The Freesurfer version we have installed is 5.1.0 if that helps.
Best,
Jeremy
---
Dear all,
I'm trying to get thickness spc stats for the individual lobe labels
(specifically the frontal lobe) I created per subject per time point (in
subject's longitudinal analysis template space) using:
mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes
I've run mris_anatomical_stats to get out the stats and put them in each
subject and time point's stats folder:
mris_anatomical_stats -a lobes.annot -f $i/stats/lh.lobes.stats $i ?h
Now I'm trying to calculate the spc using:
long_stats_slopes --qdec long.qdec.table.dat --stats lh.lobes --meas
thickness --do-spc --time years --out-spc lh.spc.lobes.txt
but I'm getting an error (it works when I use the regular aparc and aseg
stats files though). Here's my output:
---
Parsing the qdec table: long.qdec.table.dat
Working in SUBJECTS_DIR: /home/j/jy/jy72/scratch/AE/FSstruct/
Subject-Template: CISC4962plate
INFO: 2 TPs in CISC4962plate , mean age: 0.565
aparcstats2table --common-parcs --hemi lh --parc lobes --subjects
CISC4962.long.CISC4962plate CISC4962-2.long.CISC4962plate --meas
thickness --tablefile
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
-d space
SUBJECTS_DIR : /home/j/jy/jy72/scratch/AE/FSstruct/
Parsing the .stats files
Building the table..
Writing the table to
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
Writing ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat ...
mri_glmfit --table
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
--X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat
--allow-zero-dof --no-contrasts-ok --glmdir
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /mnt/lustre/scratch/jeremy/AE/FSstruct/qdec
cmdline mri_glmfit --table
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
--X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat
--allow-zero-dof --no-contrasts-ok --glmdir
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
sysname Linux
hostname apollo-login
machine x86_64
user jy72
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
logyflag 0
X ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/X-long.mat
usedti 0
glmdir ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm
Loading y from
/mnt/lustre/scratch/jeremy/AE/FSstruct/qdec/tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-stack.dat
Found 6 data colums
Found 2 data rows
Saving design matrix to
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1.76991
search space = 6.000000
DOF = 0
Starting fit and test
Fit completed in 0 minutes
Writing results
lh.lobes.thickness
lh_frontal_thickness
lh_cingulate_thickness
lh_occipital_thickness
lh_temporal_thickness
lh_parietal_thickness
lh_insula_thickness
mri_glmfit done
mri_convert --frame 0
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
mri_convert --frame 0
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 0
writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh...
mri_convert --frame 1
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
mri_convert --frame 1
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/glm/beta.mgh...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
keeping frame 1
writing to ./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh...
mris_calc -o
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/long.lh.lobes.thickness-spc.dat.mgh
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta1.mgh div
./tmp-CISC4962plate_lh.lobes_thickness_Hal4Vg/beta0.mgh
ERROR: mris_calc compute sym. pct. change (spc) problem?
---
Am I missing a step somewhere when trying to do this? Please help.
Thanks!
Jeremy
--
Jeremy Young
PhD Researcher
Behavioural and Clinical Neuroscience
School of Psychology
University of Sussex
Brighton
BN1 9QH
01273 872776
J.Young at sussex.ac.ukhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer