That does not sound right, I think that the first clustering step will probably invalidate FDR. You can use FDR to set the voxel-wise threshold when you run mri_surfcluster, but I'm not sure you can do it afterwards.
Alex Fornito wrote:
I retract the last email - it seems like I was entering the wrong sig.mgh file as input. Sorry for the confusion!!!
On a separate issue, I would like to check that I have the following correct:
I have extracted a cluster image using mri_surfcluster withouth running simulations. Say, for e.g., I use thmin 2 and minarea 30. I load the resulting output.mgh file into tksurfer. I would then like to perform FDR correction on the resulting clusters. I'm guessing that pressing the FDR button in the Overlay config menu will do the trick, since (from what I understand) the output.mgh file I have loaded assigns a zero to all vertices not in a cluster. I figure that this will therefore result in an FDR correction that accounts only for the vertices within my clusters.
However, I'm uncertain how the 'only marked' checkbox fits in. If I tick it, I get an error calculating the FDR. I'm guessing this option is relevant if you combined a stat map with a label file.
Am I on the right track?
Thanks again, Alex
On 05/12/2007, at 9:52 AM, Alex Fornito wrote:
<Pic.png>
Thanks for all your help guys, but I am still having trouble (!). This time I've tried a different dataset, again just a simple 2 group comaprison with no covariates.
Running this in qdec, and visualizing with a low threshold (min=1.3), I see a whole bunch of clusters (see attached). However, when I run mri_surfcluster, I only get one whole brain cluster again (see below). This time I smoothed with 15 mm in qdec, although I get the same if I smooth with 10mm. I have kept the thresholds low on purpose, because I expect that something should come out?? I did not run simulations in this instance, to cut processing time.
mri_surfcluster --in qdec/MF_lh_15mm/contrasts.sig.mgh --no-adjust --subject fsaverage/ --hemi l h --thmin 1.3 --minarea 15 --sum TestClusters
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_lh_15mm/contrasts.sig.mgh paint srcsubjid = fsaverage/ srcsurf = white srcframe = 0 thsign = abs thmin = 1.3 thmax = -1 fdr = -1 minarea = 15 xfmfile = talairach.xfm nth = -1 sumfile = TestClusters subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage//mri/transforms/t alairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
Reading source surface /data/kang/work/struct/alex/freesurfer/subjects_cann/fsav erage//surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/subjects_cann/fsa verage//surf/lh.white.avg.area.mgh Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 1e+10 at vertex 26 overall min = 1.75775 at vertex 126983 surface nvertices 163842 surface area 65416.985991 surface area 65416.985976 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=1.300000 (1.300000), thmax=-1.000000 (-1), thsignid=0, minarea=15.000000 Found 1 clusters Max cluster size 103339.460938 INFO: fixing MNI talairach coordinates
On 05/12/2007, at 4:19 AM, Doug Greve wrote:
There's really no such thing as an opt kernel size. The best size depends on the underlying signal and can be space variant.
doug
Alex Fornito wrote:
Yes, I selected 25 mm on qdec, based on the Lerch paper suggesting this was a generally 'optimal' kernel size. The 34.309.. was the residual output to y.fsgd.
Do you recommend a smaller kernel?
On 04/12/2007, at 5:41 PM, Pratap Kunwar wrote:
I think, one reason for getting only one big cluster is because your fwhm value is very high. By the way how did you get fwhm 34.309616??, was it produced by selecting fwhm 25 (max on Qdec)on Qdec?
Did you try fwhm 10 or 15?
Thanks for your help Pratap. I've actually been trying to follow the tutorial and was running simulations initially, but when I tried to re-trace my steps I ended omitted them because I forgot they were necessary for mri_surfcluster.
Either way, the results are the same- I still get one whole surface cluster as output even after running simulations. In this case, I re- ran it copying your commands, except I used perm because I have low numbers and no covariates. I also ran 1000 permutations, to get a quick initial result for testing. My commands and output are below.
I would appreciate further help on this, as I'm not sure where I'm going wrong!
also, I noticed that after your mri_glmfit command, you added --i divided into 5000 each. Sorry, but I'm not sure what you meant by that.
---> i had split simulation (10,000 iterations)into multiple runs csd1* (5000 iterations) and csd2* (5000 iterations) since mc-z relatively takes long time comparing to permutation. More on, https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fGroupAnalysis?action=... https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd
mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 stats/ newperm_rh/newperm_rh --glmdir stats/newperm_rh/
gdfReadHeader: reading qdec/MF_group_rh/qdec.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 group1 2 group2 INFO: gd2mtx_method is doss Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white.avg.area.mgh simbase stats/newperm_rh/newperm_rh Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white.avg.area.mgh INFO: fwhm2niters: Fixing group surface area Surface smoothing by fwhm=34.309616, niters=866.000000
$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /data/kang/work/struct/alex/freesurfer/subjects_cann cmdline mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 stats/ newperm_rh/newperm_rh --glmdir stats/newperm_rh/ sysname Linux hostname kang machine i686 user alex FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 34.309616 niters 866.000000 OneSampleGroupMean 0 y /data/kang/work/struct/alex/freesurfer/subjects_cann/qdec/ MF_group_rh/y.mgh logyflag 0 usedti 0 FSGD qdec/MF_group_rh/qdec.fsgd glmdir stats/newperm_rh/ DoFFx 0 Loading y from /data/kang/work/struct/alex/freesurfer/subjects_cann/ qdec/MF_group_rh/y.mgh Matrix condition is 1 search space = 82167.6 Smoothing input by fwhm 34.309616 Smoothing done, nsteps = 866, tsec = 1236.17 ... done DOF = 28 thresh = 2, threshadj = 2 Starting simulation sim over 1000 trials 1/1000 t=0 ------------------------------------------------ Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Diff-1-2-Intercept 0 nc=3 maxcsize=1910.81 sigmax=-3.00831 Fmax=13.551 2/1000 t=0.0572833 ------------------------------------------------ Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Diff-1-2-Intercept 1 nc=0 maxcsize=0 sigmax=1.36036 Fmax=4.46612 3/1000 t=0.0994333 ------------------------------------------------
... and so on... then
mri_surfcluster --src qdec/MF_group_lh/contrasts.sig.mgh --csd stats/ newperm_lh/newperm_lh-Diff-1-2-Intercept.csd --sum stats/newperm_lh/ newperm_lh --ocp stats/newperm_lh/newperm_lh.mgh
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = rh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 sumfile = stats/newperm_lh/newperm_lh subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/ transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000;
Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white.avg.area.mgh Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65020.838384 surface area 65020.838382 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 103836.125000 INFO: fixing MNI talairach coordinates Saving cluster pval stats/newperm_lh/newperm_lh.mgh
On 04/12/2007, at 11:30 AM, Pratap Kunwar wrote:
> Alex, > > You have to do simulations using mri_glmfit before youdo > mri_surfcluster, > > [more info in this link at > https://surfer.nmr.mgh.harvard.edu/fswiki/ > FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd > go down to [4.0 Using mri_glmfit to correct for multiple > comparisons: ] > > USAGE: ./mri_glmfit > > --glmdir dir : save outputs to dir > > --y inputfile **y.mgh > --fsgd FSGDF <gd2mtx> : freesurfer descriptor file **qdec.fsgd > --C contrast1.mat <--C contrast2.mat ...> > --fwhm fwhm : smooth input by fwhm ** your smoothing value from " > fwhm.dat" > --surf subject hemi <surfname> : needed for some flags (uses > white by > default) **lh or rh > --sim nulltype nsim thresh csdbasename : simulation perm, mc- > full, mc-z > **mc-z (i used) is faster than mc-full, minimum threshold value > ( i.e. > 1.3 for 0.05), > > My command was more like this, > > mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh -- > fwhm < ?? > >> --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd1 -- >> glmdir f11 > > > > mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh > --fwhm > 14.504073 --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd2 > --glmdir f11 > > --i divided into 5000 each > > from above mri_glmfit, i got two files starting with csd1* .csd and > csd2*.csd. > > Next one is > > mri_surfcluster, > mri_surfcluster --src contrastname/sig.mgh --csd csd1* .csd --csd > csd2* > ..csd --sum <text summary file --sum <*.sum> --ocp <*.mgh> > > the output file *.sum can be opened in text editor and *.mgh can > be seen > using tksurfer. Check the link above link for more details (i just > followed that link when i did last month). > > let me know if you get into more problems. > > pratap > >> >>> On 11/28/2007 07:43 PM, Alex Fornito wrote: >>> >>>> Hi, >>>> I have run qdec for a simple contrast comparing thickness across >>>> the >>>> cortical surface between a patient and control group. Not much >>>> survives vertex-wise FDR correction, and I would like to try >>>> cluster-based thresholding. I would like to make sure I >>>> understand the >>>> inputs to the command. Am I correct on the following? >>>> >>>> --in = the signifcance values (i.e., contrast_name.sig.mgh file) >>>> --thmin = the vertexwise threshold for determining clusters, >>>> where 2 >>>> corresponds to p=.01 >>>> --minarea = the cluster extent threshold - Am I correct in >>>> assuming >>>> this should not be smaller than the smoothing kernel? >>>> >>>> When I run the command below, I get the following output. >>>> Only one >>>> (whole hemi) cluster is identified. I'm not sure if its a >>>> problem in >>>> my command line, or with my data. Also, I seem to have the >>>> --cwsig >>>> flag wrong, but can't figure out the error (appending .w >>>> or .label to >>>> the end of the output filename does not change the error). >>>> >>>> I greatly appreciate your help. >>>> >>>> >>>> mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject >>>> fsaverage --hemi lh --surf white --annot aparc --sign abs >>>> --thmin 2 >>>> --minarea 25 --sum stats/qdec_run/cluster/summary.txt --o >>>> stats/qdec_run/cluster/cluster_output --cwsig >>>> stats/qdec_run/cluster/cwsig --olab >>>> stats/qdec_run/cluster/MF_group_lh_thk >>>> >>>> thsign = abs, id = 0 >>>> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve >>>> Exp $ >>>> hemi = lh >>>> srcid = qdec/MF_group_lh/contrasts.sig.mgh paint >>>> srcsubjid = fsaverage >>>> srcsurf = white >>>> srcframe = 0 >>>> thsign = abs >>>> thmin = 2 >>>> thmax = -1 >>>> fdr = -1 >>>> minarea = 25 >>>> xfmfile = talairach.xfm >>>> nth = -1 >>>> outid = stats/qdec_run/cluster/cluster_output paint >>>> sumfile = stats/run2/cluster/summary.txt >>>> subjectsdir = /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann >>>> FixMNI = 1 >>>> ------------- XFM matrix (RAS2RAS) --------------- >>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>> mri/transforms/talairach.xfm >>>> 1.000 0.000 0.000 0.000; >>>> 0.000 1.000 0.000 0.000; >>>> 0.000 0.000 1.000 0.000; >>>> 0.000 0.000 0.000 1.000; >>>> ---------------------------------------------------- >>>> Reading source surface >>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>> surf/lh.white >>>> reading group avg surface area 822 cm^2 from file >>>> Reading in average area >>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>> surf/lh.white.avg.area.mgh >>>> Done reading source surface >>>> Reading annotation >>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>> label/lh.aparc.annot >>>> reading colortable from annotation file... >>>> colortable with 35 entries read (originally >>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/ >>>> colortable_final.txt) >>>> Computing metric properties >>>> Loading source values >>>> number of voxels in search space = 163842 >>>> Done loading source values (nvtxs = 163842) >>>> overall max = 43.1907 at vertex 101931 >>>> overall min = 7.66111 at vertex 28089 >>>> surface nvertices 163842 >>>> surface area 65416.985991 >>>> surface area 65416.985976 >>>> NOT Adjusting threshold for 1-tailed test >>>> Searching for Clusters ... >>>> thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, >>>> minarea=25.000000 >>>> Found 1 clusters >>>> Max cluster size 103339.460938 >>>> INFO: fixing MNI talairach coordinates >>>> Saving thresholded output to >>>> stats/qdec_run/cluster/cluster_output >>>> avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 >>>> Saving cluster pval stats/qdec_run/cluster/cwsig >>>> unknown file type for file (stats/qdec_run/cluster/cwsig) >>>> LabelWrite: saving to stats/qdec_run/cluster/ >>>> MF_group_lh_thk-0001.label >>>> >>>> >>>> >>>> Alex Fornito >>>> JN Peters Research Fellow >>>> Melbourne Neuropsychiatry Centre >>>> Department of Psychiatry >>>> The University of Melbourne >>>> >>>> Postal address: >>>> Melbourne Neuropsychiatry Centre >>>> National Neuroscience Facility >>>> Levels 2 & 3, 161 Barry St >>>> Carlton South Vic 3053 Australia >>>> >>>> Ph: +61 3 8344 1861 >>>> Fax: +61 3 9348 0469 >>>> >>>> fornitoa@unimelb.edu.au mailto:fornitoa@unimelb.edu.au >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------- >>>> ----- >>>> >>>> _______________________________________________ >>>> 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 >> >> >> >
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne
Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861 Fax: +61 3 9348 0469
fornitoa@unimelb.edu.au mailto:fornitoa@unimelb.edu.au
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne
Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861 Fax: +61 3 9348 0469
fornitoa@unimelb.edu.au mailto:fornitoa@unimelb.edu.au
-- 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
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne
Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861 Fax: +61 3 9348 0469
fornitoa@unimelb.edu.au mailto:fornitoa@unimelb.edu.au
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Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne
Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861 Fax: +61 3 9348 0469
fornitoa@unimelb.edu.au mailto:fornitoa@unimelb.edu.au