External Email - Use Caution
Thank you for your confirmation! I tried the -perm as well and this error
wouldn't show after using the csd files generated from permutation.
However, I have one more question. Shall I use -perm first in order to use
-cache? If this is the case, the pial_lgi features went through well using the
permutation, but once I tried -cache afterward, it showed the error as below
with fwhm larger than 30, is there something wrong with the design? I don't
understand quite much how this fwhm became this large by the way.
Thank you so much!
cmdline mri_glmfit --y sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.mgh --fsgd
sAnalysis/g2v2DSleepiness.fsgd dods --C sAnalysis/g1g2.sleepscore.mtx --surf
fsaverage rh --cortex --glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir
--eres-save
SURFACE: fsaverage rh
log file is
sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir/cache.mri_glmfit-sim.log
cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir --cache 4 pos --cwp
0.05 --2spaces
mri_glmfit-sim 7.1.0
Wed Jan 13 14:08:23 CST 2021
Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40
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/rh.pial_lgi.g2v2DSleepiness.10.mgh --fsgd
sAnalysis/g2v2DSleepiness.fsgd dods --C sAnalysis/g1g2.sleepscore.mtx --surf
fsaverage rh --cortex --glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir
--eres-save
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 36.436322
ERROR: cannot find
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd
Regards,
Xiaoxu
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Wednesday, January 13, 2021 9:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error with no csd files generated
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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