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Hello developer, I am glad to tell you that after 3 hours, something did print more on terminal. when I was doing the GLM follow the tutorial, it only provided the example of the cortical thickness. And I did not know how to transfer it into volume. Thanks so much for your help Here is my commends
mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.PDDvsHC.volume.10.mgh
mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir lh.volume.PDDvsHC.glimdir --eres-save
mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3pos --cwp 999 --2spaces
We I check the results, it still talked about the cortical thickness , so could you tell me how to change this commends to the volume of subcortical. Or do you have the example which use GLM for comparing the difference of subcortical volume between two groups.
Thanks so much for your help
Yours
Zeng
Here is the results
ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot
1 6.960 86488 4544.63 15.7 -77.3 6.7 0.00020 0.00000 0.00040 7891 15125.67 pericalcarine
2 3.529 158070 3287.33 55.0 -52.9 8.2 0.00020 0.00000 0.00040 6796 11225.54 inferiorparietal
3 2.630 67804 1909.67 43.3 45.8 -9.3 0.00220 0.00140 0.00300 2858 4399.15 parsorbitalis
Here is the terminal output.
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Volumes/NIU20/volumetric_FS/glm
cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save
sysname Darwin
hostname dyn3199-104.wlan.ic.ac.uk
machine x86_64
user cengzhou
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y /Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
logyflag 0
usedti 0
FSGD FSGD/PDDvsHC.fsgd
labelmask /Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.PDDvsHC.volume.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
ResidualFWHM 14.826153
SearchSpace 73852.172969
anattype surface
cd /Volumes/NIU20/volumetric_FS/glm
/Applications/freesurfer/bin/mri_glmfit-sim
--glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Mon Feb 18 15:52:07 GMT 2019
Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: Wed Jul 2902:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64
cengzhou
setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm
FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line:
cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 14.506572
CSD /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd
mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh --mask rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh --sum rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary --ocn rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 999 --o rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh --no-fixmni --csd /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd --csdpdf rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat --vwsig rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh --vwsigmax rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat --oannot rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot --bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = 1
thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.57.2.32016/11/17 18:19:42 zkaufman Exp $
hemi = rh
srcid = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = pos
thmin = 1.3
thmax = -1
fdr = -1
minarea = 0
Bonferroni = 2
xfmfile = talairach.xfm
nth = -1
outid = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh MGH
ocnid = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh MGH
sumfile = rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary
subjectsdir = /Volumes/NIU20/volumetric_FS/glm
FixMNI = 0
Found 148399 vertices in mask
Found 148399 vertices in mask
Found 148399 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/Volumes/NIU20/volumetric_FS/glm/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 /Volumes/NIU20/volumetric_FS/glm/fsaverage/surf/rh.white
Done reading source surface
Reading annotation /Volumes/NIU20/volumetric_FS/glm/fsaverage/label/rh.aparc.annot
Computing metric properties
Loading source values
number of voxels in search space = 148399
Done loading source values (nvtxs = 163842)
overall max = 6.96049 at vertex 86488
overall min = -2.5107 at vertex 20214
surface nvertices 163842
metric props tot surface area 65020.839844
group_avg_vtxarea_loaded 1
masked surface area 75706.343750
Computing voxel-wise significance
CSDpvalMaxSigMap(): found 7717/163842 above 0, max=2.18117
Adjusting threshold for 1-tailed test.
If the input is not a -log10(p) volume, re-run with --no-adjust.
thminadj = 0.99897
Searching for Clusters ...
thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000
Found 38 clusters
Max cluster size 4544.626465
Pruning by CW P-Value 999
Saving thresholded output to rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh
Saving cluster numbers to rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh
Saving cluster pval rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh
Constructing output annotation
Writing annotation rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot
mri_segstats --seg rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh --exclude 0 --i rh.PDDvsHC.volume.10.mgh --avgwf rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.40924
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --seg rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh --exclude 0 --i rh.PDDvsHC.volume.10.mgh --avgwf rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.40924
sysname Darwin
hostname dyn3199-104.wlan.ic.ac.uk
machine x86_64
user cengzhou
UseRobust 0
Loading rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh
Loading rh.PDDvsHC.volume.10.mgh
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 39 segmentations
Computing statistics for each segmentation
Reporting on 38 segmentations
Using PrintSegStat
Computing spatial average of each frame
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
Writing to rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.y.ocn.dat
mri_segstats done
mri_convert rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh --frame 0
mri_convert.bin rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh --frame 0
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.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 rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh...
Mon Feb 18 15:52:07 GMT 2019
Mon Feb 18 15:52:12 GMT 2019
mri_glmfit-sim done