Just to make sure I'm doing this right, I'm going to summarize what I've taken away from your answers and to ask some new questions. In order to present the results, I need two things:
1) A set of histograms (with error bars) for each cluster figure to show the % signal change for each of the four contrasts of interest.
The cache.th20.pos.y.ocn.dat file only gives it for the condition where the cluster was significant so I can't use that.
So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the group level analysis to generate a mask for each cluster of interest.
Then I could extract the value of the voxels from each subject's cespct file for each contrast, average them across the cluster ROI, then average them across each subject, to generate the histogram?
This would suffice to give me the %age signal change?
I would be doing these computations in Matlab using MRIread.
2) A results table with the headings:
Cluster p (FWE corrected)
Cluster size
Peak Voxel p (FWE corrected)
Peak Voxel T
Peak Voxel Coords
BA
Anatomical Landmark
I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files from the group level analysis.
I can get the peak voxel coordinates from the summary files as well.
I can use this to get the peak voxel p from the group level sig.nii.gz file. Is this FWE corrected? If not, how can I get this information?
I can use these coordinates to get the peak voxel T by getting the value from the group level F.nii.gz file and taking its square root. How can I get the sign of the T statistic?
I can use the Lancaster transform to convert the MNI305 peak voxel coordinates into the Atlas coordinates to look up the putative BA and landmarks (unless there is a better way with Freesurfer? I'm seeing some references to some BA labels in the forum but it doesn't look like this is a complete set yet?).
Sorry for all these questions! I got some nice results from FSFAST and would like to get them written up.
Cheers!
Joe
On 5/29/13 10:42 PM, Joseph Dien wrote:
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
I need to extract the beta weights
from a cluster identified with
FS-Fast in order to compute percentage signal change.
1) I see a file called beta.nii.gz that appears to have the
beta
weight information. It has a four dimensional structure and
the
fourth dimension appears to be the beta weights. Is there
an index
somewhere as to which beta weight is which? Or if not, how
are they
organized?
For the first level analysis, the first N beta weights
correspond to the
N conditions in the paradigm file. The rest are nuisance
variables.
You can just use the meanfunc.nii.gz. Also, each contrasts is
computed as the simple contrast (ces) and as a percent of the
baseline at the voxel (cespct, cesvarpct).
2) In order to extract the cluster, it
looks like I would
use mri_label2vol to convert cache.th20.neg.sig.ocn.annot
into a
volume where the voxels are tagged with the number of the
corresponding cluster.
Is that from a group analysis?
Yes, that's right.
I could then use that to generate
masks to extract the information I
need for each cluster from beta.nii.gz.
If this is from a group analysis, then there should already be
a file
there (something.y.ocn.dat) that has a value for each subject
in the
rows and a value for each cluster in the columns.
I see it. Are these values already scaled as percent
signal change? If so, that would be wonderful! :)
Only if you specified it when you ran isxconcat-sess. Note that the
"non-scaled" values are actually scaled to percent of grand mean
intensity.
--------------------------------------------------------------------------------
Joseph Dien,
Senior
Research
Scientist
University of
Maryland
Phone:
301-226-8848
Fax:
301-226-8811
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Joseph Dien,
Senior Research Scientist
University of Maryland
Phone: 301-226-8848
Fax: 301-226-8811