External Email - Use Caution 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> 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 > > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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