Dear Martin,

Thank you for your helpful information. You were right that something had gone wrong with my preprocessing (for some unknown reasons). I re-run the preprocessing and was able to get the long_mris_slopes command up-and-running.

Keith

On Wed, May 8, 2013 at 4:28 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:

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.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?

---

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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: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu

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