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.eduwrote:

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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

version 4.0.5.