Thanks for your reply. it is a just a normal mri analysis, but I want to compare the subcortical volume and Cortical thinkness between PD dementia patient and healthy control group. I only got the t1image.
---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, ÄÝ 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, ÄÝ 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, ÄÝ 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, ÄÝ wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hello FreeSurfer Developers,
>>> >
>>> > I didn't cache the data during recon-all, so I ran the
>>> >
>>> > > following:
>>> >
>>> > >
>>> >
>>> > > mris_preproc ¨Cfsgd 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
>>> >
>>> >
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>>
>>
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>
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