Hi (Martin), - version 5.1 (Ubuntu 64b) - command: long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time ISI_years --qcache fsaverage - attached: first 3 lines of qdec table containing the info for subject 11298 - attached: on screen error output. - i have 2 timepoints/subject.
things go awry in the "SUBJECT 11298 Running Within-Subject GLM" step (see attachment): Reshaping mriglm->mask... ERROR: mri_reshape: number of elements cannot change what am i doing wrong? -joost
jjanssen@neurojoost:/media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA$ long_mris_slopes --qdec ./qdec/long.qdec.table.n114.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time ISI_years --qcache fsaverage Parsing the qdec table: ./qdec/long.qdec.table.n114.dat Working in SUBJECTS_DIR: /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA Subject-Template: 11298 INFO: 2 TPs in 11298 , mean age: 0.915 =============================================================================== SUBJECT 11298 Intersecting Within-Subject Cortex Label cp /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298.long.11298/label/lh.cortex.label /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label mris_label_calc intersect /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298_2.long.11298/label/lh.cortex.label /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label LabelWrite: saving to /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label =============================================================================== SUBJECT 11298 mapping label to QCache mri_label2label --srclabel /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label --srcsubject 11298 --trglabel /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label --trgsubject fsaverage --regmethod surface --hemi lh srclabel = /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label srcsubject = 11298 trgsubject = fsaverage trglabel = /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 115366 points in source label. Starting surface-based mapping Reading source registration /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/fsaverage/surf/lh.white Reading target registration /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 115366 nlabel points Performing mapping from target back to the source label Number of reverse mapping hits = 55920 Checking for and removing duplicates Writing label file /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label 171286 LabelWrite: saving to /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.fsaverage.label mri_label2label: Done =============================================================================== SUBJECT 11298 Stackinbg Within-Subject Maps mri_concat /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298.long.11298/surf/lh.thickness /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298_2.long.11298/surf/lh.thickness --o /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh =============================================================================== SUBJECT 11298 Running Within-Subject GLM Writing ./tmp-11298_lh_thickness_FC4k2V/X-long.mat ... mri_glmfit --y /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh --X ./tmp-11298_lh_thickness_FC4k2V/X-long.mat --allow-zero-dof --no-contrasts-ok --surf 11298 lh --label /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label --glmdir ./tmp-11298_lh_thickness_FC4k2V/glm Reading source surface /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.white Number of vertices 127120 Number of faces 254236 Total area 83204.789062 AvgVtxArea 0.654537 AvgVtxDist 0.885641 StdVtxDist 0.257092 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA cmdline mri_glmfit --y /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh --X ./tmp-11298_lh_thickness_FC4k2V/X-long.mat --allow-zero-dof --no-contrasts-ok --surf 11298 lh --label /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label --glmdir ./tmp-11298_lh_thickness_FC4k2V/glm sysname Linux hostname neurojoost machine x86_64 user jjanssen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh logyflag 0 X ./tmp-11298_lh_thickness_FC4k2V/X-long.mat usedti 0 labelmask /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/label/lh.long.cortex.label maskinv 0 glmdir ./tmp-11298_lh_thickness_FC4k2V/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory ./tmp-11298_lh_thickness_FC4k2V/glm Loading y from /media/LA-PUBLIC/REDES_LONGITUDINAL_BRAINVISA/11298/surf/lh.long.thickness-stack.mgh Saving design matrix to ./tmp-11298_lh_thickness_FC4k2V/glm/Xg.dat Normalized matrix condition is 1 Matrix condition is 1.0929 Found 115366 points in label. ERROR: mri_reshape: number of elements cannot change nv1 = 127120, nv1 = 123157 Pruning voxels by thr: 0.000000 Found 117047 voxels in mask Saving mask to ./tmp-11298_lh_thickness_FC4k2V/glm/mask.mgh Reshaping mriglm->mask... ERROR: mri_reshape: number of elements cannot change nv1 = 123157, nv1 = 127120 search space = 83205.454239 DOF = 0 Starting fit and test Fit completed in 0.00323333 minutes Computing spatial AR1 on surface ERROR: MRISar1: Surf/Src dimension mismatch. ERROR -11 : mri_glmfit did not work?
long.qdec.table.n114_3lines.dat
Description: Binary data
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