For thickness, you can look at the difference (or percent difference).
You would use freeview (or tksurferfv, which is a frontend for
freeview). When you run mris_preproc, you can specify that you want it
to compute the (percent) difference, or you can do it with the
multi-frame output of mris_preproc. For subcortical, it is more
difficult since you don't get a map out of it (just a single value like
total volume of hippocampus).
On 5/11/2020 3:52 PM, KennethSPrice wrote:
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is there a way to visualize the changes in thickness, area, and volume
between the 2 timepoints (cortical and subcortical)? I was under the
impression that running mri_preproc would aloow me to visualize change
in cortical thickness bt the 2 timepoints (lh.paired.thickness.mgh).
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Friday, May 1, 2020 12:14 PM, Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
Oh, right. You only have one data point (the difference) and you are
computing one parameter (the mean), so you have 0 DOF. If you only
have one data point, there are not statistical tests you can do
On 5/1/2020 3:34 AM, KennethSPrice wrote:
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In the FSGD file I have one subject pair (timepoint 1 and timepoint
2), and it is the only group. However, I removed --fsgd and replaced
it with --osgm upon your reccomendation, and am still getting the error.
I am also having an issue visualizing the output of mri_preproc in
freeview - isnt this mgh file supposed to be a volume? Is there a
way to center the freeview cursor to the middle of the current volume?
Thanks,
Ken
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Thursday, April 30, 2020 2:16 PM, Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
how many subjects are there in your fsgd? How many groups in your
fsgd file? Also, you should not use --osgm and --fsgd
On 4/30/2020 1:09 PM, KennethSPrice wrote:
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Hello Freesurfer friends!
I'm going through the "paired analysis" tutorial and am running
into an issue with the mri_glmfit. I am running on just one
subject pair.
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis#Runmriglmfit
I ran mris_preproc on my 2 timepoints and am getting an error at
mri_glmfit
mris_preproc --target fsaverage --hemi lh \
--meas thickness --out lh.paired-diff.thickness.mgh \
--fsgd pairs.fsgd --paired-diff
mri_glmfit \
--glmdir lh.paired-diff \
--y lh.paired-diff.thickness.sm05.mgh \
--fsgd paired-diff.fsgd \
--osgm \
--surf fsaverage lh
I am getting an ERROR: DOF = 0.
MRI's have been put through recon-all and are in there own directories within
SUBJECTS_DIR.
What is the cause of the error?
Thanks,
Ken
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