Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? If it is thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations?
If it does not refer to thickness, is it a statistic, etc?
# Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal
I am trying to finish writing up my results and just need answer to this question to continue.
Thanks,
Judith S. Mind Research Network
Hi Judith,
Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster.
Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region.
yes at lateral orbital frontal. The max vertex in that
cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations?
yes you are correct.
If it does not refer to thickness, is it a statistic, etc?
# Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal
I am trying to finish writing up my results and just need answer to this question to continue.
Thanks,
Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value).
doug
Pratap Kunwar wrote:
Hi Judith,
Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster.
Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region.
yes at lateral orbital frontal. The max vertex in that
cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations?
yes you are correct.
If it does not refer to thickness, is it a statistic, etc?
# Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal
I am trying to finish writing up my results and just need answer to this question to continue.
Thanks,
Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list 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
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'.
Doug:
I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual
In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh.
So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness?
Thanks,
Judith S.
On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value).
doug
Pratap Kunwar wrote:
Hi Judith,
Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster.
Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region.
yes at lateral orbital frontal. The max vertex in that
cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations?
yes you are correct.
If it does not refer to thickness, is it a statistic, etc?
# Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal
I am trying to finish writing up my results and just need answer to this question to continue.
Thanks,
Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The max is the -log10(p), bounded below by -log10(CWP) for positive correlations Hence with an -log10(CWP) of 4, the Max will be greater than 4, and will specify the maximum -log10(p) value in that cluster, occuring at VtxMax Is this right for -log10(p) kind if input? This is how i have been interpreting my results so far, and i just want to be sure...... I was also wondering why -log10(p) transformation has been used for this kind of visualization? SPM displays SPM_{z} scores, and that seems a better way to report the spms. Is -log10(p) an approximation to z-scores ? sid.
On Thu, Jun 4, 2009 at 9:53 AM, Judith Segall jsegall@mrn.org wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'.
Doug:
I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual
In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh.
So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness?
Thanks,
Judith S.
On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value).
doug
Pratap Kunwar wrote:
Hi Judith,
Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster.
Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region.
yes at lateral orbital frontal. The max vertex in that
cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations?
yes you are correct.
If it does not refer to thickness, is it a statistic, etc?
# Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal
I am trying to finish writing up my results and just need answer to this question to continue.
Thanks,
Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list 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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The Max is somewhat unrelated to the CWP. The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold. The CWP (cluster-wise p-value) which is derived from the size of the cluster, the smoothness, and the size of the search space. It is not necessary for the CWP to be greater than the Max (and often is not).
I've always found p's or (-log10(p)) to be more useful because it is the actual false-positive rate, which is the number you want for thresholding (and I have not memorized a z->p transform:). I have a matlab routine that will convert from p to z (fast_p2z.m).
doug
Siddharth Srivastava wrote:
The max is the -log10(p), bounded below by -log10(CWP) for positive correlations Hence with an -log10(CWP) of 4, the Max will be greater than 4, and will specify the maximum -log10(p) value in that cluster, occuring at VtxMax Is this right for -log10(p) kind if input? This is how i have been interpreting my results so far, and i just want to be sure...... I was also wondering why -log10(p) transformation has been used for this kind of visualization? SPM displays SPM_{z} scores, and that seems a better way to report the spms. Is -log10(p) an approximation to z-scores ? sid.
On Thu, Jun 4, 2009 at 9:53 AM, Judith Segall <jsegall@mrn.org mailto:jsegall@mrn.org> wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'. Doug: I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh. So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness? Thanks, Judith S. On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value). doug Pratap Kunwar wrote: Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. yes at lateral orbital frontal. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? yes you are correct. If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network _______________________________________________ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> _______________________________________________ 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
It is the maximum vertex-wise -log10(p) found in the cluster. Why do you think otherwise? You should be able to load the sig map into tksurfer and go to that vertex to find out.
doug
Judith Segall wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'.
Doug:
I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual
In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh.
So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness?
Thanks,
Judith S.
On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value). doug Pratap Kunwar wrote: Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. yes at lateral orbital frontal. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? yes you are correct. If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network _______________________________________________ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
Doug and freesufer list.
When I load the sig map in tksurfer i know that the CWP is displayed as the -log(10)p; however, I am not asking about visualization or the CWP. The newest version of the wiki does a great job in explaining the p values. I am only asking about the sig.cluster.summary report. It makes since that "The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold." But then what units is it in?
When I was not sure what the second column was I turned to visualization. After, loading both the sig.cluster.mgh and the group descriptor file in tksurfer and then selecting a vertex in the region with the most significance, which is based off of the CWP, it displays a scatter plot. The scatter plot does not have a label for the y-axis; however, the highest point on the y-axis is similar to the max, in column 2, of the sig.cluster.summary report. On the older wiki, there was a paragraph describing how the y was thickness. But, the sig.cluster.summary report does not have any labels for the second column. But, since the value was similar to the y-axis I began to interpret it as thickness, but wanted to clarify with the freesurfer team.
- Judith
On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It is the maximum vertex-wise -log10(p) found in the cluster. Why do you think otherwise? You should be able to load the sig map into tksurfer and go to that vertex to find out.
doug
Judith Segall wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'.
Doug:
I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual
In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh.
So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness?
Thanks,
Judith S.
On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value).
doug
Pratap Kunwar wrote:
Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. yes at lateral orbital frontal. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? yes you are correct. If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network _______________________________________________ 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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you load the FSGD and look at the scatter plot, the y-axis will be the thickness value (assuming you're doing a thickness study:).
doug
Judith Segall wrote:
Doug and freesufer list.
When I load the sig map in tksurfer i know that the CWP is displayed as the -log(10)p; however, I am not asking about visualization or the CWP. The newest version of the wiki does a great job in explaining the p values. I am only asking about the sig.cluster.summary report. It makes since that "The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold." But then what units is it in?
When I was not sure what the second column was I turned to visualization. After, loading both the sig.cluster.mgh and the group descriptor file in tksurfer and then selecting a vertex in the region with the most significance, which is based off of the CWP, it displays a scatter plot. The scatter plot does not have a label for the y-axis; however, the highest point on the y-axis is similar to the max, in column 2, of the sig.cluster.summary report. On the older wiki, there was a paragraph describing how the y was thickness. But, the sig.cluster.summary report does not have any labels for the second column. But, since the value was similar to the y-axis I began to interpret it as thickness, but wanted to clarify with the freesurfer team.
- Judith
On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is the maximum vertex-wise -log10(p) found in the cluster. Why do you think otherwise? You should be able to load the sig map into tksurfer and go to that vertex to find out. doug Judith Segall wrote: Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'. Doug: I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh. So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness? Thanks, Judith S. On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value). doug Pratap Kunwar wrote: Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carlo results, I a simple question about the sig.cluster.summary output. Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. yes at lateral orbital frontal. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? yes you are correct. If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
Doug.
Again, I am only asking about the sig.cluster.summary. This was a thickness study, where monte-carlo simulations where used to correct for multiple comparisons. Why would the *max in column 2 of the sig.cluster.summary* be derived from the sig.mgh and not the sig.cluster.mgh? Since, this report is generated at the same time as the sig.cluster.mgh. (ClusterNo *Max* VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot)
I only used the scatter plot as example as to why I has a question about how to interpret the sig.cluster.summary.
- Judith
On Thu, Jun 4, 2009 at 11:51 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you load the FSGD and look at the scatter plot, the y-axis will be the thickness value (assuming you're doing a thickness study:).
doug
Judith Segall wrote:
Doug and freesufer list.
When I load the sig map in tksurfer i know that the CWP is displayed as the -log(10)p; however, I am not asking about visualization or the CWP. The newest version of the wiki does a great job in explaining the p values. I am only asking about the sig.cluster.summary report. It makes since that "The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold." But then what units is it in?
When I was not sure what the second column was I turned to visualization. After, loading both the sig.cluster.mgh and the group descriptor file in tksurfer and then selecting a vertex in the region with the most significance, which is based off of the CWP, it displays a scatter plot. The scatter plot does not have a label for the y-axis; however, the highest point on the y-axis is similar to the max, in column 2, of the sig.cluster.summary report. On the older wiki, there was a paragraph describing how the y was thickness. But, the sig.cluster.summary report does not have any labels for the second column. But, since the value was similar to the y-axis I began to interpret it as thickness, but wanted to clarify with the freesurfer team.
- Judith
On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is the maximum vertex-wise -log10(p) found in the cluster. Why do you think otherwise? You should be able to load the sig map into tksurfer and go to that vertex to find out.
doug
Judith Segall wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'. Doug: I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual
In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh. So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness? Thanks, Judith S. On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value). doug Pratap Kunwar wrote: Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carloresults, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. yes at lateral orbital frontal. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? yes you are correct. If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
The sig.mgh is the input that creates the sig.cluster.mgh (and the summary table).
doug
On Thu, 4 Jun 2009, Judith Segall wrote:
Doug.
Again, I am only asking about the sig.cluster.summary. This was a thickness study, where monte-carlo simulations where used to correct for multiple comparisons. Why would the *max in column 2 of the sig.cluster.summary* be derived from the sig.mgh and not the sig.cluster.mgh? Since, this report is generated at the same time as the sig.cluster.mgh. (ClusterNo *Max* VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot)
I only used the scatter plot as example as to why I has a question about how to interpret the sig.cluster.summary.
- Judith
On Thu, Jun 4, 2009 at 11:51 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The Max is derived from the sig.mgh, not the sig.cluster.mgh. When you load the FSGD and look at the scatter plot, the y-axis will be the thickness value (assuming you're doing a thickness study:).
doug
Judith Segall wrote:
Doug and freesufer list.
When I load the sig map in tksurfer i know that the CWP is displayed as the -log(10)p; however, I am not asking about visualization or the CWP. The newest version of the wiki does a great job in explaining the p values. I am only asking about the sig.cluster.summary report. It makes since that "The Max is the vertex-wise maximum and is bounded below by the vertex-wise threshold." But then what units is it in?
When I was not sure what the second column was I turned to visualization. After, loading both the sig.cluster.mgh and the group descriptor file in tksurfer and then selecting a vertex in the region with the most significance, which is based off of the CWP, it displays a scatter plot. The scatter plot does not have a label for the y-axis; however, the highest point on the y-axis is similar to the max, in column 2, of the sig.cluster.summary report. On the older wiki, there was a paragraph describing how the y was thickness. But, the sig.cluster.summary report does not have any labels for the second column. But, since the value was similar to the y-axis I began to interpret it as thickness, but wanted to clarify with the freesurfer team.
- Judith
On Thu, Jun 4, 2009 at 11:15 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is the maximum vertex-wise -log10(p) found in the cluster. Why do you think otherwise? You should be able to load the sig map into tksurfer and go to that vertex to find out.
doug
Judith Segall wrote:
Thanks, for you responses Doug and Pratap. But, both of your responses need more clarification, because I believe that we are not all referring to the same 'max'. Doug: I understand that when I display the sig.cluster.mgh that the a CWP value of 0.0001 would be displayed as a 4 by the color bar in tksurfer, since it is the -log10(p). However, in this case, which is about the cluster growing summary, the -log10(p) of the CWP does not equal the Max. Max is -3.312 and the CWP is 0.08250. Or an additional example form another sig.cluster.summary, where the Max is -4.310 and the CWP is 0.0192. ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZCWP CWPLow CWPHi NVtxs Annot 1 -4.310 40526 376.78 -12.0 -66.1 5.4 0.01920 0.01750 0.02100 706 lingual
In Pratap's email his answer to my question of what is the max in the CWP is, "Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster." Which, is stating that it is both the thickness and the pvalue. I really think that it is thickness measure, but need some clarification from mgh. So, is the Max in column 2 of the cluster growing summary report, from monte carlo simulations, thickness? Thanks, Judith S. On Thu, Jun 4, 2009 at 9:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: It will be whatever you used as input. In this case, it is the -log10(p) value of the maximum in the cluster (not the thickness value). doug Pratap Kunwar wrote: Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. Hi all. After looking over our monte-carloresults, I a simple question about the sig.cluster.summary output.
Is the " Max" in column 2 below a measurement of thickness? thickness, is the correct interpretation the following: the most significant cluster is in the laterorbitofrontal region. yes at lateral orbital frontal. The max vertex in that cluster has an average thickness of 3.312 mm and the negative directionality indicates that it is thinner in that region than in the fsaverage (from freesufer) used in the group analysis/simulations? yes you are correct. If it does not refer to thickness, is it a statistic, etc? # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast lh-Avg-thickness-CAQ-CCI # CSD confint 90.000000 # Overall max 2.05497 at vertex 92846 # Overall min -3.3122 at vertex 60632 # NClusters 11 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -3.312 60632 278.00 -15.2 47.7 -15.4 0.08250 0.07900 0.08600 341 lateralorbitofrontal 2 -3.231 51202 118.54 -39.5 24.9 16.9 0.53620 0.52980 0.54260 212 rostralmiddlefrontal 3 -3.229 67407 163.06 -19.2 12.0 46.9 0.36360 0.35740 0.36980 337 superiorfrontal 4 -2.463 117667 37.51 -47.8 -50.8 8.0 0.63240 0.62620 0.63860 79 bankssts 5 -2.379 151243 12.92 -30.9 -42.8 36.6 0.63240 0.62620 0.63860 38 superiorparietal I am trying to finish writing up my results and just need answer to this question to continue. Thanks, Judith S. Mind Research Network _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto: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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Douglas N Greve
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Judith Segall -
Pratap Kunwar -
Siddharth Srivastava