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
___
umber of vertices.
> doug
>
>
>
> On 06/11/2013 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.
>>
g0001 0.3836 0. 0.1297
1.1861 1.0563
On Tue, Jun 11, 2013 at 11:44 AM, Douglas N Greve 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_se
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --sum sum.dat
On Tue, Jun 11, 2013 at 10:41 AM, Douglas Greve
wrote:
> what is your full command line?
>
>
> On 6/11/13 10:04 AM, Glen Lee wrote:
>
> thanks Doug.
> it worked and I got th
that voxel here refers to vertex since I'm submitting the
surface data.
2) what does 'found 1 segmentations mean'?
3) the dimension is 81837mm^2, correct?
On Tue, Jun 11, 2013 at 12:31 AM, Douglas Greve
wrote:
> It's --sum for this, not --o
> doug
>
>
0, 2013 at 3:39 PM, Douglas N Greve
wrote:
>
> 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
> >
>
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 I
On Wed, Jun 5, 2013 at 2:44 PM, Douglas N Greve
wrote:
> try
>
> mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2
>
> doug
>
> On 06/05/2013 02:26 PM, Glen Lee wrote:
>
>
>>
>>
>>
>> On Wed, Jun 5, 2013 at 12:12 PM, Douglas N
>
>
>
On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve
wrote:
> what was your original mri_glmfit-sim command?
>
> mri_glmfit-sim --glmdir GLM --sim perm 2 2 perm.abs.2 --sim-sign abs
>> --overwrite
>>
>
>
> Then, I tried no-sim on the generated csd file with the following command:
>
> mri_
ubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 5.124509
ERROR: cannot find any csd files
On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve
wrote:
>
> --no-sim takes an argument. Run mri_glmfit-sim with --help to get more info
> doug
>
>
> On 06/04/2013 0
t; .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
>
>
>
&g
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
wrote:
> You will need more like 1 iterations instead of 100.
> doug
>
> On 06/03/2013 04:49 PM, Glen Lee wrot
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).
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 w
Thanks Doug.
Yes, it works well now!
-Glen
On Thu, May 23, 2013 at 1:50 PM, Douglas N Greve
wrote:
> 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
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 wh
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.**edu>>
>
On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve
wrote:
>
> Does the cortex label have any holes in it and do the holes in your output
> correspond? Try it with out the --cortex flag.
> doug
> -> there was some improvement when I did smoothing after removed '--
> cortex flag', such that the number
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.
>&g
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 s
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
rh.in
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 d
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 h
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 freesurfer-L
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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