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?
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?
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)
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?
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.
Thank you so much for your support,
Avi
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 ?
- 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
- 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 list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 dgreve@mgh.harvard.edu wrote:
On 6/10/2020 9:54 AM, Avi Gharehgazlou wrote:
External Email - Use CautionHi 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 ?
- 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
- 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:
- When you run mri_glmfit-sim set the -cwp 1
- Set the overlay_threshold=0.0001,5
Thank you so much for your support,
Avi
Freesurfer mailing listFreesurfer@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
Why did you not load cache.th13.abs.sig.cluster.neg.mgh?
On 8/19/2020 1:17 PM, Avi Gharehgazlou wrote:
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 <dgreve@mgh.harvard.edu mailto:dgreve@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?YesWhen 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?Yesvglrun 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.mgh2. 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?YesWhen 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=0.0001,5Thank you so much for your support, Avi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://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
External Email - Use Caution
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:
External Email - Use CautionHi, 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:
External Email - Use CautionHi 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 ?
- 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
- 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:
- When you run mri_glmfit-sim set the -cwp 1
- Set the overlay_threshold=0.0001,5
Thank you so much for your support,
Avi
Freesurfer mailing listFreesurfer@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
Freesurfer mailing listFreesurfer@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
It looks like you are viewing the annotation. Try turning the annotation off and see what is underneath
On 8/20/2020 2:19 PM, Avi Gharehgazlou wrote:
External Email - Use Caution
- 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').
- 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').
- 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 mailto: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: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 <dgreve@mgh.harvard.edu <mailto:dgreve@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?YesWhen 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?Yesvglrun 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.mgh2. 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?YesWhen 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=0.0001,5Thank you so much for your support, Avi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://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
External Email - Use Caution
I mentioned in # 3 in my previous post what happens (and also attached images for you to see). Will you please tell me if its okay that the shades of these colours look different from my QDEC outputs?
On Mon, Aug 24, 2020 at 10:22 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
It looks like you are viewing the annotation. Try turning the annotation off and see what is underneath
On 8/20/2020 2:19 PM, Avi Gharehgazlou wrote:
External Email - Use Caution
- 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').
- 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').
- 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:
External Email - Use CautionHi, 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:
External Email - Use CautionHi 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 ?
- 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
- 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:
- When you run mri_glmfit-sim set the -cwp 1
- Set the overlay_threshold=0.0001,5
Thank you so much for your support,
Avi
Freesurfer mailing listFreesurfer@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
Freesurfer mailing listFreesurfer@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
Freesurfer mailing listFreesurfer@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
Yes, the colors will change. I should probably make it deterministic.
On 8/26/2020 12:37 PM, Avi Gharehgazlou wrote:
External Email - Use Caution
I mentioned in # 3 in my previous post what happens (and also attached images for you to see). Will you please tell me if its okay that the shades of these colours look different from my QDEC outputs?
On Mon, Aug 24, 2020 at 10:22 AM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
It looks like you are viewing the annotation. Try turning the annotation off and see what is underneath On 8/20/2020 2:19 PM, Avi Gharehgazlou wrote:External Email - Use Caution 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 <mailto: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: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 <dgreve@mgh.harvard.edu <mailto:dgreve@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?YesWhen 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?Yesvglrun 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.mgh2. 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?YesWhen 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=0.0001,5Thank you so much for your support, Avi _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://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
freesurfer@nmr.mgh.harvard.edu
-
Avi Gharehgazlou -
Douglas N. Greve