You can make the bonferroni correction from of mri_glmfit-sim the same as qdec
by not including --2spaces (the bonferroni correction in qdec is actually 1,
not 0). Also, if you want to use such a low cluster forming threshold
(1.3=p<.05), then you should use permutation and not MC (MC is not valid at
such low thresholds).
On 2/22/19 7:49 AM, Giuliana Klencklen wrote:
External Email - Use Caution
Thanks Douglas, that makes sense. I have run mri_glmfit-sim and have that table
file.
However, the cortical thickness values for each cluster displayed in that table
can’t be used because the clusters (something.sig.cluster.mgh opened with
tksurfer) do not match exactly (but are very similar to) those previously
generated with QDEC. I do not understand the cause of this issue because all
the stats I used, i.e., threshold, statistical correction, level of smooting,
seem to be the same between both qdec and mri_glmfit-sim.
I send you here a typical example of the problematic clusters, as well as the
summary for both qdec and mri_glmfit-sim. They appear similar except for the
Bonferroni correction that is set at 2 for the mri_glmfit-sim while it is set
at 0 for the qdec version? If it is the source of the current issue, how can I
configure the Bonferroni correction? If not, do you have any idea how I can
resolve the problem?
Many thanks in advance.
Regards,
Giuliana Klencklen
[QdecGroupComparison.jpg]
On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,Ph.D.
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> wrote:
This can happen if the label is small and/or you've used a lot of smoothing. It
is better to do this kind of thing in fsaverage space rather than moving the
labels back to the individual space. If you've run mri_glmfit-sim, then it
should have created a table file (something.y.ocn.dat). This file will have a
row for each subject and a column for each cluster. The value will be the mean
for that subject in that cluster.
On 2/15/19 6:23 AM, Giuliana Klencklen wrote:
External Email - Use Caution
Hi FS experts,
I did group-level, surface-based, vertex-wise analysis for baseline and
longitudinal data. I used Qdec and do the same work with the fsgd version
(mri_glmfit-sim command) to double-check the data.
I created label files with tksurfer for each of the clusters showing a
significant between-group difference. Then, I used the following command stream
to extract the cortical thickness values for each subject and cluster:
mri_label2label, mris_anatomical_stats, and aparcstats2table.
E.g.,
mri_label2label --srcsubject fsaverage --srclabel
/home/jagust/gklenck/Long_MRI/lh.ac-baseline-rostralmiddlefrontal.label
--trgsubject ${s}_tp1 --trglabel
${s}_tp1/label/lh.ac-baseline-rostralmiddlefrontal.label --hemi lh --regmethod
surface
mris_anatomical_stats -l lh.ac-baseline-rostralmiddlefrontal.label -t
lh.thickness -b -f ${s}_tp1/stats/lh.ac-baseline-rostralmiddlefrontal.stats
${s}_tp1 lh
aparcstats2table --subjects ${s}_tp1 --hemi lh --parc
ac-baseline-rostralmiddlefrontal --meas thickness --tablefile
${out_dir}/lh.ac-baseline-rostralmiddlefrontal.aparc_stats.txt
Subsequently, when I conducted between-group comparisons for each cluster, a
couple of clusters (7 out of 16) do not show a significant difference - which
does not make sense. This problem seems to appear randomly.
Help to the FS archives, I tried to use mri_segstats command but was not able
to find a correct combination of arguments. If this is the right track to solve
this problem, what combination of arguments should I use? And if this is not,
do you have any idea how I can solve this problem?
Many thanks in advance.
Regards,
Giuliana
--
Giuliana Klencklen, Ph.D.
Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu<mailto:giuliana.klenck...@berkeley.edu>
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--
Giuliana Klencklen, Ph.D.
Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu<mailto:giuliana.klenck...@berkeley.edu>
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