1. You mean I should run the below command line instead?

vglrun freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.pial:overlay=rh.lgi.TD_NDD_age_sex_SA_FWHM0.glmdir/main_effect_of_age/cache.th13.abs.sig.cluster.mgh:overlay_threshold=1.3,5:overlay=rh.lgi.TD_NDD_age_sex_SA_FWHM0.glmdir/main_effect_of_age/cache.th13.abs.sig.cluster.neg.mgh:overlay_threshold=1.3,5:annot=rh.lgi.TD_NDD_age_sex_SA_FWHM0.glmdir/main_effect_of_age/cache.th13.abs.sig.ocn.annot -viewport 3d

Regardless of whether or not I run the command line you provided (fscalc cache.th13.abs.sig.cluster.mgh mul -1 -o cache.th13.abs.sig.cluster.neg.mgh) and whether I run the above command line which includes "cache.th13.abs.sig.cluster.neg.mgh" or run the command line in my previous post which didnt include this file - the colours of my significant colours look identical in all cases (as shown in attached image labelled 'command line').

2. then is it necessary to run " fscalc cache.th13.abs.sig.cluster.mgh mul -1 -o cache.th13.abs.sig.cluster.neg.mgh" command line for visualizing my results? and also is it neccessary to add " cache.th13.abs.sig.cluster.neg.mgh" into my command line like I have in this post?

However, if I check "show outline only” (under annotation drop down menu) OR if beside annotation I choose “off”, then my clusters turn their appropriate colours (i.e. blue for negative max value, shown in attached image labelled 'command line with annot off').

3. Is this perhaps what I have to do then each time to see my sig clusters in their appropriate colours? Even in this case though, although the colours are consistent with my max value outputs (i.e. blue for negative results), the shades of the colours are different from when I conducted the exact same analysis on QDEC (shown in attached image labelled 'QDEC'). For your reference I've attached images to what I'm referring to.

On Thu, Aug 20, 2020 at 9:44 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

Why did you not load cache.th13.abs.sig.cluster.neg.mgh?

On 8/19/2020 1:17 PM, Avi Gharehgazlou wrote:
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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 <dgreve@mgh.harvard.edu> wrote:
On 6/10/2020 9:54 AM, Avi Gharehgazlou wrote:

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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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