Hi Joost, can you look at the original sig map thresholded at 1.3 to see if there is a cluster of that size?
Hi,
version 4.0.5
after:
mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh --glmdir stats/newperm_lh/
i got an csd file (attached), "stats/newperm_lh and --glmdir stats/newperm_lh/" were ignored (as expected).
i want to use this .csd file to inspect clusters: mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum qdec/summary.txt
which gives the following output (summary.txt is attached): ******************** # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ # $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ # CreationTime 2008/10/08-08:52:02-GMT # cmdline mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum q dec/summary.txt # cwd /home/neuro/joost/redes/maranon/freesurfer # sysname Linux
# hostname fedoraneuro.lim.local # machine x86_64 # FixVertexAreaFlag = 1 # # Input qdec/N83_only_boys.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/neuro/joost/redes/maranon/freesurfer # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 1000 # CSD simtype perm # CSD contrast diff-1-2.txt # CSD confint 90.000000 # Overall max 4.37947 at vertex 3484 # Overall min 1.58841e-06 at vertex 136280 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 4.379 3484 98860.55 -34.7 11.5 -6.9 0.00100 0.00000 0.00200 155267 [neuro@fedoraneuro qdec]$ cd .. [neuro@fedoraneuro freesurfer]$ mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum qdec/summary.txt thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/N83_only_boys.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 1.3 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 sumfile = qdec/summary.txt subjectsdir = /home/neuro/joost/redes/maranon/freesurfer FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /home/neuro/joost/redes/maranon/freesurfer/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 /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /home/neuro/joost/redes/maranon/freesurfer/fsaverage/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 = 4.37947 at vertex 3484 overall min = 1.58841e-06 at vertex 136280 surface nvertices 163842 surface area 65417.097656 surface area 65416.648438 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=1.300000 (1.300000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 98860.554688 INFO: fixing MNI talairach coordinates Saving cluster pval stats/cluster_map.mgh ************************
- the cluster size seems way to big.
your thoughts?
- for visualizing the cluster i thought: loading the --cwsig file (cluster_map.mgh) as an overlay on the (inflated) surface of fsaverage and then configure the overlay to set the minimal threshold to 1.3.
your thoughts?
thanks! -joost
On Tue, Oct 7, 2008 at 7:37 PM, Pratap Kunwar <pkunwar@nmr.mgh.harvard.edu mailto:pkunwar@nmr.mgh.harvard.edu> wrote:
Hi,
You have a continuous variable "age" in your fsgd file. As far as i know, permutation can't have continuous variables.
Try mc-z that should work.
pratap
> Hi, > > using version 4.0.5 > > i ran the command: > mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf > fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/ > > it worked. > > then i did: > > mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf > fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh > --glmdir stats/newperm_lh/ > > output: > > gdfReadHeader: reading qdec/qdec.fsgd > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > Continuous Variable Means (all subjects) > 0 Age 15.4819 > Class Means of each Continuous Variable > 1 control 15.0882 > 2 patient 15.7551 > INFO: gd2mtx_method is doss > Reading source surface > /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white > reading group avg surface area 822 cm^2 from file > Reading in average area > /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh > simbase stats/perm_lh > Number of vertices 163842 > Number of faces 327680 > Total area 65416.648438 > AvgVtxArea 0.399267 > AvgVtxDist 0.721953 > StdVtxDist 0.195470 > > $Id: mri_glmfit.c,v 1.138.2.1 http://1.138.2.1 2007/09/12 15:38:19 nicks Exp $ > cwd /home/neuro/joost/redes/maranon/freesurfer > cmdline mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss > --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 > stats/perm_lh > --glmdir stats/ > sysname Linux > hostname fedoraneuro.lim.local > machine x86_64 > user neuro > FixVertexAreaFlag = 1 > UseMaskWithSmoothing 1 > OneSampleGroupMean 0 > y /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh > logyflag 0 > usedti 0 > FSGD qdec/qdec.fsgd > glmdir stats/ > DoFFx 0 > Loading y from > /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh > Matrix condition is 404.504 > search space = 82220 > ERROR: design matrix is not orthogonal, cannot be used with permutation. > If this something you really want to do, run with --perm-force > > mri_info N83_only_boys.mgh gives 83 frames. > > what´s wrong with my design matrix? > > thanks! > -joost > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
version 4.0.5. http://4.0.5.
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# Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ # $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ # CreationTime 2008/10/08-08:52:02-GMT # cmdline mri_surfcluster --in qdec/N83_only_boys.mgh --csd stats/perm_lh-diff-1-2.txt.csd --cwsig stats/cluster_map.mgh --sum qdec/summary # cwd /home/neuro/joost/redes/maranon/freesurfer # sysname Linux # hostname fedoraneuro.lim.local # machine x86_64 # FixVertexAreaFlag = 1 # # Input qdec/N83_only_boys.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /home/neuro/joost/redes/maranon/freesurfer # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm2 # CSD thresh 1.300000 # CSD nreps 1000 # CSD simtype perm # CSD contrast diff-1-2.txt # CSD confint 90.000000 # Overall max 4.37947 at vertex 3484 # Overall min 1.58841e-06 at vertex 136280 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs 1 4.379 3484 98860.55 -34.7 11.5 -6.9 0.00100 0.00000 0.00200 155267
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