Yes, one more question where can I get the example of mri glimfit for ROI analysis
---Original---
From: "Greve, Douglas N.,Ph.D."<DGREVE@mgh.harvard.edu>
Date: Tue, Feb 19, 2019 22:47 PM
To: "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>;
Subject: Re: [Freesurfer] commends of GLM for volume
You can get the volumes of structures, eg, hipocampal volume, for each
structure and subject using asegstats2table, then mri_glmfit can read in
that table. But it is an ROI analysis, not a voxel-wise analysis. Is
that what you want to do?
On 2/19/19 5:20 PM, 콜 wrote:
>
> External Email - Use Caution
>
> Or I can not use mri to do the Glm for subcortical volume analysis ?
>
> ---Original---
> *From:* "Greve, Douglas N.,Ph.D."<DGREVE@mgh.harvard.edu>
> *Date:* Tue, Feb 19, 2019 21:29 PM
> *To:* "freesurfer@nmr.mgh.harvard.edu"<freesurfer@nmr.mgh.harvard.edu>;
> *Subject:* Re: [Freesurfer] commends of GLM for volume
>
> IIs this an fMRI analysis? If so, you should use permutation for both
> surface and subcort. See
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLevelPerm
>
> On 2/19/19 6:00 AM, 콜 wrote:
> >
> > External Email - Use Caution
> >
> > 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
> >
> >
> > ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi
> > NVtxsWghtVtx Annot
> >
> >
> > 16.960 86488 4544.63 15.7-77.36.70.000200.000000.00040
> > 789115125.67pericalcarine
> >
> >
> > 23.529158070 3287.33 55.0-52.98.20.000200.000000.00040
> > 679611225.54inferiorparietal
> >
> >
> > 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858
> > 4399.15parsorbitalis
> >
> > 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
> >
> >
> > sysnameDarwin
> >
> >
> > hostname dyn3199-104.wlan.ic.ac.uk
> >
> >
> > machinex86_64
> >
> >
> > usercengzhou
> >
> >
> > FixVertexAreaFlag = 1
> >
> >
> > UseMaskWithSmoothing1
> >
> >
> > OneSampleGroupMean 0
> >
> >
> > y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh
> >
> >
> > logyflag 0
> >
> >
> > usedti0
> >
> >
> > 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
> >
> >
> > 1.000000.000000.000000.00000;
> >
> >
> > 0.000001.000000.000000.00000;
> >
> >
> > 0.000000.000001.000000.00000;
> >
> >
> > 0.000000.000000.000001.00000;
> >
> >
> > ----------------------------------------------------
> >
> >
> > 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
> >
> torh.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
> >
> >
> > sysnameDarwin
> >
> >
> > hostname dyn3199-104.wlan.ic.ac.uk
> >
> >
> > machinex86_64
> >
> >
> > usercengzhou
> >
> >
> > UseRobust0
> >
> >
> > 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
> >
> >
> > Found39 segmentations
> >
> >
> > Computing statistics for each segmentation
> >
> >
> >
> > Reporting on38 segmentations
> >
> >
> > Using PrintSegStat
> >
> >
> > Computing spatial average of each frame
> >
> >
> > 0123456789 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, 콜 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, 콜 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, 콜 wrote:
> >>> >
> >>> > External Email - Use Caution
> >>> >
> >>> > Hello FreeSurfer Developers,
> >>> >
> >>> > I didn't cache the data during recon-all, so I ran the
> >>> >
> >>> > > following:
> >>> >
> >>> > >
> >>> >
> >>> > > mris_preproc 쭯fsgd PDDvsHC.fsgd --target fsaverage
> >>> >
> >>> > > --hemi lh
> >>> >
> >>> > > --meas thickness --out lh.MMSE-AD.thickness.00.mgh
> >>> >
> >>> > >
> >>> >
> >>> > > It seemed to run smoothly (I've attached the log
> >>> below)
> >>> >
> >>> > > so I
> >>> >
> >>> > > ran the next step:
> >>> >
> >>> > >
> >>> >
> >>> > > mri_surf2surf --hemi lh --s fsaverage --sval
> >>> >
> >>> > > lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex
> --tval
> >>> >
> >>> > > lh.PDDvsHC.thickness.10.mgh
> >>> >
> >>> > >
> >>> >
> >>> > > I got the following error:
> >>> >
> >>> > >
> >>> >
> >>> > > Reading source surface reg
> >>> >
> >>> > >
> >>> >
> >>> > > freesurfer/subjects/fsaverage/surf/lh.sphere.reg
> >>> >
> >>> > > Loading source data
> >>> >
> >>> > >
> >>> >
> >>> > >
> >>> >
> >>> >
> >>>
> mghRead(/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
> >>> >
> >>> >
> >>> > _______________________________________________
> >>> > Freesurfer mailing list
> >>> > Freesurfer@nmr.mgh.harvard.edu
> >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
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