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Moving Between Fsaverage Vertexwise Parcellations Without Recon-all?
by Alexander Samir Hatoum 19 Feb '19

19 Feb '19

External Email - Use Caution Hello, I am currently working with the fsaverage7 parcellation and would like to move to a lower resolution brain parcelltation (fsaverage4, 5, or 6 for example). I was wondering if there is a simple way to translate my data without rerunning recon-all? So essentially, is there a way to turn fsaverage7 parcellation into 6 or lower? Best, Alex -- <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Re: [Freesurfer] commends of GLM for volume
by 妮 19 Feb '19

19 Feb '19

External Email - Use Caution Hi, 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(a)mgh.harvard.edu> Date: Tue, Feb 19, 2019 21:29 PM To: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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/FsFastGroupLeve… On 2/19/19 6:00 AM, 妮 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(a)mgh.harvard.edu>; > *Send time:* Saturday, Feb 16, 2019 4:03 AM > *To:* "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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(a)mgh.harvard.edu> >> *Date:* Fri, Feb 15, 2019 19:01 PM >> *To:* "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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(a)mgh.harvard.edu>; >>> *Send time:* Tuesday, Feb 12, 2019 0:41 AM >>> *To:* "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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 Caution >>> > >>> > Hello 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.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(a)nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc
by 妮 19 Feb '19

19 Feb '19

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(a)mgh.harvard.edu> Date: Fri, Feb 15, 2019 19:01 PM To: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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(a)mgh.harvard.edu>; Send time: Tuesday, Feb 12, 2019 0:41 AM To: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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 Caution > > Hello 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.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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 3

average MRI scans
by Vivek Sharma 19 Feb '19

19 Feb '19

External Email - Use Caution I'm working on source reconstruction using MEG data. For which segmented T1 images of MRI scans are required. I use recon -all for individual subjects. Can we have a common average template made from MRI scans of all subjects. If I have MRI scans from 10 subjects, how can I have average template of these 10 scans. -- Vivek

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Artefacts from simultaneous MRI and EEG measurement
by Backhausen, Lea 19 Feb '19

19 Feb '19

External Email - Use Caution Dear FreeSurer experts, we recently did a simultaneous measurement of MRI and EEG in adolescent patients with obsessive-compulsive-disorder. Due to the electrode gel we see image artifacts mostly in parietal and frontal regions (please see attached images). Has anyone experience with these kinds of measurements? Is there a way to fix the artifacts? We are worried that the calculation of eTIV will also be corrupted and we cannot use it to correct for head size in the subcortical structures (which are our ROIs, mostly striatum). Thanks a lot for any advice! Lea ------------------------------ Lea Backhausen Ph.D. Student (M.Sc. Psychology/Neuroscience) Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://www.uniklinikum-dresden.de<http://www.uniklinikum-dresden.de/>

2 1

Qdecrc File
by Hua, Jessica 19 Feb '19

19 Feb '19

External Email - Use Caution Hi FreeSurfer Experts, I am trying to modify my .Qdecrc file in order to run lGI analyses. However, I cannot seem to find it. Do you know where I can find this file? Best, Jessica --- Jessica Hua, M.A.

2 2

surf2vol ERROR
by Barletta, Valeria 19 Feb '19

19 Feb '19

Dear all, I am trying to register surfaces to a volume by this command: mri_surf2vol --subject MS089_R01_29 --hemi rh --rh.MS089_R01_29.subjspace.mgh --hemi lh --surfval lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge combined-CL.nii.gz --trgsubj MS089_R01_29 And am obtaining this error: ERROR: Option --trgsubject unknown That is actually the name of my subject in $FREESURFER_HOME Also, I do not have a registration file so I used the option --trgsubject Is this correct? Why am I getting that error? Thanks, Vale

3 11

Extracting stats from palm results (.mgz)
by Daniel Leopold 19 Feb '19

19 Feb '19

External Email - Use Caution Hi all, Do you have any suggestions on how I could extract stats (e.g., thickness, area, LGI, etc.) from a cluster(s) identified via palm? I've tried mri_label2label in order to turn the palm output .mgz into a paint .label file, but mri_label2label cannot seem to read the .mgz, .mgz.nii (i.e., .mgz mri_converted to .nii), or .mgz.nii.gz files. My inputs to palm are 4D .mgh files, hence the .mgz results, which are in a data-per-vertex format. Here are the errors I get when trying convert/input .mgz and .mgz.nii files: G??M{?Kӭ7?xK/i?Mb4Ե??(???.!?t:6>|???ѧ???+F??c\Ϟ??U}??m?/8q?~ي???\???C??n?h+???~?????}?w*jo???ʵS_??_??w?????????>ԏ??N?no+?8w mri_label2label: could not scan # of lines from label file ERROR reading wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz /<??c9 mri_label2label: could not scan # of lines from label file ERROR reading wordadhd_lgi_cft3.1/wordadhd_lgi_cft3.1_lh_tfce_tstat_cfwep_c4.mgz.nii As a follow-up to this question, is it possible to threshold the input label/cluster map during the mri_label2label process? Given that my palm .mgz results were saved as logp files, I'd like to threshold the maps at 1.301. My assumption is that I'd instead have to do the following: 1) mri_binarize --i ${map} --o ${map}_bin --min 1.301 2) mri_label2label --s fsaverage --srclabel ${map}_bin --trglabel $subjects/${map}_bin.label --regmethod surface --hemi ${hemi} 3) mri_anatomical_stats -l ${map}_bin.label -f label_stats $subjects $hemi 4) aparcstats2table etc. Thank you for your attention and help! With gratitude, Dan

2 1

PETSurfer: Problem with "mri_gtmpvc --no-reduce-fov" + time consuming when using "--psf 0 --no-tfe"
by Matthieu Vanhoutte 19 Feb '19

19 Feb '19

External Email - Use Caution Dear Douglas, I wanted just to compute rescaled PET image without any PVC but following the same process as if I would have applied PVC. Moreover, I didn’t want to reduce FOV with auto mask generated (to still be in the gtmseg space). So I ran the following command: mri_gtmpvc --i PET.lps.nii.gz --reg Pet2T1.register.dof6.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --no-reduce-fov --rbv --o nopvc_nGMcerebpons --threads 4 --rescale 8 47 174 1) However, in the output directory rbv.nii.gz file still had a reduced fov: type: nii dimensions: 297 x 381 x 363 voxel sizes: 0.500000, 0.500000, 0.500000 type: FLOAT (3) fov: 148.500 Compared to the gtmseg.mgz: type: MGH dimensions: 334 x 452 x 424 voxel sizes: 0.500000, 0.500000, 0.500000 type: INT (1) fov: 226.000 I tried also to remove the —auto-mask option without success. Did I miss something? 2) I wonder why the process took so much time while there is just a rescaling to apply when using --psf 0 --no-tfe? Best, Matthieu

2 1

Difference between target surface and target of registration file in mri_surf2surf
by Alon Baram 19 Feb '19

19 Feb '19

External Email - Use Caution Hello, I am trying to understand some code I came across and am having trouble understanding the difference between the target surface in mri_surf2surf and the surface used as target for the registration. The code first uses freesurfer_registerXhem register the subject's right hemisphere to the left and register both hemispheres to fsaverage_sym, producing the registration file fsaverage_sym.sphere.reg. I then use the following command: mri_surf2surf --srcsubject $subj --hemi lh --trgsubject ico --trgicoorder 7 --surfreg fsaverage_sym.sphere.reg --srcsurfval temp.curv --src_type curv --trgsurfval tempN.curv --trg_type curv --mapmethod nnf --nsmooth-out 1 to resample the registered subject surface to ico7. To my understanding, ico7 is exactly the same as fsaverage, but fsaverage is not exactly the same as fsaverage_sym. So I find it strange that the code is using a registration file which is registered to one surface (fsaverage_sym) with a different target surface (fsaverage). I'm not sure which space the result will actually be in - fsaverage or fsaverage_sym? I'm obviously missing something basic here. Thanks very much for the help! Alon

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