Dear Freesurfer Experts,
I recently installed freesurfer. In my first subject, it did the largest
part of the calculations (recon-all all) but ended up with the following
error:
#...@# Cortical ribbon mask Tue May 12 22:29:18 CEST 2009
/Applications/freesurfer/subjects/sleep001_RJ/mri
\n mris_v
Hi Nick,
On Tuesday 12 May 2009 15:39:47 Nick Schmansky wrote:
> Martin,
>
> That etiv number seems high. Does the -tal-check stage pass? did you
> rerun the -segstats stage? that calculates etiv.
The data were first pushed through the whole FS pipeline in 2006. As I look at
the recon-all.log
Nick,
I copy this file but there is the same problem. So I try to find the
mistake.
In the file asegstats2table in $FREESURFER_HOME/bin, I do this modify:
in def write_table(options, rows, cols, table) (line 305)
I replace
r1c1 = 'Measure:%s' %( options.meas)
with this line
r1c1 = 'fsid '
a
Hi everyone,
As I dont do a study in which I compare a group of subjects with some kind
of abnormality with a control group I was looking for literature values for
cortical thickness. The only paper I found which was written by von Economo
et al. in 1925 doing a post-mortem analysis.
Are t
Hi Falk,
we published some values in our Cerebral Cortex paper , but I suspect the
effective thickness will vary a bit as a function of pulse sequence, and
certainly it will vary with things like age. Rahul has probably tabulated
by parcellation unit if that helps.
cheers
Bruce
On Wed, 13 M
Hi Falk,
We do indeed have cortical thickness values for each of the parcellation
units for a range of subjects (healthly elderly, middle age and young
controls and Alzheimer's disease subjects). Which parcellation units are
you looking for? A whole lobe?
Best,
rahul
> Hi Falk,
>
> we published
Hi Rahul and Bruce,
I'm trying to evaluate the usefulness of 7T data for the measurement of
cortical thickness. But as FreeSurfer doesn't perform too well using high
resolution data right now I'm also using a module within Slicer to get
results. Though I'm still trying to process my high resolutio
We'll need more information. What version of freesurfer was installed
and on what Mac OS (with version)? Make sure you have all the latest
Mac software updates for your Mac.
Nick
On Wed, 2009-05-13 at 10:09 +0200, Buchmann Andreas wrote:
> Dear Freesurfer Experts,
>
> I recently installed fr
So you're group analysis is in MNI152, and you want to map that to
fsaverage or back to each individual?
doug
Vina Goghari wrote:
Hello all,
I have group contrast fMRI activations analzyed by FSL Flame 1 that I
want to extract individual thickness data for each subject from data
processed by
Hi Doug,
Yes the FSL group analysis is in MN152 and then I want map that back to
each individual's brain that were analyzed and parcellated using
FreeSurfer, so I can extract thickness values from my fMRI regions of
interest if that is possible.
Thanks!
Vina
Douglas N Greve wrote:
So you're
Hi,
I want to smooth a cortical thickness map using values only in a specific
area. Basically I want to mask out all other segmentations, for example
smooth with fwhm of 20 only in the postcentral region.
I've used quite a few combinations of the -label-src and -label-trg flags
and noticed
Hi Doug and Jon,
I wanted to follow up on your last e-mail--can you tell me how you were able
to set an "anchor point" in the calcarine fissure? If you can recall why it
seemed necessary to set the calcarine fissure fieldsign to +1, I would
greatly appreciate it. This sounds potentially useful t
As a tangential follow-up question, will the longitudinal analysis
stream be discussed and demonstrated in the upcoming FSL/FreeSurfer
course in San Francisco?
-
Jim Porter
Graduate Student
Clinical Science & Psychopathology Research
University of Minnesota
Nick Schmansky wrote:
L
no, probably not, since we're still sorting out the details. We'll be happy
to chat about it in person if you like though
On Wed, 13 May
2009, James Porter wrote:
As a tangential follow-up question, will the longitudinal analysis stream be
discussed and
demonstrated in the upcoming FSL/Free
Jim,
No, I dont think there will be time, other than maybe a brief mention,
as the existing freesurfer material must fit in one day, which makes
things quite packed, as there is a ton of stuff to learn before even
thinking about longitudinal analysis.
However, maybe that day we'll ask for a show-
Hi all,
I got in the recon-all log
#...@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009
/home/gkirk/freesurfer/freesurfer/subjects/P21/mri
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41
--label_right_ribbon 42 --save_ribbon --save_distance P21
SUBJECTS_DIR
Greg,
How much memory does the system have available at the time mris_volmask
is run? It will consume about 1GB within a minute or two of starting,
and I know that the underlying code (VTK library) doesnt handle memory
alloc failures very gracefully.
If running this stage (-cortribbon) fails con
> Hello,
>
> Here is the ouput from bugr:
>
> FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer
>
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
>
> RedHat release: Fedora release 10 (Cambridge)
>
> Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64
>
> I have sets o
John,
What does the file look like when its opened in tkmedit? ie
tkmedit -f T1.mgz
does it look like our sample subject data bert? ie, a full brain t1
anatomical scan?
Nick
On Wed, 2009-05-13 at 16:41 -0400, John Drozd wrote:
>
> Hello,
>
> Here is the ouput from b
Nick,
I have 8 Gig of mem 2 quad cores, but I have been running 6 or more freesurfer
jobs concurrently, ill
run them by themselves and see if it persists and let you know.
thankx
G.
From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nick Schmansky
Se
Actually, I have also been looking for cortical
thickness normative values. We have run our
first few research subjects with FreeSurfer (a
normal control and several patients with
neurodegenerative disorders), and I wanted to see
if the thickness values we're getting are in the
normal rang
While trying to coregister a ct.nii and a orig.mgz file using the following
command:
spmregister --s SUBJECT --mov ct.nii --reg spm.reg.dat --fsvol orig
I get the following error:
>> >> >> ERROR: spm_coreg
>> ??? Undefined function or variable 'x'.
>> Finished after 0.023302 sec
>> >> Parameter
looks like it thinks the slice thickness is 0, which is probably bad
On
Wed, 13 May 2009, Nick Schmansky wrote:
John,
What does the file look like when its opened in tkmedit? ie
tkmedit -f T1.mgz
does it look like our sample subject data bert? ie, a full brain t1
anatomical scan?
Nic
We have build a normative base with 68 subjects sampled from the average
brazilian population.
we are really interested in conducting / cooperating in a multicenter study.
Enviado do meu celular Nokia
-Msg original-
De: Dana W. Moore
Enviada: 13/05/2009 18:46:08
Para: freesurfer@nmr.mg
no, we didn't use the parcellations. We binarized the sulc and used
positive/negative sulc to be sulcal/gyral
cheers,
Bruce
On Wed, 13 May 2009, Dana W. Moore
wrote:
Actually, I have also been looking for cortical thickness normative values.
We have run our first few research subjects wit
Hi,
I'm running fsv405 on a 64bit Linux centos5.
I have not had much success with using the File - Save Label - Filename within
qdec (v1.1). The gui prompt has a default filename set to lh.untitled.label and
I am unable to edit that name, but I can write the default filename to the
default dir (
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