Freesurfer February 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
196 discussions

Re: [Freesurfer] Problem with freeview in linux subsystem for
by Williamson, Brady 20 Feb '19

20 Feb '19

External Email - Use Caution Hi Falk, Thank you for the reply. Yes, I am running Xming and have set this option in the .bashrc file. I still get the same error. I have tried to research this issue extensively but cannot seem to find the answer. Thanks, Brady

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Re: [Freesurfer] Freesurfer Digest, Vol 180, Issue 5
by Bunting, Emma 20 Feb '19

20 Feb '19

External Email - Use Caution Hi, In response to: Surface to Volume conversion post, Yes, the brains were registered in fsaverage space. The issue I am facing is my sig.mgh output from GLM will not convert into a .nii file using mri_convert. I am trying to load them both as overlays not view them directly. The sig.mgh file loads fine, it is the .nii file that sees the problem. Similarly, if I do GLM directly with a .nii output, I see the same issues. You asked me to run mri_info on both the .mgh and .nii.gz files, which I gave in my previous email. Please let me know how to proceed from here! Best wishes, Emma Bunting ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: 04 February 2019 17:00 To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 180, Issue 5 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. gray matter volume of the entorhinal cortex (Laboratorio de Neurociencia Funcional) 2. Re: problem using recon-all (Shachar Gal) 3. Re: problem using recon-all (Glasser, Matthew) 4. Re: Surface to Volume conversion (Bunting, Emma) 5. Re: gray matter volume of the entorhinal cortex (Bruce Fischl) 6. Re: Surface to Volume conversion (Bruce Fischl) 7. Re: gray matter volume of the entorhinal cortex (Laboratorio de Neurociencia Funcional) 8. free surfer install issues (Jordan Fowler) 9. Re: free surfer install issues (Greve, Douglas N.,Ph.D.) 10. (no subject) (Jordan Fowler) ---------------------------------------------------------------------- Message: 1 Date: Mon, 4 Feb 2019 10:08:06 +0100 From: Laboratorio de Neurociencia Funcional <neuroaginglnf(a)gmail.com> Subject: [Freesurfer] gray matter volume of the entorhinal cortex To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CABUYonO85t9vP8NBw9HtWuET2n4i-9s-Q_LevCxZ_rK3U4YAew(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfers, gray matter volume of the entorhinal cortex (EC) can be obtained either in the ?h.aparc.stats or ?h.BA_exvivo.stats/?h.BA_exvivo.thresh.stats files. Considering that all our T1 images were manually edited on a slice-by-slice basis to correct pial surface misplacements and erroneous white matter segmentation, which volume measure of the EC would be more precise? I assume that gray matter volume contained in ?h.BA_exvivo.thresh.stats were thresholded at a specific probability value (% of case overlapping). Which probability value was used? Is there a reference paper explaining how probabilistic maps of EC were built based on ex vivo MRI contrast? Thank you in advance. Best, Jose L. Cantero

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mri_cc not giving thicker corpus callosum
by DICE Lab 20 Feb '19

20 Feb '19

External Email - Use Caution Dear FreeSurfer Developers, I am trying to run the “mri_cc” command to obtain a segmentation of the corpus callosum (CC) that is thicker then the usual 5mm (i.e. 5 voxel in my image). I would like indeed to cover the "entire" CC volume and label it with the canonical 5 values (let's say at least for the central CC, mid anterior and mid posterior). I tried mri_cc -force -T 30 -aseg aseg.mgz -o aseg.auto_CC_30seg.mgz Control001 and it prints at screen processing regardless of existence of cc in input volume setting callosum thickness to 61 mm will read input aseg from aseg.mgz writing aseg with cc labels to aseg.auto_CC_30seg.mgz reading aseg from /Users/Desktop/fsurfer/Control001/mri/aseg.mgz reading norm from /Users/Desktop/fsurfer/Control001/mri/norm.mgz 97532 voxels in left wm, 30641 in right wm, xrange [126, 142] MRIprincipleComponents: unsupported input type 1 No such file or directory searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot 6.3 global minimum found at slice 132.0, rotations (0.75, -0.50) final transformation (x=132.0, yr=0.750, zr=-0.500): 0.99988 0.00873 0.01309 -3.98366; -0.00873 0.99996 -0.00011 129.15181; -0.01309 0.00000 0.99991 129.72784; 0.00000 0.00000 0.00000 1.00000; updating x range to be [127, 129] in xformed coordinates best xformed slice 127 cc center is found at 127 0 0 MRIprincipleComponents: unsupported input type 1 No such file or directory eigenvectors: 0.00000 0.00000 0.00000; 0.00000 0.00000 0.00000; 0.00000 0.00000 0.00000; writing aseg with callosum to /Users/Desktop/fsurfer/Control001/mri/aseg.auto_CC_30seg.mgz... corpus callosum segmentation took 1.3 minutes But when I open the file asset.auto_CC_30seg.mgz on the image brain.mgz I still get a thickness of just 5 voxels. Could you please help me out in understanding why? I am wondering if this could be related to the warning MRIprincipleComponents: unsupported input type 1 No such file or directory But I do not understand to what it is referring to. The input aseg.mgz looks fine to me and the command “recon_all” did not give me any apparent issue. I hope you can help me with this and I thank you in advance for your time. Best regards, Simona

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Problem with freeview in linux subsystem for windows
by Williamson, Brady 20 Feb '19

20 Feb '19

External Email - Use Caution Hi, I am trying to run freeview in the linux subsystem (Ubuntu 18.04) for windows 10 but keep getting the following error: failed to get the current screen resources QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major code: 146 (Unknown), minor code: 20 QXcbConnection: XCB error: 170 (Unknown), sequence: 170, resource id: 90, major code: 146 (Unknown), minor code: 20 Freeview opens but there is no image. Is there a fix for this issue? Thanks, Brady

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Issue posting to the listserve
by Daniel Callow 19 Feb '19

19 Feb '19

External Email - Use Caution Hello, When trying to post to the freesurfer listserv with this account my emails don't seem to go through. When using my university email dcallow(a)umd.edu it works. Unfortunately, I don't get and can't respond to responses to emails I submit from that email so I would like to fix the issue I am having with posting to the listserv with my ddcc2442(a)gmail.com email address. Thank you, *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

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anat2dti error after dt_recon
by Daniel Davidson Callow 19 Feb '19

19 Feb '19

External Email - Use Caution Hello, I ran a successful dt_recon and then wanted to use mri_vol2vol --mov $subj_dir/dtrecons/${subj}.${cond}/lowb.nii.gz --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv --interp nearest --o $subj_dir/dtrecons/${subj}.${cond}/aparc+aseg2diff.nii.gz --reg $subj_dir/dtrecon/${subj}.${cond}/register.dat --no-save-reg to get the anatomical segmentations into diffusion space. However, when running the above code I get the following error message? echo subj = AES139 , cond = Rest subj = AES139 , cond = Rest set echo cd /Volumes/DANIEL/dti_freesurf mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/lowb.nii.gz --targ /Volumes/DANIEL/dti_freesurf/diffusion_recons/AES139.Rest/mri/aparc+aseg.mgz --inv --interp nearest --o /Volumes/DANIEL/dti_freesurf/dtrecons/AES139.Rest/aparc+aseg2diff.nii.gz --reg /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat --no-save-reg regio_read_register(): No such file or directory Could not open /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest/register.dat Matrix from regfile: MatrixPrint: mat = NULL! No such file or directory I have attached an example register.dat file in case that is the issue. also the output for ls -l register.dat -rwxrwxrwx 1 administrator staff 323 Feb 18 13:59 register.dat Any advice with troubleshooting is greatly appreciated! 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

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

19 Feb '19

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

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Re: [Freesurfer] Extracting stats from palm results (.mgz)
by Daniel Leopold 19 Feb '19

19 Feb '19

External Email - Use Caution Thank you, Doug. I'm aware of fspalm, but stayed with palm in order to take advantage of NPC and exchangeability blocks because I've got twins and singletons in the sample. Does --pargs allow for all palm functionality, including things like TFCE, eb's, and npc? Per another thread, I looked through the fspalm code and my next approach is to try mri_surfcluster or mri_volcluster with the .mgz palm results I've already got. Thanks, Dan

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

19 Feb '19

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

3 2

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

19 Feb '19

External Email - Use Caution Hi, Thanks for your reply. it is a just a normal mri analysis, but I want to compare the subcortical volume and Cortical thinkness between PD dementia patient and healthy control group. I only got the t1image. ---Original--- From: "Greve, Douglas N.,Ph.D."<DGREVE(a)mgh.harvard.edu> Date: Tue, Feb 19, 2019 21:29 PM To: "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] commends of GLM for volume IIs this an fMRI analysis? If so, you should use permutation for both surface and subcort. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLeve… On 2/19/19 6:00 AM, 妮 wrote: > > External Email - Use Caution > > Hello Greve, > I am glad to tell you that after 3 hours, something did print more on > terminal. when I was doing the GLM follow the tutorial, it only > provided the example of the cortical thickness. And I did not know how > to transfer it into volume. > Here is my commends > > mris_preproc --fsgd FSGD/PDDvsHC.fsgd --cache-in > volmue.fwhm10.fsaverage --target fsaverage --hemi lh --out > lh.PDDvsHC.volume.10.mgh > > mri_glmfit --y lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C > Contras-HC-PDD.mtx --surf fsaverage lh --cortex --glmdir > lh.volume.PDDvsHC.glimdir --eres-save > > mri_glmfit-sim --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp > 999 --2spaces > > We I check the results, it still talked about the cortical thickness , > so could you tell me how to change this commends to the volume of > subcortical. Or do you have the example which use GLM for comparing > the difference of subcortical volume between two groups. > > Thanks so much for your help > > Yours > > Zeng > > Here is the results > > > ClusterNoMax VtxMax Size(mm^2)MNIX MNIY MNIZCWPCWPLowCWPHi > NVtxsWghtVtx Annot > > > 16.960 86488 4544.63 15.7-77.36.70.000200.000000.00040 > 789115125.67pericalcarine > > > 23.529158070 3287.33 55.0-52.98.20.000200.000000.00040 > 679611225.54inferiorparietal > > > 32.630 67804 1909.67 43.3 45.8 -9.30.002200.001400.00300 2858 > 4399.15parsorbitalis > > Here is the terminal output. > > $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ > > > cwd /Volumes/NIU20/volumetric_FS/glm > > > cmdline mri_glmfit.bin --glmdir lh.PDDvsHC.volume.glmdir --y > lh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage lh --eres-save > > > sysnameDarwin > > > hostname dyn3199-104.wlan.ic.ac.uk > > > machinex86_64 > > > usercengzhou > > > FixVertexAreaFlag = 1 > > > UseMaskWithSmoothing1 > > > OneSampleGroupMean 0 > > > y/Volumes/NIU20/volumetric_FS/glm/lh.PDDvsHC.volume.10.mgh > > > logyflag 0 > > > usedti0 > > > FSGD FSGD/PDDvsHC.fsgd > > > labelmask/Volumes/NIU20/volumetric_FS/glm/fsaverage/label/lh.cortex.label > > > maskinv 0 > > > glmdir lh.PDDvsHC.volume.glmdir > > > IllCondOK 0 > > > ReScaleX 1 > > > DoFFx 0 > > > ResidualFWHM 14.826153 > > > SearchSpace 73852.172969 > > > anattype surface > > > > > cd /Volumes/NIU20/volumetric_FS/glm > > > /Applications/freesurfer/bin/mri_glmfit-sim > > > --glmdir rh.PDDvsHC.volume.glmdir --cache 1.3 pos --cwp 999 --2spaces > > > > $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ > > > Mon Feb 18 15:52:07 GMT 2019 > > > Darwin dyn3199-104.wlan.ic.ac.uk 14.5.0 Darwin Kernel Version 14.5.0: > Wed Jul 29 02:26:53 PDT 2015; root:xnu-2782.40.9~1/RELEASE_X86_64 x86_64 > > > cengzhou > > > setenv SUBJECTS_DIR /Volumes/NIU20/volumetric_FS/glm > > > FREESURFER_HOME /Applications/freesurfer > > > > Original mri_glmfit command line: > > > cmdline mri_glmfit.bin --glmdir rh.PDDvsHC.volume.glmdir --y > rh.PDDvsHC.volume.10.mgh --fsgd FSGD/PDDvsHC.fsgd --C > Contrasts/lh-thickness-HC-PDD.mtx --surface fsaverage rh --eres-save > > > > DoSim = 0 > > > UseCache = 1 > > > DoPoll = 0 > > > DoPBSubmit = 0 > > > DoBackground = 0 > > > DiagCluster = 0 > > > gd2mtx = dods > > > fwhm = 14.506572 > > > CSD > /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd > > > mri_surfcluster --in rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh > --mask rh.PDDvsHC.volume.glmdir/mask.mgh --cwsig > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh > --sum > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary > --ocn > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh > --annot aparc --cwpvalthresh 999 --o > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh > --no-fixmni --csd > /Applications/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm15/pos/th13/mc-z.csd--csdpdf > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.pdf.dat > --vwsig > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.mgh > --vwsigmax > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.voxel.max.dat--oannot > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot > --bonferroni 2 --surf white > > > Creating CDFs from CSD files > > > csd->threshsign = 1 > > > thsign = pos, id = 1 > > > version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman > Exp $ > > > hemi= rh > > > srcid= rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/sig.mgh > > > srcsubjid= fsaverage > > > srcsurf= white > > > srcframe= 0 > > > thsign= pos > > > thmin= 1.3 > > > thmax= -1 > > > fdr= -1 > > > minarea= 0 > > > Bonferroni= 2 > > > xfmfile= talairach.xfm > > > nth= -1 > > > outid= > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh > MGH > > > ocnid= > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh MGH > > > sumfile= > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.summary > > > subjectsdir= /Volumes/NIU20/volumetric_FS/glm > > > FixMNI = 0 > > > Found 148399 vertices in mask > > > Found 148399 vertices in mask > > > Found 148399 points in clabel. > > > ------------- XFM matrix (RAS2RAS) --------------- > > > /Volumes/NIU20/volumetric_FS/glm/fsaverage/mri/transforms/talairach.xfm > > > 1.000000.000000.000000.00000; > > > 0.000001.000000.000000.00000; > > > 0.000000.000001.000000.00000; > > > 0.000000.000000.000001.00000; > > > ---------------------------------------------------- > > > Reading source surface > /Volumes/NIU20/volumetric_FS/glm/fsaverage/surf/rh.white > > > Done reading source surface > > > Reading annotation > /Volumes/NIU20/volumetric_FS/glm/fsaverage/label/rh.aparc.annot > > > Computing metric properties > > > Loading source values > > > number of voxels in search space = 148399 > > > Done loading source values (nvtxs = 163842) > > > overall max = 6.96049 at vertex 86488 > > > overall min = -2.5107 at vertex 20214 > > > surface nvertices 163842 > > > metric props tot surface area 65020.839844 > > > group_avg_vtxarea_loaded 1 > > > masked surface area 75706.343750 > > > Computing voxel-wise significance > > > CSDpvalMaxSigMap(): found 7717/163842 above 0, max=2.18117 > > > Adjusting threshold for 1-tailed test. > > > If the input is not a -log10(p) volume, re-run with --no-adjust. > > > thminadj = 0.99897 > > > Searching for Clusters ... > > > thmin=1.300000 (0.998970), thmax=-1.000000 (-1), thsignid=1, > minarea=0.000000 > > > Found 38 clusters > > > Max cluster size 4544.626465 > > > Pruning by CW P-Value 999 > > > Saving thresholded output > torh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.masked.mgh > > > Saving cluster numbers to > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh > > > Saving cluster pval > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh > > > Constructing output annotation > > > Writing annotation > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.annot > > > mri_segstats --seg > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh > --exclude 0 --i rh.PDDvsHC.volume.10.mgh --avgwf > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.y.ocn.dat > --sum /tmp/mri_glmfit-sim.junk.40924 > > > > $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ > > > cwd > > > cmdline mri_segstats --seg > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh > --exclude 0 --i rh.PDDvsHC.volume.10.mgh --avgwf > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.y.ocn.dat > --sum /tmp/mri_glmfit-sim.junk.40924 > > > sysnameDarwin > > > hostname dyn3199-104.wlan.ic.ac.uk > > > machinex86_64 > > > usercengzhou > > > UseRobust0 > > > Loading > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.ocn.mgh > > > Loading rh.PDDvsHC.volume.10.mgh > > > Voxel Volume is 1 mm^3 > > > Generating list of segmentation ids > > > Found39 segmentations > > > Computing statistics for each segmentation > > > > Reporting on38 segmentations > > > Using PrintSegStat > > > Computing spatial average of each frame > > > 0123456789 10 11 12 13 14 15 16 17 18 19 > > > 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 > > > Writing to > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.y.ocn.dat > > > mri_segstats done > > > mri_convert > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh > --frame 0 > > > mri_convert.bin > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh > --frame 0 > > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > > reading from > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh... > > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > > i_ras = (-1, 0, 0) > > > j_ras = (0, 0, -1) > > > k_ras = (0, 1, 0) > > > keeping frame 0 > > > writing to > rh.PDDvsHC.volume.glmdir/rh-volume-HC-PDD/cache.th13.pos.sig.cluster.mgh... > > > Mon Feb 18 15:52:07 GMT 2019 > > > Mon Feb 18 15:52:12 GMT 2019 > > > mri_glmfit-sim done > > > > > > > ------------------ Original ------------------ > *From: * "Greve, Douglas N.,Ph.D.";<DGREVE(a)mgh.harvard.edu>; > *Send time:* Saturday, Feb 16, 2019 4:03 AM > *To:* "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>; > *Subject: * Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc > > how long? > > On 2/15/19 2:49 PM, 妮 wrote: >> >> External Email - Use Caution >> >> Hi >> Thanks for your quickly reply, yes continue to run but not print more >> on terminal anymore. >> >> ---Original--- >> *From:* "Greve, Douglas N.,Ph.D."<DGREVE(a)mgh.harvard.edu> >> *Date:* Fri, Feb 15, 2019 19:01 PM >> *To:* "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>; >> *Subject:* Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc >> >> Do you mean that it continues to run but does not do anything (eg, >> print more to the terminal) or that it has crashed? If it is hanging, >> how long? Nothing looks suspicious in the output. >> >> On 2/15/19 12:59 PM, 妮 wrote: >>> >>> External Email - Use Caution >>> >>> Hi Greve, >>> i solved this problem, but had a new one with recon-all, when i run >>> the recon-all data, sometimes it hang in the very last step of the >>> recon-all. here is the related part of output in terminal. i have >>> attached the recon-all log and status log. Have a nice weekend! >>> cheers >>> >>> #@# Curv .H and .K rh Fri Feb 15 17:30:27 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf >>> >>> \n mris_curvature -w rh.white.preaparc \n >>> >>> total integrated curvature = 11.983*4pi (150.582) --> -11 handles >>> >>> ICI = 180.5, FI = 1886.9, variation=29597.577 >>> >>> writing Gaussian curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.K...done. >>> >>> writing mean curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.white.preaparc.H...done. >>> >>> rm -f rh.white.H >>> >>> ln -s rh.white.preaparc.H rh.white.H >>> >>> rm -f rh.white.K >>> >>> ln -s rh.white.preaparc.K rh.white.K >>> >>> \n mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 >>> rh.inflated \n >>> >>> normalizing curvature values. >>> >>> averaging curvature patterns 5 times. >>> >>> sampling 10 neighbors out to a distance of 10 mm >>> >>> 148 vertices thresholded to be in k1 ~ [-1.38 0.32], k2 ~ [-0.18 0.09] >>> >>> total integrated curvature = 0.554*4pi (6.968) --> 0 handles >>> >>> ICI = 1.3, FI = 8.1, variation=139.341 >>> >>> 115 vertices thresholded to be in [-0.05 0.02] >>> >>> writing Gaussian curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.K...thresholding >>> curvature at 99.90% level >>> >>> curvature mean = 0.000, std = 0.001 >>> >>> 77 vertices thresholded to be in [-0.20 0.15] >>> >>> done. >>> >>> writing mean curvature to >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf/rh.inflated.H...curvature >>> mean = -0.018, std = 0.022 >>> >>> done. >>> >>> \n#----------------------------------------- >>> >>> #@# Curvature Stats lh Fri Feb 15 17:31:32 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf >>> >>> \n mris_curvature_stats -m --writeCurvatureFiles -G -o >>> ../stats/lh.curv.stats -F smoothwm subject lh curv sulc \n >>> >>> Toggling save flag on curvature files >>> [ ok ] >>> >>> Outputting results using filestem [ ../stats/lh.curv.stats ] >>> >>> Toggling save flag on curvature files >>> [ ok ] >>> >>> Setting surface [ subject/lh.smoothwm ] >>> >>> Reading surface... >>> [ ok ] >>> >>> Setting texture [ curv ] >>> >>> Reading texture... >>> [ ok ] >>> >>> Setting texture [ sulc ] >>> >>> Reading texture...Gb_filter = 0 >>> >>> [ ok ] >>> >>> Calculating Discrete Principal Curvatures... >>> >>> Determining geometric order for vertex faces... >>> [####################] [ ok ] >>> >>> Determining KH curvatures... >>> [####################] [ ok ] >>> >>> Determining k1k2 curvatures... >>> [####################] [ ok ] >>> >>> deltaViolations [ 213 ] >>> >>> Gb_filter = 0 >>> >>> >>> WARN: S lookup min: -0.021311 >>> >>> WARN: S explicit min: 0.000000 vertex = 907 >>> >>> \n#----------------------------------------- >>> >>> #@# Curvature Stats rh Fri Feb 15 17:31:38 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/surf >>> >>> \n mris_curvature_stats -m --writeCurvatureFiles -G -o >>> ../stats/rh.curv.stats -F smoothwm subject rh curv sulc \n >>> >>> Toggling save flag on curvature files >>> [ ok ] >>> >>> Outputting results using filestem [ ../stats/rh.curv.stats ] >>> >>> Toggling save flag on curvature files >>> [ ok ] >>> >>> Setting surface [ subject/rh.smoothwm ] >>> >>> Reading surface... >>> [ ok ] >>> >>> Setting texture [ curv ] >>> >>> Reading texture... >>> [ ok ] >>> >>> Setting texture [ sulc ] >>> >>> Reading texture...Gb_filter = 0 >>> >>> [ ok ] >>> >>> Calculating Discrete Principal Curvatures... >>> >>> Determining geometric order for vertex faces... >>> [####################] [ ok ] >>> >>> Determining KH curvatures... >>> [####################] [ ok ] >>> >>> Determining k1k2 curvatures... >>> [####################] [ ok ] >>> >>> deltaViolations [ 257 ] >>> >>> Gb_filter = 0 >>> >>> >>> WARN: S lookup min: -0.254695 >>> >>> WARN: S explicit min: >>> >>> @# Sphere lh Fri Feb 15 17:31:44 GMT 2019 >>> >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/scripts >>> >>> \n mris_sphere -rusage >>> /Users/cengzhou/Desktop/volumetric_FS/subject1/subject/touch/rusage.mris_sphere.lh.dat >>> -seed 1234 ../surf/lh.inflated ../surf/lh.sphere \n >>> >>> setting seed for random number genererator to 1234 >>> >>> $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ >>> >>> $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ >>> >>> reading original vertex positions... >>> >>> unfolding cortex into spherical form... >>> >>> surface projected - minimizing metric distortion... >>> >>> >>> == Number of threads available to mris_sphere for OpenMP = 1 == >>> >>> scaling brain by 0.321... >>> >>> MRISunfold() max_passes = 1 ------- >>> >>> tol=5.0e-01, sigma=0.0, host=cengz, nav=1024, nbrs=2, l_area=1.000, >>> l_dist=1.000 >>> >>> using quadratic fit line minimization >>> >>> complete_dist_mat 0 >>> >>> rms 0 >>> >>> smooth_averages 0 >>> >>> remove_neg 0 >>> >>> ico_order 0 >>> >>> which_surface 0 >>> >>> target_radius 0.000000 >>> >>> nfields 0 >>> >>> scale 1.000000 >>> >>> desired_rms_height -1.000000 >>> >>> momentum 0.900000 >>> >>> nbhd_size 7 >>> >>> max_nbrs 8 >>> >>> niterations 25 >>> >>> nsurfaces 0 >>> >>> SURFACES 3 >>> >>> flags 0 (0) >>> >>> use curv 0 >>> >>> no sulc 0 >>> >>> no rigid align 0 >>> >>> mris->nsize 2 >>> >>> mris->hemisphere 0 >>> >>> randomSeed 1234 >>> >>> >>> ------------------ Original ------------------ >>> *From: * "Greve, Douglas N.,Ph.D.";<DGREVE(a)mgh.harvard.edu>; >>> *Send time:* Tuesday, Feb 12, 2019 0:41 AM >>> *To:* "freesurfer(a)nmr.mgh.harvard.edu"<freesurfer(a)nmr.mgh.harvard.edu>; >>> *Subject: * Re: [Freesurfer] lh.PDDvsHC.thinckness.00.mris_preproc >>> >>> can you send the full mri_surf2surf terminal output? >>> >>> On 2/11/19 8:08 AM, 妮 wrote: >>> > >>> > External Email - Use Caution >>> > >>> > Hello FreeSurfer Developers, >>> > >>> > I didn't cache the data during recon-all, so I ran the >>> > >>> > > following: >>> > >>> > > >>> > >>> > > mris_preproc –fsgd PDDvsHC.fsgd --target fsaverage >>> > >>> > > --hemi lh >>> > >>> > > --meas thickness --out lh.MMSE-AD.thickness.00.mgh >>> > >>> > > >>> > >>> > > It seemed to run smoothly (I've attached the log >>> below) >>> > >>> > > so I >>> > >>> > > ran the next step: >>> > >>> > > >>> > >>> > > mri_surf2surf --hemi lh --s fsaverage --sval >>> > >>> > > lh.PDDvsHC.thickness.00.mgh --fwhm 10 --cortex --tval >>> > >>> > > lh.PDDvsHC.thickness.10.mgh >>> > >>> > > >>> > >>> > > I got the following error: >>> > >>> > > >>> > >>> > > Reading source surface reg >>> > >>> > > >>> > >>> > > freesurfer/subjects/fsaverage/surf/lh.sphere.reg >>> > >>> > > Loading source data >>> > >>> > > >>> > >>> > > >>> > >>> > >>> mghRead(/Users/cengzhou/Desktop/volumetric_FS/FS/lh.PDDvsHC.thickness.00.mgh, >>> >>> > -1): could not open file >>> > >>> > recon-all.log: see attached >>> > >>> > Platform: mac os 10 >>> > >>> > >>> > _______________________________________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer February 2019