Hello FreeSurfer Developers,

I have run a glm on the left hemisphere to compare cortical thickness
between 2 groups. After, I did a cluster-wise correction with permutation
testing using this command

mri_glmfit-sim --glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs

It completes without error, but I have a question about the log file and
--surf argument. My concern if about this part of the log file where it
shows "--surf fsaverage lh white" (see section from log file and complete
log file attached). White is the default I based on the help file for
mri_glmfit. Should I be running with --surf fsaverage lh pial?

Does this imply that the glm is performed on the white matter surface. I am
then visualizing on the inflated pial surface so does this cause a problem?
------------------------------------------------------------
--------------------------------------------------
1/1 Fri Mar  2 03:23:25 EST 2018
mri_glmfit --C 
lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx
--sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign
abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y
lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh
--surf fsaverage lh white
simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001
FWHM = 0.000000
gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd
INFO: gd2mtx_method is dods
Reading source surface /home1/am2359/fs6_data/fpeb_
app_fs/fsaverage/surf/lh.white
---------------------------------------------------


Thank you,
Adam
cd /home1/am2359/fs6_data/fpeb_app_fs
/home1/am2359/freesurfer_6/bin/mri_glmfit-sim
--glmdir lh.sv2a_group.glmdir.10 --perm 1000 2 abs

$Id: mri_glmfit-sim,v 1.60.2.4 2016/11/17 18:01:28 zkaufman Exp $
Fri Mar  2 03:23:25 EST 2018
Linux tauruspet.med.yale.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Mar 21 19:29:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
am2359
setenv SUBJECTS_DIR /home1/am2359/fs6_data/fpeb_app_fs
FREESURFER_HOME /home1/am2359/freesurfer_6

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.sv2a.group.thickness.10.mgh --fsgd dx_sv2a.fsgd --C sv2a_thickness_group.mtx --surf fsaverage lh --cortex --glmdir lh.sv2a_group.glmdir.10

DoSim = 1
UseCache = 0
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 0
nSimPerJob = 1000
1/1 Fri Mar  2 03:23:25 EST 2018
mri_glmfit --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white
simbase lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001
FWHM = 0.000000
gdfRead(): reading lh.sv2a_group.glmdir.10/y.fsgd
INFO: gd2mtx_method is dods
Reading source surface /home1/am2359/fs6_data/fpeb_app_fs/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65416.984375
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /home1/am2359/fs6_data/fpeb_app_fs
cmdline mri_glmfit.bin --C lh.sv2a_group.glmdir.10/tmp.mri_glmfit-sim-13158/sv2a_thickness_group.mtx --sim perm 1000 2 lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001 --sim-sign abs --fwhm 0 --fsgd lh.sv2a_group.glmdir.10/y.fsgd dods --y lh.sv2a.group.thickness.10.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --surf fsaverage lh white 
sysname  Linux
hostname tauruspet.med.yale.edu
machine  x86_64
user     am2359
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /home1/am2359/fs6_data/fpeb_app_fs/lh.sv2a.group.thickness.10.mgh
logyflag 0
usedti  0
FSGD lh.sv2a_group.glmdir.10/y.fsgd
mask lh.sv2a_group.glmdir.10/mask.mgh
maskinv 0
glmdir (null)
IllCondOK 0
ReScaleX 1
DoFFx 0
Loading y from /home1/am2359/fs6_data/fpeb_app_fs/lh.sv2a.group.thickness.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1.1
Found 149953 voxels in mask
Reshaping mriglm->mask...
search space = 74612.064358
DOF = 19
thresh = 2, threshadj = 1.69897 


Starting simulation sim over 1000 trials
mri_glmfit simulation done 20.274


Fri Mar  2 03:43:45 EST 2018
mri_surfcluster --in lh.sv2a_group.glmdir.10/sv2a_thickness_group/sig.mgh --mask lh.sv2a_group.glmdir.10/mask.mgh --cwsig lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --sum lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.summary --ocn lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --annot aparc --cwpvalthresh .05 --o lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh --no-fixmni --csd lh.sv2a_group.glmdir.10/csd/perm.th20.abs.j001-sv2a_thickness_group.csd --csdpdf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.pdf.dat --vwsig lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.voxel.mgh --vwsigmax lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.voxel.max.dat --oannot lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.annot --surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $
hemi           = lh
srcid          = lh.sv2a_group.glmdir.10/sv2a_thickness_group/sig.mgh 
srcsubjid      = fsaverage
srcsurf        = white
srcframe       = 0
thsign         = abs
thmin          = 2
thmax          = -1
fdr            = -1
minarea        = 0
xfmfile        = talairach.xfm
nth         = -1
outid    = lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh MGH
ocnid    = lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh MGH
sumfile  = lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.summary
subjectsdir    = /home1/am2359/fs6_data/fpeb_app_fs
FixMNI = 0
Found 149953 vertices in mask
Found 149953 vertices in mask
Found 149953 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/home1/am2359/fs6_data/fpeb_app_fs/fsaverage/mri/transforms/talairach.xfm
 1.00000   0.00000   0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
----------------------------------------------------
Reading source surface /home1/am2359/fs6_data/fpeb_app_fs/fsaverage/surf/lh.white
Done reading source surface
Reading annotation /home1/am2359/fs6_data/fpeb_app_fs/fsaverage/label/lh.aparc.annot
Computing metric properties
Loading source values
number of voxels in search space = 149953
Done loading source values (nvtxs = 163842)
overall max = 5.13607 at vertex 42693
overall min = -1.32724 at vertex 100014
surface nvertices 163842
metric props tot surface area 65416.984375
group_avg_vtxarea_loaded 1
masked surface area 76467.078125
Computing voxel-wise significance
CSDpvalMaxSigMap(): found 4903/163842 above 0, max=1.35655
NOT Adjusting threshold for 1-tailed test
thminadj = 2
Searching for Clusters ...
thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000
Found 27 clusters
Max cluster size 470.815887
Pruning by CW P-Value 0.05
Saving thresholded output to  lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.masked.mgh
Saving cluster numbers to lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh
Saving cluster pval lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh
Constructing output annotation
Writing annotation lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.annot
mri_segstats --seg lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --exclude 0 --i lh.sv2a.group.thickness.10.mgh --avgwf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.13158

$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd 
cmdline mri_segstats --seg lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh --exclude 0 --i lh.sv2a.group.thickness.10.mgh --avgwf lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.13158 
sysname  Linux
hostname tauruspet.med.yale.edu
machine  x86_64
user     am2359
UseRobust  0
Loading lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.ocn.mgh
Loading lh.sv2a.group.thickness.10.mgh
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found   2 segmentations
Computing statistics for each segmentation

Reporting on   1 segmentations
Using PrintSegStat
Computing spatial average of each frame
  0
Writing to lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.y.ocn.dat
mri_segstats done
mri_convert lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --frame 0
mri_convert.bin lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh --frame 0 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
keeping frame 0
writing to lh.sv2a_group.glmdir.10/sv2a_thickness_group/perm.th20.abs.sig.cluster.mgh...
Fri Mar 2 03:23:25 EST 2018
Fri Mar  2 03:43:50 EST 2018
mri_glmfit-sim done
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