What is spc? doug
On 02/04/2014 07:18 AM, Jeremy Young wrote:
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.uk https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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