When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD files as found in $FREESURFER_HOME/average/mult-comp-cor
On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:
External Email - Use Caution Dear Freesurfer Experts,
I’ve all the subjects successfully done recon-all, lgi before coming to the group analysis. The following group analysis will use the 10mm smoothing as generated in previous recon-all. Mris_preproc were implemented successfully and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed done finally, but when going back to the directory, I found out no csd files have ever been generated, and this was reported as well during the mri_glmfit-sim run. Please kindly see the log as below for details. The error was reported in the middle, so I changed it into red. It’s quite appreciated it you may help on this. Thanks a lot!
$ mri_glmfit-sim \
--glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \ --cache 4 neg \ --cwp 0.05 \ --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir SURFACE: fsaverage lh log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log
cd /home/xiaoxu/8YearOldNiiB1 /home/xiaoxu/freesurfer/bin/mri_glmfit-sim --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 --2spaces
mri_glmfit-sim 7.1.0 Tue Jan 5 15:11:00 CST 2021 Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux xiaoxu setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1 FREESURFER_HOME /home/xiaoxu/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 20.731766 CSD /home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd mri_surfcluster --in sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh --sum sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary --ocn sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh --no-fixmni --csd-out sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd --csd /home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd --csdpdf sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.pdf.dat --vwsig sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.mgh --vwsigmax sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.max.dat --oannot sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot --bonferroni 2 --surf white Merging CSD files ERROR: could not open sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version 7.1.0 hemi = lh srcid = sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 4 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh MGH ocnid = sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh MGH sumfile = sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary subjectsdir = /home/xiaoxu/8YearOldNiiB1 FixMNI = 0 Found 148772 vertices in mask Found 148772 vertices in mask Found 148772 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /home/xiaoxu/8YearOldNiiB1/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- Reading source surface /home/xiaoxu/8YearOldNiiB1/fsaverage/surf/lh.white Done reading source surface Reading annotation /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.aparc.annot mri_surfcluster supposed to be reproducible but seed not set reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Computing metric properties Loading source values number of voxels in search space = 148772 Done loading source values (nvtxs = 163842) overall max = 2.5813 at vertex 86764 overall min = -4.50366 at vertex 40067 surface nvertices 163842 metric props tot surface area 65417.000000 group_avg_vtxarea_loaded 1 masked surface area 75952.695312 Computing voxel-wise significance CSDpvalMaxSigMap(): found 8194/163842 above 0, max=-0.96614 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. thminadj = 3.69897 Searching for Clusters ... thmin=4.000000 (3.698970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000 Found 2 clusters Max cluster size 296.333069 Pruning by CW P-Value 0.05 Saving thresholded output to sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh Saving cluster numbers to sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh Saving cluster pval sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh Constructing output annotation Writing annotation sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot mri_segstats --seg sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh --exclude 0 --i sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --avgwf sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.53691
7.1.0 cwd cmdline mri_segstats --seg sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh --exclude 0 --i sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --avgwf sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.53691 sysname Linux hostname xnVMUbuntu18 machine x86_64 user xiaoxu whitesurfname white UseRobust 0 Loading sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh Loading sAnalysis/lh.area.g2v3gaCSHQ.10.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 2 segmentations Computing statistics for each segmentation
Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.y.ocn.dat mri_segstats done mri_convert sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh --frame 0 mri_convert sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh --frame 0 reading from sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 0 writing to sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh... Tue Jan 5 15:11:00 CST 2021 Tue Jan 5 15:11:03 CST 2021 mri_glmfit-sim done
Below is the mri_glmfit log. 7.1.0 cwd /home/xiaoxu/8YearOldNiiB1 cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir sysname Linux hostname xnVMUbuntu18 machine x86_64 user xiaoxu FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/xiaoxu/8YearOldNiiB1/sAnalysis/lh.area.g2v3gaCSHQ.10.mgh logyflag 0 usedti 0 FSGD sAnalysis/g2v3gaCSHQ.fsgd labelmask /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.cortex.label maskinv 0 glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir Loading y from /home/xiaoxu/8YearOldNiiB1/sAnalysis/lh.area.g2v3gaCSHQ.10.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 4709.02 Matrix condition is 1e+08 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 148772 voxels in mask Saving mask to sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh Reshaping mriglm->mask... search space = 73961.671829 DOF = 59 Starting fit and test Fit completed in 0.0714833 minutes Computing spatial AR1 on surface Residual: ar1mn=0.997889, ar1std=0.000967, gstd=8.803970, fwhm=20.731766 Writing results g1g2.sscorewithBMI MRImask(): AllowDiffGeom = 1 maxvox sig=-4.50366 F=20.3419 at index 40067 0 0 seed=1610329800 mri_glmfit done
Regards, Xiaoxu
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