Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates
and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov
/Applications/freesurfer/subjects/fsav
Hi all,
Since upgrading to Freesurfer v5.0, I have been unable to complete the first
step of recon-all ('recon-all -autorecon1 -subjid ...') when using 5
anatomical datasets (our typical load for surface reconstruction). The
problem seems to come when the third dataset is being registered, at whic
Hello,
I am trying to get a summary of beta value activation for a hand-drawn
binary mask. This mask is a sphere, so it does not correspond to a
particular anatomical label or functional contrast. Is there any way
to apply roisummary-sess to this type fo binary mask (in nii or mgz
format)? If not,
Dear FreeSurfer community,
You were very helpful for my last question, thank you.
Now I have three basic questions.
1. I would like to check the segmentation by loading T1.mgz and
aseg.mgz as an -aux volume, so that I can switch between them. How can
I do this? ( gives some king of
black and whi
If my BOLD scan has 30 slices in "interleaved" series, can I assume
the slice order is 1,3,5,7,9...29,2,4,6,8..30? In other words,
1:2:30,2:2:30?
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Dear freesurfer community,
I am currently trying to view one of the surfaces generated by recon-all
command in tksurfer but when I enter the command:
tksurfer LuceHR_FS_SURF lh inflated.nofix
I receive a series of errors that look like this:
Received X error!
Error code : 1
Request co
Dear Doug,
Thanks for your response!
Our stimuli starts with the null condition, but abblocked assumes it's the
ON condition. Is there a way to invert this?
When we look at the sig maps, how do we know what the contrast is? Which
condition does it think is null/task, negative/positive? From what
Hi,
I am trying to develop a custom software to run freesurfer, make edits if
necessary(user intervention) and rerun the freesurfer from appropriate
staring point and also, track/record the user interventions. My prime
concern is the tracking of user intervention part, and I came across
-show-edit
Hi Rita,
I would not automatically assume that regarding slice ordering with
"interleaved" acquisitions, as I don't think that there is necessarily
any "standard" that different manufacturers are committed to following.
It is actually a non-trivial issue -- e.g., how do scanner choices
regarding a
Dear freesurfer experts,
I would like to display freesurfer surfaces in the voxelspace of the
original subject image using matlab.
Which coordinate transformation do I have to apply to get the
vertex-coordinates to the RAS space and finally to the original
voxelspace of the subject? (i guess f
Hi Mahen,
4.5 is based on flirt registration which does a pairwise registration to
the first image. Since 5.0 we use the mri_robust_template tool (as it
can ignore outlier regions and produces more accurate registrations, see
Reuter et al Neuroimage 2010 "..robust registration"), but it is more
me
Dear Tanja,
Concerning your question 3 do the following:
In the System Preferences -> Keyboard & Mouse you should
select the buttons as follows:
left one: primary button,
right one: secondary button
top on: Button 3
You will now have a 3-button mouse that works fine with FreeeSurfer.
Ed
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