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Hello Greve, 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. 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 1.3 pos --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 29 02:26:53 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 1.57.2.3 2016/11/17 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
------------------ Original ------------------ From: "Greve, Douglas N.,Ph.D.";DGREVE@mgh.harvard.edu; Send time: Saturday, Feb 16, 2019 4:03 AM To: "freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu;
Subject: Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc
how long?
On 2/15/19 2:49 PM, 妮 wrote:
External Email - Use Caution Hi Thanks for your quickly reply, yes continue to run but not print more on terminal anymore.
---Original--- From: "Greve, Douglas N.,Ph.D."DGREVE@mgh.harvard.edu Date: Fri, Feb 15, 2019 19:01 PM To: "freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu; Subject: Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc
Do you mean that it continues to run but does not do anything (eg, print more to the terminal) or that it has crashed? If it is hanging, how long? Nothing looks suspicious in the output.
On 2/15/19 12:59 PM, 妮 wrote:
External Email - Use Caution Hi Greve, i solved this problem, but had a new one with recon-all, when i run the recon-all data, sometimes it hang in the very last step of the recon-all. here is the related part of output in terminal. i have attached the recon-all log and status log. Have a nice weekend! cheers
#@# Curv .H and .K rh Fri Feb 15 17:30:27 GMT 2019
/Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf
\n mris_curvature -w rh.white.preaparc \n
total integrated curvature = 11.983*4pi (150.582) --> -11 handles
ICI = 180.5, FI = 1886.9, variation=29597.577
writing Gaussian curvature to /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.K...done.
writing mean curvature to /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.H...done.
rm -f rh.white.H
ln -s rh.white.preaparc.H rh.white.H
rm -f rh.white.K
ln -s rh.white.preaparc.K rh.white.K
\n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated \n
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
148 vertices thresholded to be in k1 ~ [-1.38 0.32], k2 ~ [-0.18 0.09]
total integrated curvature = 0.554*4pi (6.968) --> 0 handles
ICI = 1.3, FI = 8.1, variation=139.341
115 vertices thresholded to be in [-0.05 0.02]
writing Gaussian curvature to /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.K...thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
77 vertices thresholded to be in [-0.20 0.15]
done.
writing mean curvature to /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.H...curvature mean = -0.018, std = 0.022
done.
\n#-----------------------------------------
#@# Curvature Stats lh Fri Feb 15 17:31:32 GMT 2019
/Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf
\n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm subject lh curv sulc \n
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/lh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ subject/lh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vertex faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 213 ]
Gb_filter = 0
WARN: S lookup min: -0.021311
WARN: S explicit min: 0.000000 vertex = 907
\n#-----------------------------------------
#@# Curvature Stats rh Fri Feb 15 17:31:38 GMT 2019
/Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf
\n mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm subject rh curv sulc \n
Toggling save flag on curvature files [ ok ]
Outputting results using filestem [ ../stats/rh.curv.stats ]
Toggling save flag on curvature files [ ok ]
Setting surface [ subject/rh.smoothwm ]
Reading surface... [ ok ]
Setting texture [ curv ]
Reading texture... [ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vertex faces... [####################] [ ok ]
Determining KH curvatures... [####################] [ ok ]
Determining k1k2 curvatures... [####################] [ ok ]
deltaViolations [ 257 ]
Gb_filter = 0
WARN: S lookup min: -0.254695
WARN: S explicit min:
@# Sphere lh Fri Feb 15 17:31:44 GMT 2019
/Users/cengzhou/Desktop/volumetric_FS/subject1/subject/scripts
\n mris_sphere -rusage /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere \n
setting seed for random number genererator to 1234
$Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading original vertex positions...
unfolding cortex into spherical form...
surface projected - minimizing metric distortion...
== Number of threads available to mris_sphere for OpenMP = 1 ==
scaling brain by 0.321...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=cengz, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 1234
------------------ Original ------------------ From: "Greve, Douglas N.,Ph.D.";DGREVE@mgh.harvard.edu; Send time: Tuesday, Feb 12, 2019 0:41 AM To: "freesurfer@nmr.mgh.harvard.edu"freesurfer@nmr.mgh.harvard.edu; Subject: Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc
can you send the full mri_surf2surf terminal output?
On 2/11/19 8:08 AM, 妮 wrote:
External Email - Use CautionHello FreeSurfer Developers,
I didn't cache the data during recon-all, so I ran the
following:mris_preproc –fsgd PDDvsHC.fsgd --target fsaverage--hemi lh--meas thickness --out lh.MMSE-AD.thickness.00.mghIt seemed to run smoothly (I've attached the log below)so Iran the next step:mri_surf2surf --hemi lh --s fsaverage --svallh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tvallh.PDDvsHC.thickness.10.mghI got the following error:Reading source surface regfreesurfer/subjects/fsaverage/surf/lh.sphere.regLoading source datamghRead(/Users/cengzhou/Desktop/volumetric_FS/FS/lh.PDDvsHC.thickness.00.mgh, -1): could not open file
recon-all.log: see attached
Platform: mac os 10
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