Thanks Pratap,
I'll try it again.
Kara
Pratap Kunwar wrote:
Kara and Lauren,
I think Doug has fixed this problem. i had similar problem but it is
working now.
pratap
Hi Lauren (and Doug),
I'm having the same issue. I ran montecarlo simulations on Friday and
then
tried to use the results in mri_surfcluster. It ran, but I also got the
same CWP values (-0.10000) for each cluster in the sum file.
Also, when it runs, it gives a CEPHES ERROR. Here is what I get:
INFO: you have selected subject average7 (and REALLY want to use it)
instead of fsaverage. So I'm going to turn off fixing of vertex area
to maintain compatibility with the pre-stable3 release.
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.39.2.2 2008/12/31 16:06:00 greve Exp
$
hemi = rh
srcid =
./group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.mgh
srcsubjid = average7
srcsurf = white
srcframe = 0
thsign = abs
thmin = 3
thmax = inf
fdr = -1
minarea = 0
xfmfile = talairach.xfm
nth = -1
outid =
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii
nii
ocnid =
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii
nii
sumfile =
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.sum
subjectsdir = /space/ventzl/1/users/SUBJECTS_DIR
FixMNI = 1
------------- XFM matrix (RAS2RAS) ---------------
/space/ventzl/1/users/SUBJECTS_DIR/average7/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
/space/ventzl/1/users/SUBJECTS_DIR/average7/surf/rh.white
Done reading source surface
Reading annotation
/space/ventzl/1/users/SUBJECTS_DIR/average7/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 85 entries read (originally
/space/neo/5/recon/christophe/Simple_surface_labels2002.txt)
Computing metric properties
Loading source values
number of voxels in search space = 163842
Done loading source values (nvtxs = 163842)
overall max = 9.2406 at vertex 150454
overall min = -4.29783 at vertex 159827
surface nvertices 163842
surface area 98024.702210
surface area 65349.801473
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=3.000000 (3.000000), thmax=inf (inf), thsignid=0, minarea=0.000000
Found 23 clusters
Max cluster size 2791.366699
INFO: fixing MNI talairach coordinates
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
***
CEPHES ERROR: bdtr (p < 0.0) domain error
***
Saving thresholded output to
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.nii
NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768.
So I'm going to put the true ncols in glmin and set dim[1]=-1.
This should be ok within FreeSurfer, but you will not be
able to use this volume with other software.
Saving cluster numbers to
/space/ventzl/8/users/oldstream/group_analysis/chronic18/glmfit/EMerror/rh.ASvfix_4.chronic18.glmdir/osgm/sig.cluster.p001.MCSIM.rh.ASvfix_4.chronic18.ocn.nii
NIFTI FORMAT WARNING: ncols 163842 in input exceeds 32768.
So I'm going to put the true ncols in glmin and set dim[1]=-1.
This should be ok within FreeSurfer, but you will not be
able to use this volume with other software.
Kara
Lauren LaCount wrote:
Hi Everyone,
I'm having a bit of a problem with mri_surfcluster. I ran it alright
last week on the right hemisphere, and now am unable to get it to run
through with the left.
First I'm running mri_glmfit to get .csd files with 10000 iterations
(split into 10 runs to speed things up), and then I'm running
mri_surfcluster with something like:
mri_surfcluster --in
../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average
--hemi lh --surf white --annot aparc.a2005s --csd
../csdfiles/mcz_SENS_lh_10000_
mfx_0.5frac_th01_1of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd
../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m
fx_0.5frac_th01 --csdpdf
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m
fx_0.5frac_th01 --vwsig
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh
--cwsig
/clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh
--o
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01
--ocn
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01
--olab
./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf
white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x
--csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out
--csdpdf it will run, but the cluster-wise probabilities in the "sum"
file are all the same (-0.1 for one time I tried it, and something
like -17 the other time), and the nrep in the sum file is -2 (or -10
the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think
everything was recently updated (probably because of the cluster size
bug?) because I can no longer re-run last week's right hemisphere
analysis using the same csd files (tried this for troubleshooting), so
maybe I have to start doing something differently with the new version
of this command with the left hemisphere?
Thank you!
-Lauren
--
Kara A. Dyckman, Ph.D.
Postdoctoral Fellow, Manoach Lab
Psychiatric Neuroimaging
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St.
Charlestown, MA 02129
email: k...@nmr.mgh.harvard.edu
phone: 617-724-4604
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Kara A. Dyckman, Ph.D.
Postdoctoral Fellow, Manoach Lab
Psychiatric Neuroimaging
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St.
Charlestown, MA 02129
email: k...@nmr.mgh.harvard.edu
phone: 617-724-4604
fax: 617-726-4078
http://nmr.mgh.harvard.edu/manoachlab
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
