Hello Freesurfer users,
I'd hope to know the RESEL number in my group GLM analysis data.
I can calculate the number of vertices and also see the fwhm.dat in the
ouput GLM folder, but I wonder if there is anyway of finding out RESEL size
if freesurfer also provides that info like SPM does.
-Glen
, Glen Lee wrote:
Thanks Doug!
I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
ERROR: Option --o unknown
I don't see --o option when I looked up mri_segstats --help either. FYI,
I'm using v5.1.
Any idea
0.3836 0. 0.1297
1.1861 1.0563
On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Did you look in the summary file? If you have questions about that, can
you send it?
doug
On 06/11/2013 11:34 AM, Glen Lee wrote:
mri_segstats --seg mask.mgh
/11/2013 04:55 PM, Glen Lee wrote:
Hi Doug --
I copied and pasted the summary file below.
It looks like mask.mgh was treated as volumetric image.
Also I'm not sure how to interpret TableCol.
# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id
Dear freesurfer users
I'm wondering if there is any way of figuring out the surface size within a
mask image (mask.mgh)
which is generated after running a group-level GLM analysis (2nd RFX) using
mri_glmfit.
As I'm thinking, this may be:
number of vertex by dimension of one vertex (1mm).
But
at 3:39 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
Hi Glen, you can use
mri_segstats --seg mask.mgh --id 1 --i
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat
doug
On 06/10/2013 03:17 PM, Glen Lee wrote:
Dear freesurfer users
I'm wondering if there is any way of figuring
, Glen Lee wrote:
Hi Doug,
I tried as you suggested, but i've got the following error: e.g.,cannot
find any csd files.
However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd ls
mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need
.05. You can change this with --cwpvalthresh to something like .99. That
should give you all the clusters. Also, you don't have to run the full
simulation again; you can use the --no-sim option and it will use the
simulation that you already did.
doug
On 6/3/13 9:45 PM, Glen Lee wrote
Hello Freesurfer experts--
I ran mri_glmfit-sim to validate the group level GLM result (which was
already done using mri_glmfit), but I was not able to get any result out of
it.
Even with a quite liberal threshold (2), no vertices came out (below is
what I typed in for the random permutation).
Indeed, I initially tried 10,000 iterations and got nothing.
What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
You will need more like 1 iterations instead of 100.
doug
On 06/03/2013 04:49 PM, Glen
Hello Freesurfer users
I'm trying to replicate my earlier findings in 3D space by warping the data
into surface using freesurfer.
Previously, the 3D data were smoothed using 4mm FWHM kernel and I'm
wondering what size of smoothing kernel for 2D would be equivalent to 4mm
for volumes.
Any help
Hello FreeSurfer experts,
I just ran smoothing on a single 2D EPI image with a binary mask (that
excludes NaN vertices), but it didn't seem work out well as the output
image (e.g., test.mgh) contains zero values throughout vertices.
Also, I've got two warning messages (see below): while one of
Thanks Doug.
Yes, it works well now!
-Glen
On Thu, May 23, 2013 at 1:50 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
The second error just means that it cannot compute the fwhm. This will
go away if you add --smoooth-only.
On 05/23/2013 01:31 PM, Glen Lee wrote:
Hello FreeSurfer
to the list and not to me directly. That way
others can benefit from the exchange and the record goes into our mail
archive.
On 05/09/2013 11:07 AM, Glen Lee wrote:
Hi Doug
See below for the command line that I used.
smoothK=4;
mri_surf2surf --hemi lh --s fsaverage_sym --fwhm
in a lot of places,
but those 0s should get smoothed with other non 0s
On 05/09/2013 02:06 PM, Glen Lee wrote:
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu
wrote:
Does the cortex label have
Hello freesurfer experts,
I'm a newbie for freesurfer and would like to ask a naive question.
I've just applied smoothing onto a single surface mgh file using
mri_surf2surf (with fwhm ==4) and examined the values in the output map.
As it turns out, values become 0 in a number of vertices after
Freesurfer users,
I'm a newbie for FS and have a rudimentary question for you.
I have to overlay the group map for right hemisphere onto the lh.inflated
(due to using sym space, where left surface map became symmetrical to the
right), but I wonder if there is any way of reverting it back to
Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf
template in either fsaverage or fsaverage_sym directory.
FYI, I'm using freeview v1.0
if anybody know, please help.
-Glen
$ freeview -f lh.inflated
2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid
Hi freesurfer experts,
I'm a newbie for the free surfer and am playing around with the freeview
GUI.
I'm having trouble moving the slide bar back to '0' by manually entering
'0' right next to the Mid point slide.
Interestingly, the slide bar moves when I entered other values like -2 or
2, but it
Dear freesurfer experts,
I'm running into installation failure and can't quite figure this out (I'm
a novice Linux user too).
It complains there is no such file or directory although I've downloaded
the file and move that to the usr/local directory, so there clearly is the
file.
Would anybody
Dear freesurfer experts,
I'm running into installation failure and can't quite figure this out (I'm
a novice Linux user too).
It complains there is no such file or directory when I simply followed the
instruction by typing the command below in the /usr/local directory.
tar xzvf
Hello,
I just installed a recent version of Ubuntu to run the freesurfer and I
know nothing about Linux yet.
But I'm seeing that the download link only specifies CenOS 4.
Does it mean that Ubuntu is not compatible with Freesurfer?
Any help would be appreciated.
Thanks,
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