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Hi, following my concern that all my significant clusters
(that have survived monte carlo p<0.05 correction in this
case) don't appear as their appropriate colours (i.e. in
yellow or blue to show positive or negative max values,
respectively), my question on how to make clusters look
their appropriate colours, you replied: fscalc
cache.th13.abs.sig.cluster.mgh mul -1 -o
cache.th13.abs.sig.cluster.neg.mgh
I tried the below steps but my significant clusters are
still not coloured appropriately when I try visualizing them
using command lines mentioned in this thread. Will you
please tell me what I am doing wrong below:
in my directory
(data9/users/avideh/data/recon/glm_PhD/lh.lgi.TD_NDD_age_sex_SA_FWHM0.glmdir/main_effect_of_age)
I ran the command line you gave:
fscalc cache.th13.abs.sig.cluster.mgh mul -1 -o
cache.th13.abs.sig.cluster.neg.mgh
and after it finished running successfully I did the following:
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/data9/users/avideh/data/recon
export WORKING_DIR=/data9/users/avideh/data/recon/glm_PhD
cd $WORKING_DIR
then:
vglrun freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.pial:overlay=lh.lgi.TD_NDD_age_sex_SA_FWHM0.glmdir/main_effect_of_age/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_NDD_age_sex_SA_FWHM0.glmdir/main_effect_of_age/cache.th13.abs.sig.ocn.annot
-viewport 3d
But the significant clusters are still not their appropriate
colours. I'd really appreciate your help on how I can
visualize my significant clusters in their appropriate colours.
Thank you so much
On Fri, Jun 12, 2020 at 10:39 AM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
On 6/10/2020 9:54 AM, Avi Gharehgazlou wrote:
External Email - Use Caution
Hi experts,
I am a bit confused with visualizing my significant
clusters after having corrected my results for multiple
comparisons. after running mri_glmfit, I corrected with
monte carlo and permutation as explained below, will
you please confirm my understanding below is correct ?
1. I ran monte carlo simulation (1.3 sig level). My
understanding is that
"cache.th13.abs.sig.cluster.summary" shows the clusters
that are significant after correction for multiple
comparisons. I have 1 cluster listed in this file.
Thus, I am interpreting this as having 1 significant
cluster after correction at p<0.05, is this correct?
Yes
When I want to visualize my corrected results I use the
command line below. I am assuming this command line
displays only the significant clusters that survived
multiple comparison correction because only the cluster
that is listed in my
"cache.th13.abs.sig.cluster.summary" file appears on
the brain here, and because I have put "
cache.th13.abs.sig.cluster.mgh" and as overlay "
cache.th13.abs.sig.ocn.annot" and set the threshold to
1.3 in my command line. Is it correct that the cluster
that appears when running the below command line is my
significant cluster surviving multiple comparisons
correction at p<0.05?
Yes
vglrun freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/cache.th13.abs.sig.ocn.annot
-viewport 3d
also, how can I get the clusters to look their
appropriate colours when I am vieweing them with the
command line above? all my clusters appear gray
(regardless of whether they have positive or negative
max values, in which case they should be yellow and
blue, respectively)
fscalc cache.th13.abs.sig.cluster.mgh mul -1 -o
cache.th13.abs.sig.cluster.neg.mgh
2. I then ran permutation testing. My
"perm.th13.abs.sig.cluster.summary" file is blank. I
interpret this as no clusters having survived multiple
comparison correction with permutation testing. Am I
correct?
Yes
When I use the below command line to visualize my
result I see a blank brain (with no clusters coloured).
Which makes sense to me because my
"perm.th13.abs.sig.cluster.summary" also showed no
significant clusters. is this interpretation and the
command line I am using below correct?
vglrun freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.lgi.TD_PTSD_age_SA_IQ_FWHM0.glmdir/group.diff/perm.th13.abs.sig.ocn.annot
-viewport 3d -layout 1
I think my understanding is correct, but I am confused
because the FreeSurfer instructions state that the
above command lines will display "all clusters,
regardless of significance"... but using the above
command lines seems to only display my significant
clusters. I am assuming this is because I set my
threshold to 1.3 (the same threshold I used to correct
for multiple comparisons in 1 and 2 above). But wanted
to make sure I am correct before proceeding.
If you want all clusters regardless of sig, you have to
do two things:
1. When you run mri_glmfit-sim set the -cwp 1
2. Set the overlay_threshold=0.0001,5
Thank you so much for your support,
Avi
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