Hi Wilder
Fsaverage doesn't really have a thickness associated with it. I guess we could
comput the mean thickness of the subjects that went into it, but I'm not sure
how useful that would be as they are intentionally varied in terms of age and
pathology
Cheers
Bruce
> On Aug 12, 2014, at 3:5
Dear Zeke,
Thanks for your email. For some reasons your email went to the spam folder
The build-stamps.txt file contents:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0
>freeview does not work
Thanks,
Ali
On Tue, Aug 5, 2014 at 11:44 PM, Z K wrote:
> Just so its clear.. You have insta
Dear Bruce,
Thanks for your email, for some reasons your email went to the spam folder.
Yes, all PC are running Ubuntu.
The ram is: 7.6 GiB
Processor: Intel® Core™ i7-3770 CPU @ 3.40GHz × 8
The graphic card: Intel® Ivybridge Desktop
*-display
description: VGA compatible controller
Dear Freesurfers,
I’m struggling with finding a way of getting a table of the cluster maxima of
FEAT functional data registered to (reg-feat2anat) and resampled to (feat2surf)
reconstructed surfaces. I want to extract cluster maxima for single subjects
but preferentially NOT in fsaverage group
That thickness file is already there, for what it is worth.
doug
On 8/12/14 4:59 AM, Bruce Fischl wrote:
Hi Wilder
Fsaverage doesn't really have a thickness associated with it. I guess
we could comput the mean thickness of the subjects that went into it,
but I'm not sure how useful that would
mri_surfcluster will probably do what you need though there are some
caveats:
- You will not be able to get the results corrected for multiple comparisons
- If you are looking at the z-score, then this will not be as powerful
as it could be because you applied no smoothing (unless you applied
Dear Freesurfers,
I am trying to flip an overlay (.mgh) to the contralateral hemisphere.
The overlay is in fsaverage-space.
I am using it only for visualization (and not doing any statistics).
I noticed that there was a program that could achieve this:
ftp://surfer.nmr.mgh.harvard.edu/transfer/
Hello Carolina,
Freesurfer will run on Mavericks. However, you may run into a small
hiccup regarding XQuartz... If after the upgrade you get a segfault
error when attempting to open any of the freesurfer GUIs then please
reinstall XQuartz v2.7.5 (http://xquartz.macosforge.org/trac/wiki/Releases
Ali,
I have not encountered this issue before. Could you please provide a
screencapture or copy/paste of the terminal output when you type:
$> tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz
-Zeke
On 08/12/2014 06:48 AM, Ali Radaideh wrote:
> Dear Zeke,
>
> Thanks for your email. For so
I've refreshed those links, try now
doug
On 08/12/2014 09:40 AM, Bastian Cheng wrote:
> Dear Freesurfers,
>
> I am trying to flip an overlay (.mgh) to the contralateral hemisphere.
>
> The overlay is in fsaverage-space.
> I am using it only for visualization (and not doing any statistics).
>
> I
sorry, I should have given you a new make_average_volume.
you can get it from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume
On 08/11/2014 07:52 AM, angela.fav...@unipd.it wrote:
> Hi Doug, I am having a problem with the last step of building my own
> sym
thank you!
> sorry, I should have given you a new make_average_volume.
>
> you can get it from here
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume
>
>
> On 08/11/2014 07:52 AM, angela.fav...@unipd.it wrote:
>> Hi Doug, I am having a problem with the last ste
great, thank you!!
On 12 August 2014 17:11, Douglas N Greve wrote:
>
> I've refreshed those links, try now
> doug
>
> On 08/12/2014 09:40 AM, Bastian Cheng wrote:
>> Dear Freesurfers,
>>
>> I am trying to flip an overlay (.mgh) to the contralateral hemisphere.
>>
>> The overlay is in fsaverage-sp
segmentation vs parcellation:
Segmentation appears to mean identifying and assigning voxels to a label which
maps to a gross structure like thalamus, left cortex, etc. Parcellation
appears to mean the same but for mappings at higher resolution, e.g. L V1. Is
this correct?
surface vs volume:
Hey Bruce,
Is there anyway I can make edits to the grey matter to help with the
segmentation errors (i.e reclassify grey matter in the brainmask with voxel
edit so they are included in the pial layer). Even with the addition of
control points and wm edits I'm still not getting a proper segmentati
Hi Bruce and others,
Thanks for the reply! I cloned in all of the brain to the brainmask and ran
-autorecon2. What I have so far looks a lot better, but -autorecon2 exited with
errors. In recon-all.log it looks like mris_curvature_stats went fine, then it
says "INFO: mri_segstats will not calcu
Hi Matt
Not really. Is the white matter in those regions already 110?
Bruce
> On Aug 12, 2014, at 8:21 PM, "Walton, Matt" wrote:
>
> Hey Bruce,
>
> Is there anyway I can make edits to the grey matter to help with the
> segmentation errors (i.e reclassify grey matter in the brainmask with voxel
Hey,
Bruce, yes WM is already classified as 110 in the regions, but grey matter
is still being excluded.
Matt
On Tue, Aug 12, 2014 at 2:08 PM, Bruce Fischl
wrote:
> Hi Matt
> Not really. Is the white matter in those regions already 110?
> Bruce
>
> On Aug 12, 2014, at 8:21 PM, "Walton, Matt"
If you upload the subject and send us the voxel coords we will have a look
Bruce
> On Aug 12, 2014, at 10:55 PM, "Walton, Matt"
> wrote:
>
> Hey,
>
> Bruce, yes WM is already classified as 110 in the regions, but grey matter is
> still being excluded.
>
> Matt
>
>
>> On Tue, Aug 12, 2014
Dear FS experts.
I am trying run trac-all - the longitudinal version - on the cluster and not by
using the dmrirc file. I am looking at the 'trac-all -help' and also the wiki,
but I couldn't find a flag or option where I could specify the use of
unbiased-template (e.g. [subjectID-base]) and oth
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