Hi there,
I am using freesurfer for datas of two year olds.
- Is there a special command to run freesurfer on children's data?
- When I checked the seg.stats for volumes, I got a higher value for
BrainSegVolNotVentSurf (value: 845377 mm3), than for the BrainSegVol (value:
839497) in one patient.
Hi Panos
the first two are basic differential geometric measures (H and K are the
typical symbols for them). The second two come from a David Van Essen paper
I think in the late 90s. Sorry, I don't remember the exact reference
cheers
Bruce
On Mon, 5 May 2014, pfot...@nmr.mgh.harvard.edu wrote:
Hi Kristina
do the results look accurate. 2 is pretty close to (or past) the limit of
where we generate reliable results.
Not sure about your other question - I don't remember how they are
calculated. Someone else should know, although note that we are putting on
a class this week so response
Hi Bruce,
That's actually great, thanks for your help!
Best,
Panos
Hi Panos
the first two are basic differential geometric measures (H and K are the
typical symbols for them). The second two come from a David Van Essen
paper
I think in the late 90s. Sorry, I don't remember the exact
Dear group,
when using the qdec gui interface, I was wondering where the button or
the likes is to change the estimation from its standard doss to dods
(different osnet, different slope). I believe I can do this somewhere on
the qdec gui without changing to mri_glmfit?
Dear FS experts,
I have a question about the way contrasts work in an event-related design. I am
wondering if freesurfer is doing some sort of weighing when it compares two
different conditions with incomparable number of trials. For example condition
A is represented by 10 trials in the
For the contrast AB, the number of trials is not considered. When you
contrast A and B, you are assessing the mean response to trials of
condition A to the mean response to trials of condition B. You wouldn't
want to weight this by the number of trials as then the contrast would not
make sense.
Any other thoughts as to what might be going wrong with our coordinate
transformations / any other transformations that we might not be taking
into account?
Thanks,
Isaac
On Tue, Apr 29, 2014 at 4:52 PM, ISAAC PEDISICH i...@sas.upenn.edu wrote:
The purpose of what I'm trying to do is getting
Hi everybody,
I have a question about optseq2.
In order to calculate ntp, I need to know the total time that my run lasts.
Thus, I do not know whether I have to include in the total trial time the
fixation cross time (500 ms) + event (1000 ms) + variable ISI average (1 s,
ranging from 500 to
Lukas,
The Mac build does not support openmp. This is because the initial
version of gcc we were using for the Mac build did not support it. We
are now using a version of gcc for the Mac build which does support
oppenmp so the current plan is that any subsequent releases of
freesurfer will
Hi Cesar
what command lines did you run to register and sample?
Bruce
On Mon, 5 May 2014,
Cesar Echavarria wrote:
Hello freesurfer experts,
The functional overlay for one of our subjects looks like the image attached.
You'll notice
the holes on the overlay that have a value of 0. I'm
Hi Bruce,
After unpacking the data, I simply run the selxavg command below and allow
it to do the automatic pre-processing.
selxavg3-sess -s Subjects/myla -a LOC_fsaverage_5p3.rh
The analysis was generated with the following command:
mkanalysis-sess -analysis LOC_fsaverage_5p3.rh -surface
On 04/30/2014 11:38 PM, charujing123 wrote:
Hi FS experts and users
I have done the each subjects' surface regestration on fsaverage
surface, and merge all of them into a *.mgh. Group analysis is also
completed.
Now I have two questions:
1,I want to extract the VtxMax vertex number
The total time is the time from when you start the scanner until the
scanner turns off. The duration of the stimulus should be the just that
of the stimulus. If you want to have a minimum amount of fixation
between events, then use --tnullmin.
doug
On 05/05/2014 12:53 PM, Conchy PF wrote:
I've looked at the actual editing of voxels (ie, erasing and deleting)
vs putting control points in terms of their effect on a group analysis
of aging. CPs have an appreciable effect. I could not find much of an
effect of editing, probably because the edits rarely lined up across
subject. I
DOSS is not working in QDEC. It should be disabled in 5.3
doug
On 05/05/2014 09:39 AM, Anna Jonsson wrote:
Dear group,
when using the qdec gui interface, I was wondering where the button
or the likes is to change the estimation from its standard doss to
dods (different osnet, different
It could be that the brain mask is too aggressive. Try looking at
Subjects/myla/bold/RRR/masks/brain.nii.gz
doug
On 05/05/2014 03:17 PM, Cesar Echavarria wrote:
Hi Bruce,
After unpacking the data, I simply run the selxavg command below and
allow it to do the automatic pre-processing.
They are not computed in exactly the same way, but the results are still
a little surprising. What is the value of BrainSegVolNotVent? That
should always be less than BrainSegVol.
On 05/05/2014 08:22 AM, Bruce Fischl wrote:
Hi Kristina
do the results look accurate. 2 is pretty close to (or
Hi Zeke!Thanks a lot for the response. Better a late response than none :o)!
Do you have any vague estimate when a new release will be available?
So far I did not try to compile it from the sources, because it is not my
daily business and for an inexperienced it most likely ends up with pure
Thanks Donald for the clarification. In our design, for the condition A (errors
in a memory task), number of trials depends on subjects' performances and
therefore we've got some between subject variability there. If the number of
trials is not considered and as long as it is sufficient to
I used the command below to check the brain mask relative to the subject's
anatomy:
tkmedit myla_anat orig.mgz -over Subjects/myla/bold/masks/brain.nii.gz
The mask looked fine in that no portion of the brain appeared to lie
outside the mask.
Cesar
On Mon, May 5, 2014 at 3:43 PM, Douglas N
I do not have any information to give in regards to when a new release
would be available. Compiling freesurfer from source is not exactly
something I would call fun. That said, I have been working on a brief
how-to-guide on how to build freesurfer on Mac OSX and I have already
packaged the
Have you checked the registration? If so, are you sure that the
activation is exactly 0? Also, look at cortex.label to check whether
somehow those vertices were not labeled.
On 05/05/2014 04:08 PM, Cesar Echavarria wrote:
I used the command below to check the brain mask relative to the
And fun, right?
On May 5, 2014, at 5:48 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
I do not have any information to give in regards to when a new release
would be available. Compiling freesurfer from source is not exactly
something I would call fun. That said, I have been working on a
Dear FreeSurfer community,
We are having some issues registering our functional data (or masks) from FSL
to an inflated brain in FreeSurfer. Some of our masks, when registered to the
inflated brain and viewed in FreeSurfer, are not showing up on the cortical
surface. We have followed
Hi all,
Earlier today, I posted the message listed below. However, we discovered part
of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat
file created. Therefore, we have no registration matrix to use. Before, we
were inadvertently using the anat2std file instead.
Hi Douglas and all,
I have used the ‘recon-all’ command to segment the gray matter of 140 subjects.
I have three questions:
(1) as the segmentation is done in the individual space, how can I register the
results into the template brain? The results includes the surface and the
vertex. Is it
Can you tell us specifically what you have done? I mean command lines ...
doug
On 5/5/14 6:57 PM, Sherryse Corrow wrote:
Dear FreeSurfer community,
We are having some issues registering our functional data (or masks)
from FSL to an inflated brain in FreeSurfer. Some of our masks, when
Dear Freesurfer:
I have some problems with using mri_surf2vol .I'd like to ask if you
could help me with this.--volreg Contains the matrix that maps XYZ in the
reference anatomical to XYZ in the functional volume. And to get this reg I
use bbregister. But the result of bbregister is functional
Dear Freesurfer:
I have some problems with using mri_surf2vol .I'd like to ask if you
could help me with this.--volreg Contains the matrix that maps XYZ in the
reference anatomical to XYZ in the functional volume. And to get this reg I
use bbregister. But the result of bbregister is functional
Run reg-feat2anat. If that does not work, then send the command line and
terminal output. Just saying that something does not work will not get
you closer to a solution. We need to know what you did and what happened
doug
On 5/5/14 7:55 PM, Sherryse Corrow wrote:
Hi all,
Earlier today, I
On 5/5/14 10:41 PM, Caka wrote:
Hi Douglas and all,
I have used the ‘recon-all’ command to segment the gray matter of 140
subjects. I have three questions:
(1) as the segmentation is done in the individual space, how can I register
the results into the template brain? The results
Dear all,
Two positions are available @ Queensland Brain Institute.
*POSITION 1:*
Postdoctoral Fellow Position in Neuroimaging and Brain Network Analysis at
Queensland Brain Institute
The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute
(QBI) and Centre for Advanced
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