that looks okay. What about the last two lines?
On Thu, 17 Apr 2008, Sky
Raptentsetsang wrote:
Hi Bruce,
Here are the first few lines of the lh.cortex.label:
#label , from subject ??
149955
==>/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_a
nd_S_occipital_inferior.label <==
161841 -37.845 -74.578 -13.988 0.000000
161842 -37.786 -74.111 -14.300 0.000000
161843 -37.811 -73.715 -14.628 0.000000
161844 -37.907 -73.352 -14.952 0.000000
161865 -37.824 -71.907 -13.407 0.000000
161867 -37.788 -71.373 -13.692 0.000000
161868 -38.012 -72.139 -13.895 0.000000
161869 -38.155 -72.375 -14.413 0.000000
161870 -38.143 -72.648 -14.845 0.000000
161871 -38.084 -72.975 -15.268 0.000000
==>/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_a
nd_S_transverse_frontopolar.label <==
146036 -10.156 67.319 -1.698 0.000000
146037 -9.764 67.608 -2.021 0.000000
146038 -9.389 67.908 -2.304 0.000000
146039 -8.876 67.922 -0.865 0.000000
146040 -8.929 68.036 -1.708 0.000000
146041 -9.014 68.059 -2.603 0.000000
146042 -8.649 68.148 -2.940 0.000000
146043 -8.286 68.109 -3.301 0.000000
146044 -7.962 67.947 -3.652 0.000000
146045 -7.753 67.564 -3.208 0.000000
At 06:05 PM 4/16/2008, Bruce Fischl wrote:
Hi Sky,
what are the first few lines of:
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
is your partition full?
Bruce
On Wed, 16 Apr 2008, Sky Raptentsetsang wrote:
Hello Freesurfers,
I am having troubles analyzing some data in the
qdec tool. I have two
groups of the same subjects that were run with
different versions of FS
and I have put them in the same SUBJECTS_DIR and
smoothed and created an
average subject. I have made a qdec.table.dat
file and the appropriate
.levels files. The qdec.table.dat file seems to
load okay but once I try
to run an analysis i get the attached error
messages.
Any ideas on where this error is coming from? It
is stating that the
error is coming from a line in text that I don't
think exists.
(I have also included the qdec.table.dat)
erorr.log:
mri_glmfit: could not parse 149955th line in
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
Command print out:
[EMAIL PROTECTED] subjects]$ qdec &
[1] 20069
[EMAIL PROTECTED] subjects]$ Using Freesurfer version
4.
Subjects Directory is
/cind/00/FSv4Test/Freesurfer/subjects
Sessions Directory is /home/sky/sessions
Reading /opt/freesurfer4.0.2/lib/tcl/tkUtils.tcl
Using /opt/freesurfer4.0.2/lib/tcl/fsgdfPlot.tcl
Loading data table
/cind/00/FSv4Test/Freesurfer/subjects/qdec.table.dat...
Number of columns: 5
fsid column: 1
Number of factors: 4
Number of subjects: 68
.
.
.
.
.
$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19
nicks Exp $
cwd /cind/00/FSv4Test/Freesurfer/subjects
cmdline mri_glmfit --y
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh
--fsgd
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/qdec.fsgd
--glmdir
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version
--surf average lh --label
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label--C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Avg
-In
tercept-thickness.mat--C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Dif
f-v
3-v4-Intercept-thickness.mat
sysname Linux
hostname polaris.v21.med.va.gov
machine x86_64
user sky
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh
logyflag 0
usedti 0
FSGD
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/qdec.fsgd
labelmask
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
maskinv 0
glmdir
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version
DoFFx 0
Creating output directory
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version
Loading y from
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh
Matrix condition is 1
mri_glmfit: could not parse 149955th line in
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
ERROR reading
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
Error in Analyze: command failed: mri_glmfit --y
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh
--fsgd
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/qdec.fsgd
--glmdir
/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version
--surf average lh --label
/cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label--C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Avg
-In
tercept-thickness.mat--C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Dif
f-v
3-v4-Intercept-thickness.mat
Thanks in advance.
Sky Raptentsetsang
Staff Research Associate
CIND, San Francisco VAMC
Department of Radiology, UCSF
4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop
114M
San Francisco, CA 94121
Phone 415.221.4810 ext. 4186
Fax 415.386.3954
Sky Raptentsetsang
Staff Research Associate
CIND, San Francisco VAMC
Department of Radiology, UCSF
4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M
San Francisco, CA 94121
Phone 415.221.4810 ext. 4186
Fax 415.386.3954
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