Hello Freesurfer experts--
I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it.
Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation).
mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite
What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right?
FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table.
Any of your help would be greatly appreciated. -Glen
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
You will need more like 10000 iterations instead of 100. doug
On 06/03/2013 04:49 PM, Glen Lee wrote:
Hello Freesurfer experts--
I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it.
Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation).
mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite
What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right?
FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table.
Any of your help would be greatly appreciated. -Glen
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
You will need more like 10000 iterations instead of 100. doug
On 06/03/2013 04:49 PM, Glen Lee wrote:
Hello Freesurfer experts--
I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it.
Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation).
mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite
What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right?
FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table.
Any of your help would be greatly appreciated. -Glen
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug
On 6/3/13 9:45 PM, Glen Lee wrote:
Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You will need more like 10000 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: > Hello Freesurfer experts-- > > I ran mri_glmfit-sim to validate the group level GLM result (which was > already done using mri_glmfit), but I was not able to get any result > out of it. > > Even with a quite liberal threshold (2), no vertices came out (below > is what I typed in for the random permutation). > > mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign > abs --overwrite > > What is strange is that I was clearly see a number of clusters when I > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster > shows up in perm.abs.2.sig.cluster.mgh. > I should be able to see the identical map between those right? > > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. > As can be seen, nothing is listed in the stats table. > > Any of your help would be greatly appreciated. > -Glen > > > > > > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > # CreationTime 2013/06/03-20:19:31-GMT > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white > # cwd /glen/2D/results/LH > # sysname Linux > # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu> <http://sumo.uphs.upenn.edu> > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input GLM/osgm/sig.mgh > # Frame Number 0 > # srcsubj fsaverage_sym > # hemi lh > # surface white > # annot aparc > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects > # SearchSpace_mm2 59961.4 > # SearchSpace_vtx 82070 > # Bonferroni 0 > # Minimum Threshold 2 > # Maximum Threshold infinity > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # CW PValue Threshold: 0.05 > # Area Threshold 0 mm^2 > # CSD thresh 2.000000 > # CSD nreps 100 > # CSD simtype perm > # CSD contrast osgm > # CSD confint 90.000000 > # Overall max 3.495 at vertex 61659 > # Overall min -4.18843 at vertex 73402 > # NClusters 0 > # Total Cortical Surface Area 59961.4 (mm^2) > # FixMNI = 0 > # > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need to define the path for this csd folder?
Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite
-Glen
On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug
On 6/3/13 9:45 PM, Glen Lee wrote:
Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong?
FYI, I use v5.1.0.
On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
You will need more like 10000 iterations instead of 100. doug
On 06/03/2013 04:49 PM, Glen Lee wrote:
Hello Freesurfer experts--
I ran mri_glmfit-sim to validate the group level GLM result (which was already done using mri_glmfit), but I was not able to get any result out of it.
Even with a quite liberal threshold (2), no vertices came out (below is what I typed in for the random permutation).
mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign abs --overwrite
What is strange is that I was clearly see a number of clusters when I overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster shows up in perm.abs.2.sig.cluster.mgh. I should be able to see the identical map between those right?
FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. As can be seen, nothing is listed in the stats table.
Any of your help would be greatly appreciated. -Glen
# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ # CreationTime 2013/06/03-20:19:31-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname sumo.uphs.upenn.edu http://sumo.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 100 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug
On 06/04/2013 09:11 AM, Glen Lee wrote:
Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need to define the path for this csd folder?
Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite
-Glen
On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote:Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: You will need more like 10000 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: > Hello Freesurfer experts-- > > I ran mri_glmfit-sim to validate the group level GLM result (which was > already done using mri_glmfit), but I was not able to get any result > out of it. > > Even with a quite liberal threshold (2), no vertices came out (below > is what I typed in for the random permutation). > > mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign > abs --overwrite > > What is strange is that I was clearly see a number of clusters when I > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster > shows up in perm.abs.2.sig.cluster.mgh. > I should be able to see the identical map between those right? > > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. > As can be seen, nothing is listed in the stats table. > > Any of your help would be greatly appreciated. > -Glen > > > > > > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > # CreationTime 2013/06/03-20:19:31-GMT > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white > # cwd /glen/2D/results/LH > # sysname Linux > # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu> <http://sumo.uphs.upenn.edu> > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input GLM/osgm/sig.mgh > # Frame Number 0 > # srcsubj fsaverage_sym > # hemi lh > # surface white > # annot aparc > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects > # SearchSpace_mm2 59961.4 > # SearchSpace_vtx 82070 > # Bonferroni 0 > # Minimum Threshold 2 > # Maximum Threshold infinity > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # CW PValue Threshold: 0.05 > # Area Threshold 0 mm^2 > # CSD thresh 2.000000 > # CSD nreps 100 > # CSD simtype perm > # CSD contrast osgm > # CSD confint 90.000000 > # Overall max 3.495 at vertex 61659 > # Overall min -4.18843 at vertex 73402 > # NClusters 0 > # Total Cortical Surface Area 59961.4 (mm^2) > # FixMNI = 0 > # > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Doug -- Sorry for asking your help again as I can't seem to resolve this on my own.
I looked up the mri_glmfit-sim --help and added the path of csd file in the argument, but it still fails to find .csd file. Can you let me know once again what I did wrong? (see the command line below).
mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim /csd/mc-z.negative.j001-osgm.csd --overwrite
Also see the output below. -------- Original mri_glmfit command line: cmdline mri_glmfit --y Bb_Bp_sm8_i6_n13_L.mgh --osgm --glmdir GLM --surf fsaverage_sym lh
DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 5.124509 ERROR: cannot find any csd files
On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug
On 06/04/2013 09:11 AM, Glen Lee wrote:
Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below:
/2D/results/LH/GLM/csd> ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd
I'm guessing that I need to define the path for this csd folder?
Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite
-Glen
On Mon, Jun 3, 2013 at 11:03 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote:Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote:
You will need more like 10000 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: > Hello Freesurfer experts-- > > I ran mri_glmfit-sim to validate the group level GLM result (which was > already done using mri_glmfit), but I was not able to get any result > out of it. > > Even with a quite liberal threshold (2), no vertices came out (below > is what I typed in for the random permutation). > > mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign > abs --overwrite > > What is strange is that I was clearly see a number of clusters when I > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster > shows up in perm.abs.2.sig.cluster.mgh. > I should be able to see the identical map between those right? > > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. > As can be seen, nothing is listed in the stats table. > > Any of your help would be greatly appreciated. > -Glen > > > > > > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > # CreationTime 2013/06/03-20:19:31-GMT > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd > GLM/csd/perm.abs.2.j001-osgm.**csd --mask GLM/mask.mgh --cwsig > GLM/osgm/perm.abs.2.sig.**cluster.mgh --vwsig > GLM/osgm/perm.abs.2.sig.voxel.**mgh --sum > GLM/osgm/perm.abs.2.sig.**cluster.summary --ocn > GLM/osgm/perm.abs.2.sig.ocn.**mgh --oannot > GLM/osgm/perm.abs.2.sig.ocn.**annot --annot aparc --csdpdf > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o > GLM/osgm/perm.abs.2.sig.**masked.mgh --no-fixmni --surf white > # cwd /glen/2D/results/LH > # sysname Linux > # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu> <http://sumo.uphs.upenn.edu> > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input GLM/osgm/sig.mgh > # Frame Number 0 > # srcsubj fsaverage_sym > # hemi lh > # surface white > # annot aparc > # SUBJECTS_DIR /usr/local/freesurfer5-1/**subjects > # SearchSpace_mm2 59961.4 > # SearchSpace_vtx 82070 > # Bonferroni 0 > # Minimum Threshold 2 > # Maximum Threshold infinity > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # CW PValue Threshold: 0.05 > # Area Threshold 0 mm^2 > # CSD thresh 2.000000 > # CSD nreps 100 > # CSD simtype perm > # CSD contrast osgm > # CSD confint 90.000000 > # Overall max 3.495 at vertex 61659 > # Overall min -4.18843 at vertex 73402 > # NClusters 0 > # Total Cortical Surface Area 59961.4 (mm^2) > # FixMNI = 0 > # > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
what was your original mri_glmfit-sim command?
On 06/05/2013 12:10 PM, Glen Lee wrote:
Doug -- Sorry for asking your help again as I can't seem to resolve this on my own.
I looked up the mri_glmfit-sim --help and added the path of csd file in the argument, but it still fails to find .csd file. Can you let me know once again what I did wrong? (see the command line below).
mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim /csd/mc-z.negative.j001-osgm.csd --overwrite
Also see the output below.
Original mri_glmfit command line: cmdline mri_glmfit --y Bb_Bp_sm8_i6_n13_L.mgh --osgm --glmdir GLM --surf fsaverage_sym lh
DoSim = 0 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 5.124509 ERROR: cannot find any csd files
On Tue, Jun 4, 2013 at 11:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
--no-sim takes an argument. Run mri_glmfit-sim with --help to get more info doug On 06/04/2013 09:11 AM, Glen Lee wrote: Hi Doug, I tried as you suggested, but i've got the following error: e.g.,cannot find any csd files. However, I can see them stored in csd folder as shown below: /2D/results/LH/GLM/csd> ls mc-z.negative.j001-osgm.csd perm.abs.2.j001-osgm.csd I'm guessing that I need to define the path for this csd folder? Here is the command line that I typed in: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite -Glen On Mon, Jun 3, 2013 at 11:03 PM, Douglas 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: hi Glen, no cluster will show up if the p-value for all clusters is above .05. You can change this with --cwpvalthresh to something like .99. That should give you all the clusters. Also, you don't have to run the full simulation again; you can use the --no-sim option and it will use the simulation that you already did. doug On 6/3/13 9:45 PM, Glen Lee wrote: Indeed, I initially tried 10,000 iterations and got nothing. What else then could have gone wrong? FYI, I use v5.1.0. On Mon, Jun 3, 2013 at 5:32 PM, 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: You will need more like 10000 iterations instead of 100. doug On 06/03/2013 04:49 PM, Glen Lee wrote: > Hello Freesurfer experts-- > > I ran mri_glmfit-sim to validate the group level GLM result (which was > already done using mri_glmfit), but I was not able to get any result > out of it. > > Even with a quite liberal threshold (2), no vertices came out (below > is what I typed in for the random permutation). > > mri_glmfit-sim --glmdir GLM --sim perm 100 2 perm.abs.2 --sim-sign > abs --overwrite > > What is strange is that I was clearly see a number of clusters when I > overlaid sig.mgh at a matched threshold (e.g., p>2), but no cluster > shows up in perm.abs.2.sig.cluster.mgh. > I should be able to see the identical map between those right? > > FYI, I also pasted the content in perm.abs.2.sig.cluster.summary below. > As can be seen, nothing is listed in the stats table. > > Any of your help would be greatly appreciated. > -Glen > > > > > > > # Cluster Growing Summary (mri_surfcluster) > # $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > # $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ > # CreationTime 2013/06/03-20:19:31-GMT > # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd > GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig > GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig > GLM/osgm/perm.abs.2.sig.voxel.mgh --sum > GLM/osgm/perm.abs.2.sig.cluster.summary --ocn > GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot > GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf > GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o > GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white > # cwd /glen/2D/results/LH > # sysname Linux > # hostname sumo.uphs.upenn.edu <http://sumo.uphs.upenn.edu> <http://sumo.uphs.upenn.edu> <http://sumo.uphs.upenn.edu> > # machine x86_64 > # FixVertexAreaFlag 1 > # FixSurfClusterArea 1 > # > # Input GLM/osgm/sig.mgh > # Frame Number 0 > # srcsubj fsaverage_sym > # hemi lh > # surface white > # annot aparc > # SUBJECTS_DIR /usr/local/freesurfer5-1/subjects > # SearchSpace_mm2 59961.4 > # SearchSpace_vtx 82070 > # Bonferroni 0 > # Minimum Threshold 2 > # Maximum Threshold infinity > # Threshold Sign abs > # AdjustThreshWhenOneTail 1 > # CW PValue Threshold: 0.05 > # Area Threshold 0 mm^2 > # CSD thresh 2.000000 > # CSD nreps 100 > # CSD simtype perm > # CSD contrast osgm > # CSD confint 90.000000 > # Overall max 3.495 at vertex 61659 > # Overall min -4.18843 at vertex 73402 > # NClusters 0 > # Total Cortical Surface Area 59961.4 (mm^2) > # FixMNI = 0 > # > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > CWPLow CWPHi NVtxs Annot > > > _______________________________________________ > 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 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what was your original mri_glmfit-sim command?
mri_glmfit-sim --glmdir GLM --sim perm 20000 2 perm.abs.2 --sim-sign abs
--overwrite
Then, I tried no-sim on the generated csd file with the following command:
mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite /csd/perm.abs.2.j001-osgm.csd
try
mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2
doug
On 06/05/2013 02:26 PM, Glen Lee wrote:
On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what was your original mri_glmfit-sim command? mri_glmfit-sim --glmdir GLM --sim perm 20000 2 perm.abs.2 --sim-sign abs --overwrite Then, I tried no-sim on the generated csd file with the following command: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite /csd/perm.abs.2.j001-osgm.csd
thanks Doug. just tried, but I still got no clusters.
below is the output of perm.abs.2.sig.cluster.summary.
# CreationTime 2013/06/05-18:52:23-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname rage.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /derek/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 20000 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
On Wed, Jun 5, 2013 at 2:44 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
try
mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2
doug
On 06/05/2013 02:26 PM, Glen Lee wrote:
On Wed, Jun 5, 2013 at 12:12 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
what was your original mri_glmfit-sim command? mri_glmfit-sim --glmdir GLM --sim perm 20000 2 perm.abs.2 --sim-sign abs --overwrite Then, I tried no-sim on the generated csd file with the following command: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite /csd/perm.abs.2.j001-osgm.csd-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
you need to set the clusterwise threshold to something close to 1 (eg, --cpwvalthresh .99) On 06/05/2013 03:20 PM, Glen Lee wrote:
thanks Doug. just tried, but I still got no clusters.
below is the output of perm.abs.2.sig.cluster.summary.
# CreationTime 2013/06/05-18:52:23-GMT # cmdline mri_surfcluster --in GLM/osgm/sig.mgh --csd GLM/csd/perm.abs.2.j001-osgm.csd --mask GLM/mask.mgh --cwsig GLM/osgm/perm.abs.2.sig.cluster.mgh --vwsig GLM/osgm/perm.abs.2.sig.voxel.mgh --sum GLM/osgm/perm.abs.2.sig.cluster.summary --ocn GLM/osgm/perm.abs.2.sig.ocn.mgh --oannot GLM/osgm/perm.abs.2.sig.ocn.annot --annot aparc --csdpdf GLM/osgm/perm.abs.2.pdf.dat --cwpvalthresh .05 --o GLM/osgm/perm.abs.2.sig.masked.mgh --no-fixmni --surf white # cwd /glen/2D/results/LH # sysname Linux # hostname rage.uphs.upenn.edu http://rage.uphs.upenn.edu # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input GLM/osgm/sig.mgh # Frame Number 0 # srcsubj fsaverage_sym # hemi lh # surface white # annot aparc # SUBJECTS_DIR /derek/freesurfer5-1/subjects # SearchSpace_mm2 59961.4 # SearchSpace_vtx 82070 # Bonferroni 0 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 20000 # CSD simtype perm # CSD contrast osgm # CSD confint 90.000000 # Overall max 3.495 at vertex 61659 # Overall min -4.18843 at vertex 73402 # NClusters 0 # Total Cortical Surface Area 59961.4 (mm^2) # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
On Wed, Jun 5, 2013 at 2:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
try mri_glmfit-sim --glmdir GLM --no-sim perm.abs.2 doug On 06/05/2013 02:26 PM, Glen Lee wrote: On Wed, Jun 5, 2013 at 12:12 PM, 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: what was your original mri_glmfit-sim command? mri_glmfit-sim --glmdir GLM --sim perm 20000 2 perm.abs.2 --sim-sign abs --overwrite Then, I tried no-sim on the generated csd file with the following command: mri_glmfit-sim --cwpvalthresh 0.99 --glmdir GLM --no-sim --overwrite /csd/perm.abs.2.j001-osgm.csd -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Glen Lee