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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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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