Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

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

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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/>

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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.

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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

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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

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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

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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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Group level T map
by Lauri Tuominen 19 Feb '19

19 Feb '19

External Email - Use Caution Dear freesurfers, I am trying to find a t-map for my group level test. In a one sample group mean test folder I have: gamma.nii.gz gammavar.nii.gz cnr.nii.gz sig.nii.gz F.nii.gz The gamma.nii.gz corresponds to the beta.nii.gz from the folder above, which I take means that it is the beta coefficient map. Which one would be the t-value map or should I calculate this separately? Thank you so much!! Lauri Tuominen

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

19 Feb '19

External Email - Use Caution For more than 3 hours ---Original--- From: "Greve, Douglas N.,Ph.D."<DGREVE(a)mgh.harvard.edu> Date: Fri, Feb 15, 2019 20:03 PM 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

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Freesurfer February 2019