Doug,
For the PCA residuals we found 37% for the first component.
The same analysis has been done for FreeSurfer v4.5.0,
and we found a residual FWHM of 15.27 and 30% for the
first PCA component. The time courses showed some outliers
for both versions, very much dependent on the position on
the
Dear FS:
We compared two groups using cluster-wise Montecarlo simulation.
Clusters obtained are extended for more than one region of aparc.2009
atlas. How to identify automatically those regions in each cluster?May I
get a file with list of aparc.2009 regions and corresponding clusters?
Dear FS:
We compared two groups using cluster-wise Montecarlo simulation.
Clusters obtained are extended for more than one region of aparc.2009
atlas. How to identify automatically those regions in each cluster?May I
get a file with list of aparc.2009 regions and corresponding clusters?
Hi Martin,
I am a little confused about these mapped files in the base directories
you are referring to. How would I check them?
-Shannon K.
On Fri, Sep 28, 2012 at 4:08 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:
I see,
Usually people look at thickness maps and volume on an ROI
Hi Gari, you can use the data from the surf2surf in qdec/mri_glmfit. If
you are using qdec, you might want to let qdec generate the file for you
to make sure they are consistent. It is just running mris_preproc and
should give an identical file, but just to make sure.
doug
On 09/29/2012
Hi Maryam, I must confess ignorance on search-light analysis. Can you
give me more background on what it is, the output data, and what you
want mri_glmfit to tell you?
doug
On 09/30/2012 09:46 PM, Maryam Vaziri Pashkam wrote:
Hi Dough,
I have run a searchlight analysis on 10 subjects and
Hi Yawu, there is a file in the output called
subject/stats/lh.aparc.stats (there is an rh.aparc.stats too as well as
?h.aparc.a2009s.stats files).
doug
ps. Please send emails to the FreeSurfer list instead of directly to me.
Thanks!
On 10/01/2012 03:36 AM, Liu Yawu wrote:
Hi Douglas,
After
wow, that is a big difference. Can you just subtract the y.mgh of the
4.5 version from that of the 5.0 version and see where the differences
are? Also, if you take the y.mgh of 4.5 and run it in the mri_glmfit of
5.0, do you see the same FWHM as in the mri_glmfit of 4.5?
doug
On 10/01/2012
I put a new version of mri_glmfit-sim which will do what you want. Use
it by adding the --a2009s flag
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim
doug
On 10/01/2012 12:16 PM, jm wrote:
Dear FS:
We compared two groups using cluster-wise Montecarlo
Hi Doug,
The output of the analysis is a volume with performance values in each
voxel. the performance ranges between 0 to 1 and I want to see if across
subjects there is any region with above chance performance (Chance is 0.5).
Maryam
On Mon, Oct 1, 2012 at 6:10 PM, Douglas N Greve
So it is only one volume? This won't work with mri_glmfit. glmfit needs
to have a value for each subject so that it can compute the variance
across subjects (needed to infer whether a difference from 0 is
significant). I don't know of any software that will do it.
doug
On 10/1/12 6:59 PM,
Its one value per voxel per subject. So there is variane across subjects.
and I want to see weather that value is different from 0.5 instead of 0.
Maryam
On Mon, Oct 1, 2012 at 8:54 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
So it is only one volume? This won't work with mri_glmfit.
Hi Martin,
Thanks for your reply.
My iMac has 14 GB of RAM. However, the Mac OS version of FreeSurfer is only
available as a 32-bit version, and thus any time FreeSurfer requires more than
approximately 3.5 GB of memory it will exit with an error. Are there any plans
yet for a 64-bit Mac OS
Dear FreeSurfer Users,
I have created a binary mask for the hippocampi and now i want to create
the
triangulated surfaces of the hippocampi?
An one know how to do it?
Thanks,
Efrat
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mri_mc should do the trick
Cheers
Bruce
P.s. it is a marching cubes tessellation algorithm. You could also try
mri_tessellate
On Oct 1, 2012, at 10:10 PM, Efrat Kliper e.kli...@gmail.com wrote:
Dear FreeSurfer Users,
I have created a binary mask for the hippocampi and now i want to
Dear all,
I need to mark the cortical extent of a lesion (intersection of the lesion
and pial surface, where lesion represent a epilepsy related resection).
After the pial labeling of the resection, I need to register the labeled
surface to the fsaverage.
I completed recon-all routine on the
Hello,
I'm having a problem similar to the one outlined here:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error ERROR: Option --keep-precision
unknown
I looked for the newer version of mri_vol2vol described in the previous
post,
You can subtract .5 from the volume (fscalc vol.mgh sub .5 -o
vol-minus.5.mgh), then do a one-sample group mean (--osgm). You should
do a permutation test to correct for multiple comparisons because the
residuals definitely won't be Gaussian.
doug
On 10/1/12 9:11 PM, Maryam Vaziri Pashkam
I just put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
doug
On 10/1/12 10:56 PM, Andrew Bock wrote:
Hello,
I'm having a problem similar to the one outlined here:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
Dear FreeSurfers Users,
When i am using the dt_recon function to create adc map i get quite a lot
negative values,
dose anyone encounter this problem?
Thanks,
Efrat
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I have download the latest verion of mri_segstats from the release
notes. But it does not generate asegstats.
4 x86_64 x86_64 GNU/Linux
#
#@# ASeg Stats Tue Oct 2 07:36:17 CEST 2012
/home/knutjb/freesurfer/20_ucsd_automatic_version2/004
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