Hi,
We are using freesurfer version 4.4. We did fully run recon-all, but not clear
which file should be used to get label of 4 main lobes; frontal, occipital,
temporal and parietal. Could you please give some instruction on marking the
lobes. Thank you.
Naza
The University of Aberdeen is
Mustafa,
There are a couple of relevant pages with information on this.
These:
http://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13908.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg04901.html
Allison
--
On Wed,
You can break the aparc.annot into individual labels with
mri_annotation2label, then merge the labels of each lobe into a single
lobe label with mri_mergelabels, then combine the lobe labels into an
annotation with mris_label2annot. The 3rd link below is probably the
most useful one for this.
Two suggestions:
1. Can you temporarily change the spm path to spm5 to see if that fixes
the problem?
2. Can you send me your command line, directory you ran it from,
SUBJECTS_DIR, and terminal output?
doug
Chindhuri Selvadurai wrote:
The path to spm2 was not originally in my startup.m file,
This is a standard type of group analysis using a single covariate. You
can set up an FSGD file specifying the groups as classes and using
allele load as a continuous variable. If you're not interested in the
differences between the slopes, then use a DOSS model when you run
mri_glmfit.
Hi FreeSurfers,
I have done my DTI analyses (dt_recon with TBSS) and the statistical analyses
in FreeSurfer.
Now I have defined the clustersize with mri_volcluster, but I find this rather
arbitrary.
Is there a way to calculate a minimum size cluster threshold (by using for
example a Monte
Hi Heidi, I'm not sure what you are asking for. Do you want to find a
p-value for the cluster you have found in your TBSS analysis? If so, you
can use mri_glmfit-sim to perform a simulation (monte carlo or permutation).
doug
Jacobs H (NP) wrote:
Hi FreeSurfers,
I have done my DTI analyses
Hi Doug,
Thank for you answer. Let me clarify a bit more.
I want to know if there is a statistical way to define relevant clusters
(instead of doing a bonferonni correction).
I can imagine that cluster with a few voxels cannot be considered as
statistical significant.
Heidi
You can try to add voxels to the wm.mgz in the area that you know is wm.
If that's already there or you tried that already, let us know.
Allison
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On Wed, 6 Oct 2010, Soon Hock Wei wrote:
Dear All:
Just to follow up with my previous enquiry, is there any suggestion/advice over
this pial
