Hi Pedro,
Have a look at this article:
http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours
I think this is the same you'd like to do (or you can change some steps
easily).
Hope it helps!
All the best,
Anderson
On 05/07/12 20:44, Pedro Paulo de Magalhães Oliveira Junior wr
ok, just posted... please, see here: http://brainder.org
On 08/05/12 15:51, Anderson Winkler wrote:
Hi Gabriel,
Please, try downloading from here:
http://dl.dropbox.com/u/2785709/aseg2srf
http://dl.dropbox.com/u/2785709/srf2obj
Right-click and click Save As, to avoid Windows opening it up
a link to the
downloading page? That way I can try again and see what happens. I did
check in my Linux distribution and is just as you said, the gawk is
the default, so I have no any other idea for this.
Regards,
Gabriel
El 08/05/12, *Anderson Winkler * escribió:
Hi Gabriel,
This sou
rfer/bin/srf2obj:2:
' invalid on the expressionrfer/bin/srf2obj:2: ^ character '
Regards,
Gabriel
El 07/05/12, *Anderson Winkler * escribió:
Hi Gabriel,
Attached is a script that probably does what you need. Just make it
executable and call it without arguments to get usage inf
Hi Gabriel,
Attached is a script that probably does what you need. Just make it
executable and call it without arguments to get usage information. The
label indices you can get from the aseg.stats file or from
FreeSurferColorLUT.txt.
The surfaces will be saved in a subdirectory called "ascii
;mri_convert" then I'm using your script to convert that surface
to an object file but always renturns the following error:
aplication srf2obj
gawk: /root/trabajo/freesurfer/bin/srf2obj:2:
' inválido en la expresiónrfer/bin/srf2obj:2: ^ caracter '
I'm working under cent
Hi Mahinda,
For question 1, if you use the new mris_preproc, as described here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19821.html
then yes, you are safe in computing the areas for each vertex.
We have a recent paper that discuss current matters on pointwise area
stuff, a
*De:* Anderson Winkler
*Para:* freesurfer@nmr.mgh.harvard.edu
*Enviado:* Lunes 26 de marzo de 2012 13:56
*Asunto:* Re: [Freesurfer] Cortical Normalization Questions
Hi Jeff and all,
For normalization (i.e., divide the
is flawed, I'd be curious to know what the reason was...
>>>
>>> cheers,
>>> -MH
>>>
>>> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote:
>>>> Hi Jeff
>>>>
>>>> yes, I think this is still our recommendation
Hi Darshan,
If you'd like to go directly from FreeSurfer .asc to OBJ, the attached
little script should do the trick...
Hope it helps!
All the best,
Anderson
On 21/02/12 16:59, Pedro Paulo de Magalhães Oliveira Junior wrote:
There's a how-to in the FreeSurfer website:
http://surfer.nmr.m
oops, sorry list, this was supposed to go to Pedro...
On 15/10/11 17:39, Anderson Winkler wrote:
Ah Pedro,
Se era isso que você precisava, poderia ter falado. Eu tenho isso
pronto, que pode ser chamado via linha de comandos. Foi usado no paper
que vc deve ter visto...
Abração,
Anderson
On
wrote:
Thanks.
I suppose I can't do this without matlab. Right?
-- iOS 5.0
Em 08/10/2011, às 19:29, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>> escreveu:
there is a write_annotation.m file you can use
ops, it seems the comments inside the dpxwrite.m no longer reflect what
it does. You probably don't need this, but anyway, the version attached
is more up-to-date.
Anderson
On 08/10/11 17:28, Anderson Winkler wrote:
Hi Pedro,
There is probably a way to do that using FS tools from the co
Hi Pedro,
There is probably a way to do that using FS tools from the command line,
but the attached script should do the same. The result is a
"data-per-vertex" file, which is the same as the .asc files from
mris_convert. There is no geometry input, hence the vertex coordinates
are all set to
swiki/FreeSurferAnalysisPipelineOverview#TheVolume-based.28Subcortical.29Stream
You may want also to have a look at this paper:
http://dx.doi.org/10.1016/S0896-6273(02)00569-X
Hope this helps!
All the best,
Anderson
On 29/08/11 03:38, Lucas Eggert wrote:
Dear Anderson Winkler,
thank you very much for your quick res
Hi Lucas,
To know if a given structure is gray or white matter you can look in any
reasonable anatomy textbook. In any case, the question itself is
somewhat ill-posed, because some of the subcortical structures have
heterogeneous tissue composition and can't really be labeled entirely as
gray
re subtle but spread across the
brain, which covariate would you use?
thanks,
Alan
[Beth Israel Deaconess Medical Center]
On Wed, Aug 24, 2011 at 12:43 PM, Anderson Winkler
mailto:andersonwink...@hotmail.com>> wrote:
A side note: If you are using FS 4.5.0 or earlier, there is also
A side note: If you are using FS 4.5.0 or earlier, there is also
BrainSegVolNotVent, which discount ventricles. If you want to capture
effects of aging or atrophy, perhaps this could be more sensitive than
BrainSegVol.
On 24/08/11 12:32, Anderson Winkler wrote:
Hi Zuzana,
Yes, you can use
Hi Zuzana,
Yes, you can use BrainSegVol as a measurement of brain volume (I'd
assume you are using FS <=4.5.0). Note that there is another measurement
that you might be interested in, the IntraCranialVol. These measurements
tell different things and not necessarily correlate well one with
ano
Hi Jeff,
Not sure where you can find a verbose documentation, but you can figure
out by looking at the file read_surf.m in the ${FREESURFER_HOME}/matlab
directory. It's straightforward.
All the best,
Anderson
On 08/17/2011 04:32 PM, Jeff Eriksen wrote:
Where may I find the documentation expla
Hi Allison,
A suggestion is to use the surface area of each hemisphere as the
weighting factor. The global average thickness for both hemispheres is
then given by:
bh.thickness = (lh.thickness*lh.surfarea + rh.thickness*rh.surfarea) /
(lh.surfarea + rh.surfarea).
If you use the data in the ?h
*Imaging Genomics Post-Doctoral Fellowship*
**
A postdoctoral fellowship in Imaging Genetics at the Olin
Neuropsychiatric Research Center, Institute of Living, and the
Department of Psychiatry, Yale University, is currently available. The
two-year NIH-funded fellowship, under the direction of
Dear Andrei,
Do you need any specific feature from VRML? If not, and you simply need
to import the mesh into Blender, you can do this:
1) Convert the mesh to ASCII format:
/mris_convert somesurface somesurface.asc/
2) Save the attached script somewhere, make it executable with chmod,
then us
Hi Joakim,
I think you can remove entirely the -t option. The area will be one of
the fields in the table, regardless of this option, as it depends on the
mesh that is used to derive all other measurements except thickness. If
you specify an ?h.area file with -t, it will instead output incorre
with that, though. I see no reason why thickness
measurements wouldn't be normal.
All the best!
Anderson
On 05/16/2011 03:18 PM, Ilana Hairston wrote:
thanks! very helpful.
not to be argumentative, but if my Z distribution is not normal, is there
meaning to FDR?
On May 16, 2011, at
Hi Ilana,
I'll let the first question to the FS experts to answer. For the second:
> 1. Is it legitimate toconclude from this that the regressor's overall effect
> is that it's associated with a thinner cortex (e.g., older subjects have a
> thinner cortex), eventhough most of the cortex does no
Hi Boris,
For now I am taking the geometric average between pial and white
surface coordinates.
Is that the right way to do it, or is there a more precise way?
To obtain a surface that lies in the geometric middle between white and
pial surfaces, it is correct to take the average of the coor
We still have here an old, but very good dual-core PPC that we use to
work with tksurfer, tkmedit, qdec, glmfit and other utilities. If not at
all hard to compile, it would be good to continue having FreeSurfer
available... At some point we'll inevitably have to turn that machine
off, but it co
Hi Catherine,
When setting the variable, drop the "$" sign. So, type simply:
setenv SUBJECTS_DIR /media/external/data/Ventricle-freesurfer
Anderson
On 04/23/2011 04:04 PM, Rongxiang Tang wrote:
Hi Krish,
Thanks for the help. It's calculating now...
One more questions...I noticed that when I
o the trick,
> maybe you used the hex-number instead of decimal for the tag code?
>
> - Manfred
>
>
> Anderson Winkler wrote:
>
>> Hi Graham and Manfred,
>>
>> Thanks for the help! Interesting is that the .tif created with
>> mris_make_template in
gt; Hi Anderson,
>>
>> This might be helpful (beware datedness though).
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/TemplateTifImageFiles
>>
>> The data at the time I did that goc was evidently stored in 32-bit float
>> format... that could lead to your
straight variances. Are the
> means large too? Make sure there are no byte-swapping issues
>
> On Mon, 21 Mar 2011, Anderson Winkler wrote:
>
>
>> Hi Bruce,
>>
>> Thanks! They appear to be stored as 32-bits integers and when I open I
>> get very large nu
se are stored for curv, sulc and inflated curvature.
>
> cheers
> Bruce
>
> On Mon, 21 Mar 2011, Anderson Winkler wrote:
>
>> Hi all,
>>
>> The .tif files (templates) contain 9 pages each, which seem to be
>> organized as 3+3+3. I think I understand that they are
Hi all,
The .tif files (templates) contain 9 pages each, which seem to be
organized as 3+3+3. I think I understand that they are equirectangular
projections of the latitude/longitude of curvature and sulcal depth, is
this correct? But what exactly each of these 9 frames contain?
Thanks!
Ander
Hi Ritobrato,
We have one that may too interest you:
Winkler AM, Kochunov P, Blangero J, Almasy L, Zilles K, Fox PT,
Duggirala R, Glahn DC. Cortical thickness or grey matter volume? The
importance of selecting the phenotype for imaging genetics studies.
Neuroimage. 2010 Nov 15;53(3):1135-46.
h
Dear all,
The B&H procedure is dependent on the number of tests and, for
neuroimaging methods, more tests is often equivalent to higher
resolution, either in voxel-based or surface-based representations of
the brain. The question that arises is whether this would influence
sensitivity and/or p
Dear Lars, Pedro and all,
There should be no problem in using different thresholds for each of
these pairwise comparisons.
Let's consider the following extreme case: Suppose in one of these
comparisons you have a strong effect (say, "activation") that comprises
large brain regions. Suppose t
sue is something the FreeSurfer community
want but it's not so easy to implement in this situation.
Best Regards,
Pedro Paulo Jr.
---
Pedro Paulo de M. Oliveira Junior
Diretor de Operações
Netfilter & SpeedComm Telecom
On Mon, Ja
Dear all,
We are considering to buy a blade system, and FreeSurfer would be one of the applications to run on it. We know that a 3D graphics card, with support for OpenGL and built-in memory+GPU, is recommended. What we are not sure is whether it is mandatory for all the FreeSurfer routines, of if
Hi,
I edited the recon-all, omitting the --conform option, and the pipeline failed
shortly after.
So, is there a way to run the volume processing pipeline (in particular, the
subcortical segmentation), without resampling to 1mm^3 voxels, keeping the
native format 0.8^3 mm^3?
Anderson
Dear all,
Is there a way to have all the results from recon-all in the native image space
(in our case, 0.8x0.8x0.8mm), rather than conformed to 1mm^3?
Looking at the script, I'm worried that replacing the --conform to --noconform
option to mri_convert may prevent the downstream steps to work c
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