Hi Keith,
your longitudinal qdec file looks OK. Something must have gone wrong
before (in the processing, e.g. maybe the base was reprocessed and the
longs were not updated or things were renamed?)
I would create a new directory with only this subject, then start from
scratch. create both cross (kp5 and kp5b), the base (kp5_base) and both
longs with the correct naming . Then check if the long_mris_slopes
command still fails.
Best, Martin
On 05/01/2013 12:11 PM, Qi Wu wrote:
Dear Freesurfer experts,
I have a dataset of 2 time points. I ran into problems when I tried to
use the two-stage approach to pull out statistics such as the rate of
change in Freesurfer 5.1.
I could not even get the first stage working. The error messages I got
were "ERROR: MRISar1: Surf/Src dimension mismatch" "ERROR -11 :
mri_glmfit did not work?"
I did further trouble-shooting for this particular message "nv1 =
140942, nv1 = 143525", and I found out that "143525" was in the "base"
folder (kp5_base), and "140942" was for the two longitudinally
registered images (kp5.long.kp5_base, and kp5b.long.kp5_base).
The command line I used was : "long_mris_slopes --qdec
./qdec/AS_long_qdec.dat --meas thickness --hemi lh --do-avg --do-rate
--do-pc1 --do-spc --do-stack --do-label --time weeks --nosmooth".
The first three lines in the qdec file:
"fsid fsid-base weeks age sex FSS avgPain
kp5 kp5_base 0 48 0 4.1 7
kp5b kp5_base 20 48 0 8.6 6"
This error was similar to what was in a previous post
(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024576.html
by joost janssen Jun 29, 2012). I tried to fix any similar problems,
but still wasn't able to get it working.
What else could I have been doing wrong?
The on screen error output is provided as follows
Many thanks
Keith
Postdoctoral fellow
Toronto Western Hospital
Toronto, Ontario
Canada
***********************************
Parsing the qdec table: ./qdec/AS_long_qdec.dat
Working in SUBJECTS_DIR:
/data/keith/freesurferdata/subjects_longitudinal_5.1_old
Subject-Template: kp5_base
INFO: 2 TPs in kp5_base , mean age: 10.0
===============================================================================
SUBJECT kp5_base Intersecting Within-Subject Cortex Label
cp
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/label/lh.cortex.label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
mris_label_calc intersect
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/label/lh.cortex.label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
LabelWrite: saving to
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
===============================================================================
SUBJECT kp5_base Stackinbg Within-Subject Maps
mri_concat
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5.long.kp5_base/surf/lh.thickness
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5b.long.kp5_base/surf/lh.thickness
--o
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
===============================================================================
SUBJECT kp5_base Running Within-Subject GLM
Writing ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat ...
mri_glmfit --y
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
--X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof
--no-contrasts-ok --surf kp5_base lh --label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
--glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm
Reading source surface
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.white
Number of vertices 143525
Number of faces 287046
Total area 91438.851562
AvgVtxArea 0.637094
AvgVtxDist 0.873064
StdVtxDist 0.245806
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /data/keith/freesurferdata/subjects_longitudinal_5.1_old
cmdline mri_glmfit --y
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
--X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat --allow-zero-dof
--no-contrasts-ok --surf kp5_base lh --label
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
--glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm
sysname Linux
hostname davissvr1.uhnres.utoronto.ca
<http://davissvr1.uhnres.utoronto.ca>
machine x86_64
user qwu
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
logyflag 0
X ./tmp-kp5_base_lh_thickness_6PR2rH/X-long.mat
usedti 0
labelmask
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/label/lh.long.cortex.label
maskinv 0
glmdir ./tmp-kp5_base_lh_thickness_6PR2rH/glm
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory ./tmp-kp5_base_lh_thickness_6PR2rH/glm
Loading y from
/data/keith/freesurferdata/subjects_longitudinal_5.1_old/kp5_base/surf/lh.long.thickness-stack.mgh
Saving design matrix to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/Xg.dat
Normalized matrix condition is 1
Matrix condition is 10
Found 131455 points in label.
ERROR: mri_reshape: number of elements cannot change
nv1 = 143525, nv1 = 140942
Pruning voxels by thr: 0.000000
Found 134956 voxels in mask
Saving mask to ./tmp-kp5_base_lh_thickness_6PR2rH/glm/mask.mgh
Reshaping mriglm->mask...
ERROR: mri_reshape: number of elements cannot change
nv1 = 140942, nv1 = 143525
search space = 91439.090793
DOF = 0
Starting fit and test
Fit completed in 0.0042 minutes
Computing spatial AR1 on surface
ERROR: MRISar1: Surf/Src dimension mismatch.
ERROR -11 : mri_glmfit did not work?
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--
Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology - Harvard Medical School
MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.edu
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