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.htmlb... 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
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?