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.htmlby 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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