Martin is the one to ask
Bruce
On Thu, 4 Nov 2010, Alan Francis wrote:
> Hi Bruce, Doug:
>
> I am planning to process scans in a longitudinal study on First break SZ. I
> heard that FS 5.1 will have features that will be better than 5.0. Any idea
> on when 5.1 will be released?
>
> thanks much,
>
Hi Bruce, Doug:
I am planning to process scans in a longitudinal study on First break SZ. I
heard that FS 5.1 will have features that will be better than 5.0. Any idea
on when 5.1 will be released?
thanks much,
Alan
BIDMC
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F
Hi Martin,
Thanks for the detailed explanation!
I think I've got it down now.
Best,
Lisa
__
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
P Please consider the environment before printing this e-
use stable5
Adam Nitenson wrote:
> Hey Doug,
>
> Everything is working out well with this pathwaybut beta2sxa is not
> recognized as a valid command. I've sourced to nmr (Stable 4 if that
> matters at all) and have been on the same terminal on which I've done the
> previous steps. Any ideas?
>
Hey Doug,
Everything is working out well with this pathwaybut beta2sxa is not
recognized as a valid command. I've sourced to nmr (Stable 4 if that
matters at all) and have been on the same terminal on which I've done the
previous steps. Any ideas?
Specifically, I entered:
beta2sxa -b 12ConT.
Basically yes,
but the 3x3 submatrix can be more than just rotation and scaling (there
can be shearing in a 9 degree of freedom linear transform).
So the 12 DOFs are 3 rotation, 3scaling,3 shearing,3 translation. Only
the translation parameters can be read directly from the matrix (as you
corre
Hi Lisa,
this is an affine transformation. Usually there is a 4th row containing
0 0 0 1
A point at position x,y,z is mapped to the target location via
M * (x,y,z,1)^t
where M is the 4x4 matrix and (x,y,z,1)^T is the column vector of the
coordinates of the point with a 1 in the 4th row.
The top
Nothing is transformed during the reconstruction. The transform is
computed but not applied. If you want to transform the results into any
other space, then you need a registration matrix to that space and then
you can run mri_vol2vol or mri_label2vol.
doug
Lisa F. Akiyama wrote:
> Hi FreeSurf
Hi FreeSurfers,
Is it possible to tranform a MRI to an atlas that is not "talairach" (MNI305
atlas) using the talairach_avi command or using
another command in FreeSurfer?
Thank you.
Best,
Lisa
__
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Br
Hello,
Could someone inform me what each value of the 3x4 talairach transformation
matrix signifies (e.g. translation, rotation in specific directions)?
Here's an example of an talairach.xfm output.
MNI Transform File
> % tkregister2
>
> Transform_Type = Linear;
> Linear_Transform =
>1.055506
The -hrf flag is not necessary.
Adam Nitenson wrote:
> Ok, I have previously created these group specific concatenations, but not
> with the -hrf flag. Would I need to reconcatenate them with this flag or
> does your method not require it?
>
> -Adam
>
>
>> Create two contrasts, A-vs-fixation an
Ok, I have previously created these group specific concatenations, but not
with the -hrf flag. Would I need to reconcatenate them with this flag or
does your method not require it?
-Adam
> Create two contrasts, A-vs-fixation and B-vs-fixation, then run
> isxconcat-sess separately for each group.
Create two contrasts, A-vs-fixation and B-vs-fixation, then run
isxconcat-sess separately for each group. This will create ces files for
each contrast. There will be a ces file for each time point in the FIR;
each of these will have a frame for all the members of the group.
1. Compute the mean
In fact, I had to use selxavg-sess and not selxavg3-sess to do the FIR
analysis because fast-selxavg3-sess failed during the FIR analysis (I dont'
have the error on me right now, but I can send it in tomorrow if it's
important).
Katie
On Thu, Nov 4, 2010 at 12:29 PM, Katie Bettencourt wrote:
>
OK. I'll put that on my list.
On 11/04/2010 11:56 AM, f.le...@donders.ru.nl wrote:
> Yup, indeed. There are slight differences in there, but not really clear.
>
> Yup again, a customized color mapping for overlays would fulfill all my
> visualization wishes, that would be great!
>
> kind
>
>
> I'm not sure about the diffs with version 3. Why are you using such an old
> version?
>
>
I'm not sure I understand your question, why am I using the "old version"
selxavg-sess or selxavg3-sess? I'm using Freesurfer 4.5, but I tried using
selxavg-sess because I was confused by the results I
Yes, exactly...and if possible A1, A2, B1, and B2 simultaneously.
-Adam
> Do you mean something like you have two conditions (say A and B) and two
> groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
>
> Adam Nitenson wrote:
>> Hello Freesurfers,
>>
>> I'm been experime
Yup, indeed. There are slight differences in there, but not really clear.
Yup again, a customized color mapping for overlays would fulfill all my
visualization wishes, that would be great!
kind regards,
Frank
- Original Message -
From: "Ruopeng Wang"
To: "Frank Leoné
We always recommend to reprocess. In some cases it works to take older cross
sectional data from an older version for longitudinal processing, but since
4.0.2 is rather old I would definitely recommend to reprocess.
Maybe best is to wait for 5.1 which will be out in a couple of weeks, if you
re
Do you mean something like you have two conditions (say A and B) and two
groups (say 1 and 2), you want to plot A1 and A2 instead of just A and B?
Adam Nitenson wrote:
> Hello Freesurfers,
>
> I'm been experimenting with creating timecourses for tksurfer and
> tkmedit using the -hrf flag. How
You mean even after you adjust the range of the scale, you still can
only see a binary-like overlay colors? That seems to be odd.
As to visualize your circular data, you just need a customized color
mapping, is that right?
On 11/4/10 11:15 AM, f.le...@donders.ru.nl wrote:
> Hi Ruopeng,
>
> Than
Hi Doug,
I'm sorry about using the term "subcortical white matter". It
was due to misunderstanding your response, viz.
"the white matter volume computed from the pial-white
includes subcortical structures".
It's settled now, see response by Michael Harms and
my reponse to that.
Ed
On 4 Nov 2010,
Hello Freesurfers,
I'm been experimenting with creating timecourses for tksurfer and
tkmedit using the -hrf flag. However I've noticed that the h.nii files
created provide the HDR timecourse are only based on the original
analysis under which isxconcat-sess was run (in my case, error vs
correc
Hi Ed,
What do you mean by subcortical white matter? Do you mean cerebellar
white matter? The mris_volume command will give you the entire volume
inside the white surface, which will include all gray matter structures.
This will not include cerebellar white matter.
doug
Ed Gronenschild wrote:
Hi Ruopeng,
Thanks for the answer. Actually, the results I describe are already with
changes to the color scale. It is still quite coarse though in my opinion.
Actually have an added wish now: I want to be able to plot circular data in
freeview (retinotopic mapping), is this possible?
kind
If you load the data as overlay in freeview, you should be able to
adjust the color scale to see the gradient.
On 11/4/10 6:18 AM, f.le...@donders.ru.nl wrote:
> Hi everyone,
>
> I saw there has been posts on this before, and I know more people here at the
> center have this request, so I wanted
Dear FreeSurfers,
I have one question, related to longitudinal data processing. According to
the wiki page about Longitudinal Processing, as the first step, all time
points should be processed with the default workflow.
All of my data, including all time points, were already processed using
FreeS
Hi Michael,
Thanks for your explanation. It was rather confusing
but the picture is now clear:
for the total cerebral white matter I should take the
measure "CorticalWhiteMatter" in the aseg.stats.
Ed
On 4 Nov 2010, at 15:05, Michael Harms wrote:
>
> Hi Ed,
> Is there a distinction in FreeSurf
Hi Ed,
Is there a distinction in FreeSurfer between "cortical" and
"subcortical" white matter? I thought that white matter was simply
white matter...
You wrote that the white matter values in aseg.stats are identical to
the output of mris_wm_volume, which is exactly what I would expect.
You do
Hi, doug
Thanks so much for your answer. Acctually I use the volume-based
registration in order to get the talairach coordinate for each vertex in the
label. As the *.label file provide the vertex number and R,A,S positions.
How could I get the corresponding position in Talairach coordinates for ea
Hi everyone,
I saw there has been posts on this before, and I know more people here at the
center have this request, so I wanted to ask it again, now also for freeview:
is it possible to have custom coloring on the surfaces? It is not that I need
specific colors, it is just that I find the defa
Hi Doug,
This thread about GM and WM volumes was initiated by my question
on how to get the total cerebral GM and WM volumes.
From what I understand now is that for the GM I should take the
volume named "TotalGray" in the aseg.stats file. In the example
below that would be 710389.282729.
Howeve
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