Dear list members,
as you know, the hippocampal subfields given back by FreeSurfer
(posterior_left_CA1.mgz, posterior_left_CA2-3.mgz, etc.) are posterior
probability maps in the range [0-255] (i.e. [0-1] with 8 bit of
quantization).
Although there is a way to calculate the volume (
kvlQuantifyPost
When doing a FC analysis, there is no need to run mkcontrast.
selxavg3-sess figures out that you are doing a FC analysis and creates
the appropriate contrast. The name of the contrast automatically created
will be the name of the FC passed to fcseed-config, eg, if you used
-fcname L_Posteriorc
The WhiteSurfaceArea is the area of the cortical surface defined as the
boundary between the WM and the GM. Is this what you want?
On 8/27/14 6:56 PM, will brown wrote:
Sorry, my mistake. I did mean surface area rather than volume. I am
unsure as to how to find the total surface area of the cor
volcluster is only used for volume-based (ie, 3D) analysis, eg, an fMRI
analysis of subcortical structures. surfcluster is used for surfaces
doug
On 8/28/14 4:33 AM, Katharina Zech wrote:
Dear all,
I run the surfcluster analysis (mri_surfcluster). But the tutorial
tells me that there exists a
Not that I know of. I've done some of this type of analysis. I've found
few effects on group analysis of erasing and cloning but there are
effects of putting control points. Of course, it is hard to say how
general these results are.
doug
On 8/28/14 6:54 AM, Kasper Jessen wrote:
Hi,
Thank yo
If you know the vertex you want to extract, then you can run something like
mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf out.dat
where y.mgh is the stack created by qdec and out.dat is the data file
you want
doug
On 8/28/14 8:37 AM, Abrishamchi, Aurash David wrote:
Hello,
I still c
It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in
/usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001
does that file exist? Have you run preproc-sess?
doug
On 8/28/14 9:49 AM, Francesca Strappini wrote:
> Dear all,
>
> I've run selxavg3-sess and I got this error me
Sorry, 7th order, not 12th
doug
On 8/29/14 11:51 AM, Douglas Greve wrote:
>
> It is based on the 12th order icosahedral surface from which the
> surface atlas is constructed (fsaverage).
> doug
>
>
>
> On 8/29/14 4:06 PM, shinj...@andrew.cmu.edu wrote:
>> Hello,
>>
>> I was still wondering about
Thank you, now it works!
Best
Francesca
2014-09-08 15:24 GMT+03:00 Douglas Greve :
> It is not looking for fmc.sm5.DM.lh.nii.gz but rather fmcsm5.nii.gz in
>
> /usr/local/freesurfer/fsfast/MeytalRetinotopy/SUBJ01/bold/001
>
> does that file exist? Have you run preproc-sess?
> doug
>
> On 8/28/14
Hi David
what is the annot you are using in mris_label2annot? is it the
?h.BA.annot?
cheers
Bruce
On Mon, 8 Sep 2014, David Provencher wrote:
> Hi,
>
> I am new to freesurfer and I am trying to figure our how to extract 3d
> masks in native space for the visual cortex (BA 17,18,19) of individua
Use mri_glmfit with the --pvr option. You would use one of the modes as
the input (--y) and one of the modes as the per-voxel regressor (--pvr).
When you make a contrast, you need to include elements for each PVR (the
PVR forms a vertex-specific regressor in the design matrix)
doug
On 8/31/
Run mri_glmfit-sim with --cwp 1
This sets the clusterwise threshold to 1, meaning to keep all clusters
regardless of their p-values
doug
On 9/1/14 9:40 AM, Robby De Pauw wrote:
Dear FS-community
Thx to Doug I was able to successfully run a first analysis. However,
I'd like to have a table
Dears experts,
I would be very grateful if help me with the following doubts:
1- My data was collected with a 0.23T scan. How i can process it?,Should i
make any kind of pre-process before to begin with recon-all?
2- I want only to get the statistics of the caudate nucleus. Is there any
way to obt
Hi Merlin
hmmm, I 've never seen data from such a low field scanner. Have you tried
running it through recon-all? I would worry that it is quite noisy. Try it
and see how it goes.
And no, there is no way to only get caudate - you need to run at least
through the end of autorecon2 to get the co
Dear all,
I just found that the equivalence Volume/integral isn't quite correct. The
equivalence must be between the volume and something like an expected value
of the histogram V = E[H] = ∫xH(x)*dx* (where x is the greyscale value).
So, the point 2) described in my previous email becomes (with s
Dear Luigi,
the MAP solution (which maximizes the posterior probability of the segmentation
given the image and the atlas) is to assign to each voxel the label with the
highest posterior probability. The expected value of the volume of a structure
is indeed the integral of the its posterior acro
Hi Lucy
Jon Polimeni (ccd) probably has the most experience processing 7T data.
Jon: can you comment?
thanks
Bruce
On Sun, 7 Sep 2014, Lucy Hiscox wrote:
> Dear Freesurfer experts,
>
> I am currently trying to segment a 7T image at 0.8 isotropic
> resolution. I have an MPRAGE scan and a Gradie
p.s. probably you should use the ?h.BA.thresh.annot, which is the annot
containing the labels thresholded to have the correct area
cheers
Bruce
On Mon, 8 Sep 2014, Bruce Fischl wrote:
> Hi David
>
> what is the annot you are using in mris_label2annot? is it the
> ?h.BA.annot?
>
> cheers
> Bruc
You need to load it as an overlay onto a surface. If you mapped your FC
onto the native subject space, then use the subject's surface. If you
used fsaverage, then use the fsaverage surface.
doug
On 09/03/2014 11:58 AM, Martin Scherr wrote:
> Dear Freesurfer experts,
>
> We are trying to perform
That was an oversight. I've attached a version that should work. Can you
test it for me? Once I know it works I'll check it in to tree.
doug
On 09/03/2014 12:30 PM, Eryilmaz, Huseyin Hamdi wrote:
Dear FS experts,
I have a question about a MC output file. When I run the MC sim
(using mri_
Is that all it says? There is no error msg? That is all it prints to the
terminal? It should not matter, but try it without the quotes.
On 09/03/2014 01:23 PM, Nooshin Zadeh wrote:
> Dear FreeSurfer experts,
>
>
> I get a new message when I use "mri_convert" command to convert dicom
> to mgz. I
Hi Bruce,
First of all, thanks for the reply! There was a typo in my initial
question, so I rewrote it to make it clearer :
# convert labels to annotation (outputs lh.myAnnot.annot & rh.myAnnot.annot)
mris_label2annot --s --h lh --l lh.V1.label --l lh.V2.label --l
lh.label --ctab BA.ctab --
Hi David - On the difference between .thresh and "not .thresh" labels: The
BA labels come from averaging histologically derived labels from a set of
post mortem brains. The non-thresholded version is just the sum of the
corresponding labels from the different brains in fsaverage space. So
vert
Hi Laura - Apologies, I just found your email and realized I hadn't
answered earlier. Which tract are you concerned about being contaminated
by CSF?
a.y
On Wed, 27 Aug 2014, Laura Christine Anderson wrote:
Dear Tracula users, does anyone know whether or not Tracula uses any
corrections fo
Hi Peggy - It's hard to diagnose the problem by seeing only the tracts and
not the rest of the data, but this does look very strange. 1.5T is not a
problem, but anisotropic resolution is not optimal for tractography, as it
can bias the amount of diffusion measured in the direction that the voxe
Thanks for the reply Anastasia, that makes it more clear.
I realized that I was confused due to my inexperience with freesurfer
and was using the wrong approach. I did not realize I could simply use
the segmented volumes in aseg.mgz corresponding to the visual cortex
using http://ftp.nmr.mgh.ha
Hi Peggy - I looked at the data. Unfortunately, the voxel size is
0.9x0.9x4 in the first time point and 0.9x0.9x5.2 in the second. So not
only is the resolution extremely anisotropic, which is problematic for
tractography, but it's also different between scans, which almost
guarantees that you
Hello Freesurfer Community!
Thank you Anastasia and Christopher, I am still getting ending with errors
and the log file gives no clue that I have been able to detect, see
attached.
Any help would be appreciated!
On Thu, Sep 4, 2014 at 4:29 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> w
Do you know where can I get the BA28a and BA28b ROIs?
【小孔成像】http://www.conxz.net
From: Douglas N Greve
Date: 2014-08-08 00:22
To: freesurfer
Subject: Re: [Freesurfer] Brodmann Area stats to table
There should already be ?h.BA.stats and ?h.BA.thresh.stats. Do those work?
On 08/07/2014 09:45 A
Thanks very much Andreia, yes this does look like what I want. I haven't
had a chance to test it yet but it does indeed appear to answer my
question. Thanks to those that have offered answers, to clarify, I did
indeed mean the surface area of the pial surface rather than the white/grey
boundary.
W
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