Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

[All] postdoctoral position in PET imaging available at MGH / Martinos Center
by Bruce Fischl 22 Feb '19

22 Feb '19

Postdoctoral position in integrated PET/MRI at Massachusetts General Hospital / Harvard Medical School The Loggia and Hadjikhani Labs are inviting applications for a Post-Doctoral Research Fellow in the Department of Radiology at Massachusetts General Hospital (A.A. Martinos Center for Biomedical Imaging) and Harvard Medical School. The candidate will use state-of-the-art integrated PET/MRI scanners to image neuroinflammation in the central nervous systems of migraine patients, and the effect of nonpharmacological therapies. The candidate will collaborate with Dr. Julie Price and several other members of the Martinos Center. Requirements include a Ph.D. in Neuroscience, Physics, Chemistry, Engineering, or a related field, as well as good command of written and oral English. Experience with Positron Emission Tomography is preferred. Compensation is competitive and commensurate with experience. If interested, please email Marco Loggia (marco(a)nmr.mgh.harvard.edu) with your CV. _______________________________________________________ Marco L. Loggia, PhD Assistant Professor of Radiology, Harvard Medical School Associate Director, Center for Integrative Pain NeuroImaging (CiPNI) A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth Street, Room 2301 Charlestown, MA 02129 Phone: (617) 643-7267 Fax: (617) 726-7422 Email: marco.loggia(a)mgh.harvard.edu Web: http://scholar.harvard.edu/loggia _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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Templates used for eTIV computation in recon-all
by Ami Tsuchida 22 Feb '19

22 Feb '19

External Email - Use Caution Dear experts, We were comparing recon-all output of Freesurfer 5.3 and 6.0 in our database, and found that eTIV values can increase by up to 40% going from 5.3 to 6.0. However, closer inspection revealed that it was not due to the version per se, but how we call recon-all. We had computed one version with recon-all -all, and the other with recon-all -autorecon1, thinking that eTIV output from these two were identical. Some testing in two versions with two flags showed that in both versions, using -all flag automatically add --atlas 3T18yoSchwartzReactN32_as_orig in the talairach_avi command, while -autorecon1 does not. The talairach_avi.log indicates that the former set the target to 3T18yoSchwartzReactN32_as_orig, while the latter use the 711-2C_as_mni_average_305. My first question is, is this some kind of bug or is it intentional? We thought that the difference in the templates caused the change in the estimates, but it looks like that's not the only answer: We still get very different eTIV values from -autorecon1 option in FS5.3 and 6.0, even though the target images are the same. The results from -all option are more comparable. Here is the eTIV from one subject we tested: -FS5, autorecon1: 1318267 -FS6, autorecon1: 1561456 -FS5, -all: 1662005 -FS6, -all:1678336 Here I attached the shortened recon-all log files from two versions of Freesurfer, with with -all or -autorecon1, as well as eTIV output from the four variations we tested in one subject. Could you help us resolve why we get the varying estimates? Thank you!

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Re: [Freesurfer] commends of GLM for volume
by 妮 22 Feb '19

22 Feb '19

External Email - Use Caution Yes, one more question where can I get the example of mri glimfit for ROI analysis ---Original--- From: "Greve, Douglas N.,Ph.D."<DGREVE(a)mgh.harvard.edu> Date: Tue, Feb 19, 2019 22:47 PM To: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)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, 妮 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(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 > > _______________________________________________ > 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 1

dt_recon registration check
by Daniel Davidson Callow 22 Feb '19

22 Feb '19

External Email - Use Caution Hello, I have run through dt_recon and want to use anatomically based segmentations (aseg) to create ROIs for the diffusion-weighted data using mri_vol2vol. I ran mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv --interp nearest --o $subj_dir/dtrecon/${subj}.${cond}./aparc+aseg2diff.nii.gz --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg Which worked. I now want to quality check and make sure the ROIs I make from the aseg2diff segmentation is accurately aligned in diffusion space (such as making sure the hippocampal ROIs for aseg are actually going to overlay the hippocampal region of the diffusion data). My question is what is the best way to quality check for quality registration between the diffusion and anatomical data? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park dcallow(a)umd.edu <dcallow(a)gmail.com> 443-254-6298

2 1

PETSurfer: Needs for gtmseg
by Matthieu VANHOUTTE 22 Feb '19

22 Feb '19

External Email - Use Caution Dear FS's experts, In the perspective of correcting generated surfaces errors or defects, does the gtmseg command need corrected surfaces or could it be launch independently before having these corrected surfaces ? Best, Matthieu

2 1

Registering from subjects to a common volume
by Tim Schäfer 22 Feb '19

22 Feb '19

External Email - Use Caution Dear list, I would like to register volume data from several subjects to a common volume, e.g., the volume of the fsaverage subject. The volume data contains some marked voxels and is in the same space as the orig.mgz of the respective subject. I would like to find/see the positions of the voxels in a volume like $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz. This would require a non-linear, inter-subject registration I guess. How can I do this in FreeSurfer? Most likely I can somehow use mri_vol2vol to achieve this, but I don't see how. Is the talairach transform what I want? -- Tim

2 2

Recon-all XL defect detected...
by Matthieu VANHOUTTE 22 Feb '19

22 Feb '19

External Email - Use Caution Dear Freesurfer's experts, I have run recon-all on one subject and it stopped with a "XL defect detected..." (please see below the log): /#@# Fix Topology lh Sat Feb 16 08:22:31 CET 2019// // // mris_fix_topology -rusage /FS6.0.1/awellv3s013/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 awellv3s013 lh // // //reading spherical homeomorphism from 'qsphere.nofix'// //using genetic algorithm with optimized parameters// //setting seed for random number genererator to 1234// // //*************************************************************// //Topology Correction Parameters// //retessellation mode: genetic search// //number of patches/generation : 10// //number of generations : 10// //surface mri loglikelihood coefficient : 1.0// //volume mri loglikelihood coefficient : 10.0// //normal dot loglikelihood coefficient : 1.0// //quadratic curvature loglikelihood coefficient : 1.0// //volume resolution : 2// //eliminate vertices during search : 1// //initial patch selection : 1// //select all defect vertices : 0// //ordering dependant retessellation: 0// //use precomputed edge table : 0// //smooth retessellated patch : 2// //match retessellated patch : 1// //verbose mode : 0// // //*************************************************************// //INFO: assuming .mgz format// //$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $// // $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $// //before topology correction, eno=-112 (nv=135382, nf=270988, ne=406482, g=57)// //using quasi-homeomorphic spherical map to tessellate cortical surface...// // //Correction of the Topology// //Finding true center and radius of Spherical Surface...done// //Surface centered at (0,0,0) with radius 100.0 in 10 iterations// //marking ambiguous vertices...// //39303 ambiguous faces found in tessellation// //segmenting defects...// //22 defects found, arbitrating ambiguous regions...// //analyzing neighboring defects...// // -merging segment 16 into 2// //21 defects to be corrected // //0 vertices coincident// //reading input surface FS6.0.1/awellv3s013/surf/lh.qsphere.nofix...// //reading brain volume from brain...// //reading wm segmentation from wm...// //Computing Initial Surface Statistics// // -face loglikelihood: -9.1744 (-4.5872)// // -vertex loglikelihood: -6.3047 (-3.1523)// // -normal dot loglikelihood: -3.6091 (-3.6091)// // -quad curv loglikelihood: -5.8524 (-2.9262)// // Total Loglikelihood : -24.9405// // //CORRECTING DEFECT 0 (vertices=41, convex hull=76, v0=1825)// //After retessellation of defect 0 (v0=1825), euler #=-4 (114791,342427,227632) : difference with theory (-18) = -14 // // //CORRECTING DEFECT 1 (vertices=22, convex hull=53, v0=6219)// //After retessellation of defect 1 (v0=6219), euler #=-3 (114805,342485,227677) : difference with theory (-17) = -14 // // //CORRECTING DEFECT 2 (vertices=19736, convex hull=2755, v0=16117)// //normal vector of length zero at vertex 115020 with 0 faces// //vertex 115020 has 0 face// //XL defect detected...// //No such file or directory// //Linux hpc1.cyceron.fr 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux// // //recon-all -s awellv3s013 exited with ERRORS at Sat Feb 16 10:17:17 CET 2019/ I looked at the ?h.orig.nofix but didn't see anything wrong, despite the fact that these surfaces are very not smooth. What could I do ? Best, Matthieu

2 4

How to get gray matter tissue via freesurfer?
by 潘祖江 22 Feb '19

22 Feb '19

External Email - Use Caution Hi all, I have came across a problem. As we know, by using recon-all command we can get white matter segmentation, but what I need to use is gray matter segmentation, so what could I do to get ideal segmentation? Hope to get response from someone who concerns. Thanks. -- -------------------------------- 潘祖江 Zujiang Pan 清华大学计算机科学与技术 Department of Computer Science and Technology Tsinghua University, 100084 +86 15600487317

2 1

Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
by Yi Leng Fung 22 Feb '19

22 Feb '19

External Email - Use Caution Dear FreeSurfer Developers, Prior to extracting the gray volume numbers of the entorhinal and perirhinal cortex from ?h.BA_exvivo.thresh.stats file, I was examining the entorhinal and perirhinal cortex on the ?h.BA.thresh.annot on Freeview. However, I noted that their locations on the annot file did not correspond to the (non-overlapping) locations indicated by ?h.entorhinal.thresh.label and ?h.perirhinal.thresh.label. I have also loaded the annot files and label files from the fully recon-ed subject named "bert" on Freeview and observed the same mismatch in the labeling. I am curious why this might be the case. I have searched the archive and have not been able to find any similar queries on this, hence it would be of tremendous help if someone could clarify this observation. If it is of interest, I am running freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 on Ubuntu 16.04. Thank you for your assistance and I look forward to hearing from you. Best regards, Yi-Leng

3 16

Issue posting to Freesurfer support
by Daniel Callow 22 Feb '19

22 Feb '19

External Email - Use Caution Hello, I am signed up to post emails to Freesurfer support list < freesurfer(a)nmr.mgh.harvard.edu> which I have cced in this email. However, when I submit my questions they do not seem to show up or go to the listserv. Is there someone I could contact to help with this? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

2 1

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Freesurfer February 2019