Hi
We have just updated one of our Linux servers from OpenSuse v. 12.1 to
12.3. After the update we get the following license error message for
some of the freesurfer commands:
csvarer@hevesy:/usr/local/nru/freesurfer> tkmedit -help
---
Hello all,
I am having a problem with generating values of the vertices at the
hippocampal area. I believe it is a masking issue as reviewing the mask
after the glmfit analysis I see that the mask does not cover the entire
medial region excluding the corpus callosum. Can I do anything to change
th
Hi Joerg
I think Jon Polimeni (ccd) might have some tools for this, but it's not
something we routinely do
cheers
Bruce
On Tue, 11 Jun 2013, Jörg Pfannmöller wrote:
Hello FSexperts,
I am investigating a small area on the cortex. If this area is diplayed by
tksurfer the lable outlines and
Hi Anupa
sorry, I don't understand the question. Fsaverage is the average of a
bunch of subjects (40 or so I think). What do you mean by "size"? It
certainly has less surface area than any individual in it, since the
averaging smnooths it. We store this in the surface so that we can correct
fo
Hi Joshua
are you using the surfaces for this? If so, you shouldn't as they are
undefined in those regions (since they have internal laminar structure
that is different than what we expect). What are you trying to achieve?
cheers
Bruce
On Tue, 11 Jun 2013, Joshua deSouza wrote:
> Hello all,
>
Dear Doug,
Thanks you for your e-mail and sorry for the inconvenience. Here is the
code again.
In this line of code we included the fixed duartion of the fix (1.0) in the
event duration specification (summing to 5.0) and asked Optseq to insert
null events of a minimum duration of 0.0 in 25% of th
Dear FS experts
After the installation of the newest Mac OS X security updates, the
following error occurred:
[Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
tksurfer bert lh pial
dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib
Referenced from: /usr/X11/lib/li
Hi Doug,
I have the v5.3 and the same problem in -qcache step (number of vertices do
not match surface).
I tried some suggestions such as "recon-all -s -vno-check";
"recon-all ..-make all"; "recon-all -s -surfvolume" and I have the same
results: Error: number of vertices do not match surface. How
Dear all,
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PS. If you also go to attend the OHBM 2013 in Seattle, you can find us at
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brainnet...@gma
Dear Freesurfer experts,
I am trying to install free surfer.
It seems that my downloaded version does not have a .cshrc file. I only have an
.sh and .csh file.
All the edits (i.e.,setenv FREESURFER_HOME Applications/freesurfer/ source
Applications/freesurfer/SetUpFreeSurfer.csh) that I trie
thanks Doug.
it worked and I got the following result on which I have clarifying
questions:
--
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
0 1 81837 81837
1) I'm assuming that v
what is your full command line?
On 6/11/13 10:04 AM, Glen Lee wrote:
thanks Doug.
it worked and I got the following result on which I have clarifying
questions:
--
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segm
Hi Claus, I have never seen this before. Maybe Zeke has an idea?
doug
On 6/11/13 5:02 AM, Claus Svarer wrote:
Hi
We have just updated one of our Linux servers from OpenSuse v. 12.1 to
12.3. After the update we get the following license error message for
some of the freesurfer commands:
Hi, Eugenio,
TY again for your help. I did the computing without errors after your
suggestions. I also computed the intensities based on nu.mgz, norm.mgz
and T1.mgz. I would like to know the best measure I should consider,
including because I intend to compare these values with intensity data
from
Hi Doug
After having sent the message to the mailing list this morning I found
another mail sent to the mailing list a month ago about same problem:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28264.html
I have tried to follow the thread but can't see that a solution was
de
yes, this probably relates to the recent crypt problems. Zeke: do you
know how this was resolved? Unfortunately Nick is away for a while longer
and won't be responding
Bruce
On Tue, 11 Jun 2013, Claus Svarer wrote:
Hi Doug
After having sent the message to the mailing list this morning I found
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 the following result on
I'm re-sending an old problem, because I received no answer.
Cheers,
Gabriel
- Mensaje original -
De: Gabriel Gonzalez Escamilla
Fecha: Lunes, 10 de Junio de 2013, 4:56 pm
Asunto: Re: [Freesurfer] autorecon3 error
A: Bruce Fischl
CC: freesurfer@nmr.mgh.harvard.edu
> Dear Doug
>
> Sorr
Hi Gabriel
something is wrong with some surface in the lh. Maybe your disk was full?
Can you go through each of them and visualize them in tksurfer? One
should fail (lh.orig, lh.white, lh.smoothwm, lh.inflated. lh.sphere,
lh.sphere.reg)
sorry I can't be more specific. I've never seen this pa
Dear all,
I'm trying to import my data in Freesurfer. I have it on a folder on my
desktop. I set my SUBJECTS_DIR variable to my subjects directory (other
folder on my desktop). When I run recon-all -i paths_to_myimputfiles
-subjid my_sub_name, I got:
[cpellica@wmen-ps2208 freesurfer]$ recon-all -
Clelia,
Ide be willing to bet the error has something to do with the "%" sign in
the path to the data file. Would it be possible for you to place the
file somewhere such the the absolute path does not contain a "%" sign?
-Zeke
On 06/11/2013 12:37 PM, clelia pellicano wrote:
> Dear all,
>
> I'm
Hi clelia
can you ls that file and confirm that exists? And check the permissions?
Also, note that even if it had found it you didn't tell it to do anything.
You probably want to specify -all on the recon-all command line as well.
cheers
Bruce
On Tue, 11 Jun 2013, clelia pellicano wrote:
D
Hi,
thank you so much, now it's working! I have deleted the "%" from the path
(moving the files), and now it's ok.
Thank you again,
C.
On Tue, Jun 11, 2013 at 5:43 PM, Bruce Fischl wrote:
> Hi clelia
>
> can you ls that file and confirm that exists? And check the permissions?
> Also, note that
thanks Zeke!
Bruce
On Tue, 11 Jun 2013, clelia pellicano wrote:
Hi,
thank you so much, now it's working! I have deleted the "%" from the path
(moving the files), and now it's ok.
Thank you again,
C.
On Tue, Jun 11, 2013 at 5:43 PM, Bruce Fischl
wrote:
Hi clelia
can you ls that
Hi Peter, what scanner are you using? You might be better off with using
a 3T atlas. Spec -schwartzya3t-atlas with recon-all and see if that
cleans it up. You can run just the talairaching with
recon-all -s subject -schwartzya3t-atlas -talairach
doug
On 06/11/2013 01:03 PM, Peter Boulos wrot
Regarding any license issue under Opensuse 12.3 and the libcrypt
incompatibility.
So grab a libcrypt from an older opensuse (one where freesurfer was working,
for me, I used libcrypt.so from 11.3, but 12.1 may be a better candidate if it
works). Place it somewhere ($FREESURFER_HOME/lib is a go
Has anyone published the mean cortical thickness of healthy older adults
for all the Freesurfer ROI? I've only been able to find papers that report
a of subset of the ROIs.
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts Ge
Thank you Nick for informing the list of this workaround.
-Zeke
On 06/11/2013 01:48 PM, Nick Jones wrote:
> Regarding any license issue under Opensuse 12.3 and the libcrypt
> incompatibility.
>
> So grab a libcrypt from an older opensuse (one where freesurfer was
> working, for me, I used libcryp
David might know
Bruce
On Tue, 11 Jun 2013, MCLAREN, Donald wrote:
> Has anyone published the mean cortical thickness of healthy older adults for
> all the Freesurfer ROI? I've only been able to find papers that report a of
> subset of the ROIs.
> Best Regards, Donald McLaren
> =
>
Thank you for your answer. There is another issue I am needing help with. As I
have edited the .csh file from FreeSurfer I am not able to make it work any
more. Is there a way to have a copy of the SetUpFreeSurfer.csh?I have
downloaded the last version of Freesurfer for OSX 10.6.8Thank you so mu
Pablo,
Attached are the original SetUpFreeSurfer.csh and SetUpFreeSurfer.sh
files that come with the Freesurfer5.3 installation package.
-Zeke
On 06/11/2013 02:56 PM, pablo najt wrote:
Thank you for your answer. There is another issue I am needing help
with. As I have edited the .csh fil
Dear Bruce et al.,
Submitting a paper in which I use freesurfer for the analysis of the
auditory cortex, I was asked how freesurfer actually takes individual
boundaries (e.g. of Heschl's gyrus) into account? Both atlases (Desikan and
Destrieux) are based on about 10-20 subjects. How are these boun
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: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks E
Dear Marcos,
these are just mean and standard deviations of intensities of the images
at different levels of processing. What the best measure is depends on
what you want to do with them.
Cheers,
/Eugenio
On Tue, 2013-06-11 at 11:46 -0300, Marcos Martins da Silva wrote:
> Hi, Eugenio,
> TY again f
Dear All,
If I had to choose between longitudinal processing v4.4 or cross-sectional
processing v5.1 for analyzing longitudinal data, what processing stream
should I choose?
Best Regards, Donald McLaren
=
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts
Got it.
Thanks for the prompt answer!
By the way, I tried mri_segstats with --accumulate flag, but it says option
'--accumulate' is unknown.
I don't seem to find it when I looked up mri_segstas --help either.
On Tue, Jun 11, 2013 at 5:05 PM, Douglas N Greve
wrote:
>
> Right, so in this case, th
Hi Holger
You should read the spherical warping and parcellation papers. The secret is
not using landmarks but instead using the entire folding pattern
Cheers
Bruce
On Jun 11, 2013, at 4:51 PM, "Klein, Holger"
wrote:
> Dear Bruce et al.,
>
> Submitting a paper in which I use freesurfer for
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