013 at
web page.
> doug
>
>
> On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote:
>
>> Thanks, Doug.
>>
>> I'm not planning to use qdec. It's just that I used to generate the
>> ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we
>> n
the mris_preproc command followed by
> mri_glmfit.
> doug
>
>
> On 03/28/2013 12:51 PM, Douglas N Greve wrote:
> > On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote:
> >> Dear Freesurfer experts,
> >>
> >> I'm trying to investigate lh-to-rh asymmetry, so
Dear Freesurfer experts,
I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to
the subject of fsaverage_sym following the instructions on this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg
commands I've got ?h.thickness files in subjid/xhemi/surf.
Hi Doug,
Thanks for replying. Yet I have a question on this matrix. From what I see,
each row corresponds to one contrast, which has one df. Thus why are we
having 8 rows while the interaction has a df of 4?
Thanks,
Cherry
On Sun, Nov 18, 2012 at 6:23 PM, Douglas Greve wrote:
>
> Hi Bo, you can
Hi Bo,
I'm definitely not an expert of this, but I see that you really nead some
help, so I tried to look at your matrix. From my humble opinion it doesn't
look correct. Firstly, the first 9 groups are male groups and the last 9
are female groups. Then why are all female groups assigned 0 in the m
Hi Jurgen,
I actually just came across a similar situation in which I tried to
convince my PI that a paired t test is more appropriate. In my humble
opinion, if you are applying an independent group test, than the matching
design is irrelevant in this analysis because you're not taking any
advanta
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