Instead of --2spaces, use --bonferroni 2

On 5/26/16 10:30 AM, Hao wen wrote:

Hello:

Freesurfers, follow the tutorial '

FsTutorial
GroupAnalysis', my task is to find the thickness differences between groups(Controls(30) & AD(30)), and it works well for the first part which is to fit the linear model and get the uncorrected P_values, and I got the expected P-value map, but when I followed the clusterwise correction for multiple comparision, with this command below:

mri_glmfit-sim \

--glmdir lh.gender_age.glmdir \

--cache 4 neg \

--cwp 0.05\

--2spaces

I got two questions:

1) with the flag --2spaces, i got the error that this command not found;

2) also, with or without the --2spaces, after the freeview open, i got another error, which said did not find any volume geometry information in the surface, I googled, and I know Doug has answered in this post:

http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, but I think my freesurfer is the newest version:freesurfer-5.3.0-15052013-x86_64-centos!

As below, these are my command and the output:

§§Command:

export SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/

cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE

mri_glmfit-sim \

--glmdir lh.AD_CN_NO_COVARIATE.glmdir \

--cache 1.3 neg \

--cwp 0.05\

--2spaces

# load the cluster annotation in freeview

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot -viewport 3d

§§Output:

cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir

SURFACE: fsaverage lh

log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log

cd /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE

/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim

--glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

Thu May 26 16:20:39 CEST 2016

Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

wen

setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/

FREESURFER_HOME /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos

Original mri_glmfit command line:

cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir

DoSim = 0

UseCache = 1

DoPoll = 0

DoPBSubmit = 0

DoBackground = 0

DiagCluster = 0

gd2mtx = dods

fwhm = 22.776285

CSD /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd

mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh --csd /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd --mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --vwsig lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.voxel.mgh --sum lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary --ocn lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --oannot lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot --annot aparc --csdpdf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.pdf.dat --cwpvalthresh 0.05 --o lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh --no-fixmni --surf white

Creating CDFs from CSD files

csd->threshsign = -1

thsign = neg, id = -1

version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $

hemi = lh

srcid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh

srcsubjid = fsaverage

srcsurf = white

srcframe = 0

thsign = neg

thmin = 1.3

thmax = -1

fdr = -1

minarea = 0

xfmfile = talairach.xfm

nth = -1

outid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh MGH

ocnid = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh MGH

sumfile = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary

subjectsdir = /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/

FixMNI = 0

Found 149955 vertices in mask

Found 149955 vertices in mask

Found 149955 points in clabel.

------------- XFM matrix (RAS2RAS) ---------------

/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/mri/transforms/talairach.xfm

1.000 0.000 0.000 0.000;

0.000 1.000 0.000 0.000;

0.000 0.000 1.000 0.000;

0.000 0.000 0.000 1.000;

----------------------------------------------------

Reading source surface /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/surf/lh.white

Done reading source surface

Reading annotation /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output//fsaverage/label/lh.aparc.annot

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 = 149955

Done loading source values (nvtxs = 163842)

overall max = 8.58718 at vertex 22205

overall min = -1.57802 at vertex 24019

surface nvertices 163842

surface area 65417.097656

surface area 65416.648438

Computing voxel-wise significance

CSDpvalMaxSigMap(): found 0/163842 above 0

Adjusting threshold for 1-tailed test.

If the input is not a -log10(p) volume, re-run with --no-adjust.

Searching for Clusters ...

thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=-1, minarea=0.000000

Found 2 clusters

Max cluster size 132.153870

Pruning by CW P-Value 0.05

Saving thresholded output to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh

Saving cluster numbers to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh

Saving cluster pval lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh

Constructing output annotation

Writing annotation lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot

mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2688

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $

cwd

cmdline mri_segstats --seg lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh --exclude 0 --i /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh --avgwf lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.2688

sysname Linux

hostname HP1973

machine x86_64

user wen

UseRobust 0

Loading lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh

Loading /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE/lh.AD_CN_NO_COVARIATE.thickness.15.mgh

Voxel Volume is 1 mm^3

Generating list of segmentation ids

Found 1 segmentations

Computing statistics for each segmentation

Reporting on 0 segmentations

Computing spatial average of each frame

Writing to lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.y.ocn.dat

mri_segstats done

mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --frame 0

mri_convert lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --frame 0

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.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 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh...

Thu May 26 16:20:39 CEST 2016

Thu May 26 16:20:45 CEST 2016

mri_glmfit-sim done

./cluster_wise_correction_for_multiple_comparisons.sh: line 23: --2spaces: command not found

Did not find any volume geometry information in the surface

p?CBreading colortable from annotation file...

colortable with 1 entries read (originally none)

colortable with 1 entries read (originally none)

CTABisEntryValid: index -1 was OOB

Resource temporarily unavailable

Resource temporarily unavailable

B

ginally none)

CTABisEntryValid: index -1 was OOB

Resource temporarily unavailable

Resource temporarily unavailable

B

ginally none)

CTABisEntryValid: index -1 was OOB

Resource temporarily unavailable

Resource temporarily unavailable

B

ginally none)

CTABisEntryValid: index -1 was OOB

Resource temporarily unavailable

Resource temporarily unavailable

B

ginally none)

Can you give me some answer? Thank you very much!
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