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

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?