Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Glm for volume
by 妮 19 Feb '19

19 Feb '19

External Email - Use Caution Hello developer, 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. Thanks so much for your help 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 1.3pos --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 ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 6.960 86488 4544.63 15.7 -77.3 6.7 0.00020 0.00000 0.00040 7891 15125.67 pericalcarine 2 3.529 158070 3287.33 55.0 -52.9 8.2 0.00020 0.00000 0.00040 6796 11225.54 inferiorparietal 3 2.630 67804 1909.67 43.3 45.8 -9.3 0.00220 0.00140 0.00300 2858 4399.15 parsorbitalis 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 sysname Darwin hostname dyn3199-104.wlan.ic.ac.uk machine x86_64 user cengzhou FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh logyflag 0 usedti 0 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 2902:26:53 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 1.57.2.32016/11/17 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 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- 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 to rh.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 sysname Darwin hostname dyn3199-104.wlan.ic.ac.uk machine x86_64 user cengzhou UseRobust 0 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 Found 39 segmentations Computing statistics for each segmentation Reporting on 38 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 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

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Re: [Freesurfer] zero values when run recon-all with T2pial flag (V6.0)
by Morgan Botdorf 19 Feb '19

19 Feb '19

External Email - Use Caution Thanks for taking a look at the file I sent! I think I have figured out the issue for the most part. While it shows that there is data in the recon-all log for the various cortical regions and eTIV, the data I extracted using aparcstats2table gives me zeros. Part of the problem seems to be that in the table aparcstats2table produces using the Destrieux atlas, some variables are listed twice, but in a different format. For example, frontomarginal thickness is listed as both rh_G_and_S_frontomargin_thickness and as rh_G_&_S_frontomargin_thickness. Some subjects have data for one variable and some for the other variable. This happened for 13 variables. I've attached an excel file with data from 2 subjects that shows the variables that are listed twice and how some subjects have data for some variables and others have data for other variables. Please let me if you have any ideas of why this may have happened. Thanks! Morgan -- Morgan Botdorf, M.S. Graduate Student Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

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recon-all -all
by 妮 19 Feb '19

19 Feb '19

External Email - Use Caution Hello FreeSurfer Developers, when i was run the recon-all -all, sometimes the terminal would show randomSeed 1234, and stop running the process here is my #@# 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: 0.000000 vertex = 112 #-------------------------------------------- #@# 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> i have attached the recon-all log cheers Zeng

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fcseedcor_multiple runs
by Nasiriavanaki, Zahra 19 Feb '19

19 Feb '19

Dear Freesurfers Hi I have been doing seed to seed connectivity analysis using fcseedcor. I have multiple runs for each subject, and based on the fcseedcor help, I am supposed to average runs before comparing across subjects. So, does it mean I should average all seed.dat files and the regressors (including vscf,wm,global waveform, mcprextreg) across runs? I appreciate your time and consideration. Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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partial FoV - registration failure
by Francesca Strappini 19 Feb '19

19 Feb '19

External Email - Use Caution Dear freesurfer experts, I am using freesurfer to analyze some fMRI data collected on two monkeys. My runs have a partial field of view, since just the posterior part of the brain was scanned. Unfortunately, no full-head EPI was collected. The registration between the processed functional data and the T1 is bad. All the values in the register.dof6.mincost file are above 0.8 and also visually I can see some mismatch. I though to run bbregister, could you suggest me which is the best procedure and which steps of the preprocessing I should re-run after? Thanks -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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mris_preproc calling on incorrect target surface
by Bunting, Emma 19 Feb '19

19 Feb '19

External Email - Use Caution Hi Freesurfer Pros, I'm trying to perform mris_preproc with an average subject that I created called 'avgsubject.Patients_EB', as my target. Although it appears to take avgsubject.Patients_EB as the target subject, and VIPD_010 (the first subject in my fsgd file) as the source subject, it then somehow swaps the target and source surfaces (sphere.reg's) it is trying to call upon. I am therefore getting an error because there is no avgsubject.Patients_EB.sphere.reg file within the VIPD_010 subject folder. The commands I use for the mri_preproc are below, with the sections I am referring to highlighted in bold. ebunting@img-140:.../MRI_data/freesurfer$ mris_preproc --fsgd PDonly_Liu_EB.fsgd \ > --target avgsubject.Patients_EB \ > --hemi lh \ > --meas thickness \ > --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh \ > nsubjects = 97 tmpdir is ./tmp.mris_preproc.12493 /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer Log file is lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mris_preproc.log Tue Feb 12 11:20:49 GMT 2019 setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer /var/drc/software/64bit/freesurfer-6.0.0//bin/mris_preproc --fsgd PDonly_Liu_EB.fsgd --target avgsubject.Patients_EB --hemi lh --meas thickness --out lh.PDonly_Liu_AvgSubjectPatients_EB.thickness.00.mgh Linux img-140.drc.ion.ucl.ac.uk 2.6.32-279.el6.x86_64 #1 SMP Wed Jun 13 18:24:36 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.12493 Src lh avgsubject.Patients_EB.sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/97 VIPD_010 Tue Feb 12 11:20:49 GMT 2019 -------------- ----------------------- mri_surf2surf --srcsubject VIPD_010 --srchemi lh --srcsurfreg avgsubject.Patients_EB.sphere.reg --trgsubject avgsubject.Patients_EB --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.12493/VIPD_010.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness --sfmt curv --noreshape --cortex MRISread(/var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg): could not open file Source registration surface changed to avgsubject.Patients_EB.sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer cd /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer mri_surf2surf --srcsubject VIPD_010 --srchemi lh --srcsurfreg avgsubject.Patients_EB.sphere.reg --trgsubject avgsubject.Patients_EB --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.12493/VIPD_010.1.mgh --sval /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname img-140.drc.ion.ucl.ac.uk machine x86_64 user ebunting srcsubject = VIPD_010 srcval = /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.thickness srctype = curv trgsubject = avgsubject.Patients_EB trgval = ./tmp.mris_preproc.12493/VIPD_010.1.mgh trgtype = srcsurfreg = avgsubject.Patients_EB.sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg No such file or directory mri_surf2surf: could not read surface /var/drc/research/visioninpd/home_study_2017_data/MRI_data/freesurfer/VIPD_010/surf/lh.avgsubject.Patients_EB.sphere.reg No such file or directory n.b. that the lh.avgsubject.Patients_EB.sphere.reg file can be found within the avgsubject.Patients_EB/surf folder, so I believe this is an issue of simply mixing the target and source surfaces. It is also worth noting that I have found your bug fix for the make_average_surface script, which now completes without errors. However, the make_average_subject script still completes with errors, and when I try to use the average_surface output as my target I get the same errors. Please let me know if there is something I am doing wrong here, or if there is a way to fix the error I am getting! Many thanks, Emma Bunting

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commends of GLM for volume
by 妮 19 Feb '19

19 Feb '19

External Email - Use Caution ---Original--- From: "妮"<646102581(a)qq.com> Date: Tue, Feb 19, 2019 11:00 AM To: "Greve, Douglas N.,Ph.D."<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Re: commends of GLM for volume Hello developer, 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. Thanks so much for your help 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 ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 6.960 86488 4544.63 15.7 -77.3 6.7 0.00020 0.00000 0.00040 7891 15125.67 pericalcarine 2 3.529 158070 3287.33 55.0 -52.9 8.2 0.00020 0.00000 0.00040 6796 11225.54 inferiorparietal 3 2.630 67804 1909.67 43.3 45.8 -9.3 0.00220 0.00140 0.00300 2858 4399.15 parsorbitalis 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 sysname Darwin hostname dyn3199-104.wlan.ic.ac.uk machine x86_64 user cengzhou FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh logyflag 0 usedti 0 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 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; ---------------------------------------------------- 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 to rh.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 sysname Darwin hostname dyn3199-104.wlan.ic.ac.uk machine x86_64 user cengzhou UseRobust 0 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 Found 39 segmentations Computing statistics for each segmentation Reporting on 38 segmentations Using PrintSegStat Computing spatial average of each frame 0 1 2 3 4 5 6 7 8 9 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

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fixing errors with pial boundary
by Morgan Botdorf 19 Feb '19

19 Feb '19

External Email - Use Caution Dear Freesurfer Experts, We have come across several subjects where the pial boundary line does not extend far enough outward and misses some gray matter. We know that control points can be used to fix a similar issue with white matter boundaries. Are there any tools that can be used to fix this type of gray matter error? Thank you, Morgan Botdorf

2 1

overlay cortical thickness estimates
by forsteca＠hu-berlin.de 19 Feb '19

19 Feb '19

External Email - Use Caution Hello Freesurfer Community, I want to view my cortical thickness estimates (I calculated standard deviations for different subjects) on a 3D file. I thought I could replace the lh.thickness part in the following code by my own estimations: freeview -f \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial:annot=aparc.a2009s.annot:name=pial_aparc_des:visible=0 \ /Datasets/SUBJ_DAY_01_01/surf/lh.inflated:overlay=lh.thickness.asc:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.inflated:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.white:visible=0 \ /Datasets/sSUBJ_DAY_01_01/surf/lh.pial \ --viewport 3d I tried loading a binary mat, as lh.thickness is a binary file as well. I got the following error: couldn't determine type of file Can you clarify what file structure the thickness overlay file should be, so that Freesurfer is able to read the thickness information ? Thank you so much. (addional info: mat file 163842x1 double)

2 1

hippocampal subfield segmentation input mask?
by Malone, Ian 19 Feb '19

19 Feb '19

External Email - Use Caution Dear FreeSurfer list, I'm wondering if there is any way to input different starting segmentations for the hippocampus into the hippocampal subfield segmentation? We've got a hippocampus specific segmentation algorithm which we'd like to try as input to see if it provides a better starting point than whole brain labels. Are there any other inputs we'd need? Best wishes, Ian Malone -- Research Associate Dementia Research Centre Queen Square Institute of Neurology UCL London WC1N 3BG

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Freesurfer February 2019