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
[EMAIL PROTECTED] qdec]$ cd ..
[EMAIL PROTECTED] 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
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> 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.>
------------------------------------------------------------------------
# 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
------------------------------------------------------------------------
1 -1
------------------------------------------------------------------------
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j janssen wrote:
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
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
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