Hello,
I'm facing the same problem for one of my subjects. Is there a general solution
for this problem or would you solve this problem on a case by case basis? I saw
posts from others with the same problem.
Thanks for your help,
Nasim
On Nov 29, 2010, at 7:55 AM, Bruce Fischl wrote:
> Hi Jenn
Hi Nasim,
can you tar and gzip the entire subject dir and send it to us? I'll try
to track it down. In the mean time if you just rerun with the old topo
fixer it should work. Nick can post the appropriate flags
cheers
Bruce
On Tue, 15 Feb
2011, Nasim Maleki wrote:
> Hello,
>
> I'm facing the
Hi,
I was trying to use the FreeSurfer tutorials for the first time, and had a
problem whenever I tried to use the command tksurfer.
After I defined FREESURFER_HOME, TUTORIAL_DATA and SUBJECTS_DIR I tried to
visualise a surface. The result was that a window opened where the surface
should ha
Dear Doug
Thanks for your response. What I meant is, for example, some voxels
would be "occupied" by edges of the mesh even if they are not occupied
by any vertices. As you move to higher and higher resolutions,
presumably more and more voxels would fall into this category. That
being said, I under
Yes, that all looks correct. The only other thing you may want to do is
to demean (ie, remove the mean from) your continuous variables. When you
test for a difference in thickness (as opposed to slope), you are
implicitly testing at your variables=0. Eg, if age is one of your
variables, then yo
Hi all,
there is an open position to fMRI-EEG,
http://www.eracareers.pt/ opportunities/index.aspx?task= global&jobId=22187
Best,
Jose
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Hi Freesurfers,
I'm trying to analyze functional data in Stable 5, but have noticed
that the func2roi command is no longer used. My analysis involves 9
conditions (not including Fixation) and 1 timepoint for each. The
steps I used in Stable 4 to generate this data are as follows:
func2roi-ses
Dear FS experts,
I run recon all on several patients, manual edited all the outputs and
rerun recon all. I'm interested in subcortical segmentation and I
extracted all the data with the aseg stats command. Is it now possible
to select a structure (let's say the accumbens) and save it as a .ni
Hello All!
I am currently trying to create a high resolution anatomy by manually
changing some parameters throughout the recon-all process. I have currently
hit a road block at the fill portion of the recon-all process. So far I have
tried this high resolution reconstruction on two subject's anato
Hi Fabrizio,
You can use mri_extract_label for this. You need to specify the index
number of the structure which you can find here:
$FREESURFER_HOME/FreeSurferColorLUT.txt
On Tue, 15 Feb 2011, fabrizio piras wrote:
> Dear FS experts,
> I run recon all on several patients, manual edited all the o
sure. mri_binarize or mri_extract_label will do this for you (see the
FreeSurferColorLUT.txt file for the correct indices to use)
cheers
Bruce
On Tue, 15 Feb
2011, fabrizio piras wrote:
> Dear FS experts,
> I run recon all on several patients, manual edited all the outputs and
> rerun recon all
Hi Bruce,
We have two studies being conducted (one cross-sectional and one
longitudinal)
Some of the subjects in have a lot of atrophy and have large ventircles.
For the cross-sectional analysis stream are there many differences between
4.5 and the forthcoming 5.1 ? Or would it be fine to use 4.5
Hi Mehul,
I think 5.1 will work better for large ventricles than 4.5, but I'll be
interested to hear your experience.
cheers
Bruce
On Tue, 15 Feb 2011, Mehul Sampat wrote:
> Hi Bruce,
> We have two studies being conducted (one cross-sectional and one
> longitudinal)
> Some of the subjects in ha
Hi Evan
can you send some coronal images showing where it is slanted? I also
don't understand why you can't use the aseg. What resolution are you
acquiring the data at?
cheers
Bruce
On Tue, 15 Feb 2011, Evan Luther wrote:
> Hello All!
>
> I am currently trying to create a high resolution anatom
Hi All,
I've been doing whole-brain functional analyses using glmfit and
mri_volcluster. As I understand it, correction for multiple comparisons is
done on a cluster level with this command, by specifying a minimum cluster
size and then applying a threshold within each cluster. This is working o
Nothing that is easy to do. You can compute your own voxel-wise
Bonferroni threshold based on the search space and then use mri_binarize
to do the thresholding. I don't have a command-line that computes FDR,
but you can get the threshold for a given FDR in matlab with
fast_fdrthresh, then app
Yes, I see what you mean now. Currently, there is nothing that vol2surf
does to account for this. One thing that can be done is to super-sample
the mesh so make the distance between vertices smaller (this is what Jon
Pollemeni does -- and he's certainly working at fMRI resolutions where
this ki
You need to specify a threshold (-thresh) with a contrast. This is the
equivalent to the -min in funcroi-sess. There was a bug in
funcroi-config that prevented it from catching that you did not specify
a threshold (which has been fixed now).
thanks
doug
Adam Nitenson wrote:
> Hi Freesurfers,
>
Hi all,
We are attempting to do an analysis for subjects that came in on two
different days to perform two similar but different tasks (one
learning condition, one control). Each of the tasks is structured
such that there are 30sec rest epochs alternating with 30sec active
(typing) epochs for a t
In principle you can do it either way and get the same result. From a
practical standpoint, it is probably easier to do the day2-day1
subtraction, then do the group analysis.
doug
Mandy Nagy wrote:
> Hi all,
>
> We are attempting to do an analysis for subjects that came in on two
> different da
what does the aseg look like n that case? And what resolution is your
data?
On Tue, 15 Feb 2011, Evan Luther wrote:
> Hey Bruce,
>
> I also do not understand why I could not use the aseg but if I do not set
> the noaseg flag I get a result like the picture I have attached where no cut
> is made.
can you load them with the -segmentation flag in tkmedit so I can see them
as a color overlay? And is there a reason you need 0.7mm data? That's why
it is *so* noisy
On Tue, 15 Feb 2011, Evan Luther wrote:
> Hey Bruce,
>
> Here are the aseg and aseg.auto_noCCseg files. Our data is at a .7 mm
> r
but who decided 0.7mm iso was the right setting for the scanner? Can you
change that? what kind of scanner and coil is it?
On Tue, 15 Feb 2011, Evan Luther wrote:
> Sorry about that! Hear they are. The reason why we want .7 mm resolution is
> because that is the resolution of the volume anatomi
I guess Dr. Ress decided on that resolution in order to obtain the high
resolution anatomies. It is a GE scanner and we are using an 8 channel head
coil.
On Tue, Feb 15, 2011 at 5:05 PM, Bruce Fischl wrote:
> but who decided 0.7mm iso was the right setting for the scanner? Can you
> change that?
I see. Unless there's a compelling reason to be doing high res I would
avoid it. Things will work *much* better for you if you acquire 1mm
isotropic. Or even acquire that in addition to the 0.7mm since it should be
quite fast relative to the high res
On Tue, 15 Feb 2011, Evan Luther wrote:
> I
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