Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

Errors in WM surface persistent after manual edits to wm.mgz
by Rachel Hoel 29 Dec '18

29 Dec '18

External Email - Use Caution Dear Freesurfer Developers, Our study is implementing the longitudinal processing pipeline in FS 6.0. When attempting to make manual white matter edits to our subjects, the edits save but do not appear to impact the white matter surface. We are using the voxel-edit tool in freeview and recon-editing is selected, and the edits are made on the wm.mgz volume. Below are the commands we use to make and submit the edits... Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Thank you in advance, Rachel Hoel Research Assistant Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces
by Neva M Corrigan 28 Dec '18

28 Dec '18

External Email - Use Caution Hi, I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes for all of my subjects. The pial surfaces look very good, but the white matter surfaces are poor. Notably, the wm.mgz volume and the lh.orig and rh.orig surfaces seem to correctly include all of the white matter in the temporal lobe. However, the rh.white and lh.white surfaces miss a substantial portion of the white matter. On the ReconAllDevTable I see that the ?.orig surfaces are generated before the ?.white surfaces. Can you suggest how I might be able to fix the ?.white surfaces? In case it is relevant, I had to create an xopts.txt file with the following options in order to obtain correct skull-stripping and pial surfaces for this data: mri_normalize -mprage -b 2 -n 5 I am using freesurfer development version with a date of 05-03-2018. I have attached an image of the ?.orig and the ?.white surfaces superimposed on the wm.mgz and brainmask.mgz volumes. Thank you, Neva

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How to visualise DTI
by Renew Andrade 27 Dec '18

27 Dec '18

External Email - Use Caution Dear community! I would like to know how can I use Freeview or any tool of FreeSurfer to visualise preprocessed DTI files from a database. They are in a standard output like it appears in Tracula output page of FreeSurfer wiki. It shouldn’t be a problem to use these files in FreeSurfer. Everything (details of output and preprocessing stages) is explained in this website. https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc <https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc> Thanks for your help!

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mpr2mni305 failed, during recon-all
by Shachar Gal 24 Dec '18

24 Dec '18

External Email - Use Caution hello, I'm running the hcp's FreeSurfer pipeline, and for some reason, after working successfully several times, on different subjects, im getting this error: *** /Users/georgieboy/Research/Piano/test/222/222/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin medical613-6.tau.ac.il 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64 recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018 *** the information in the talairach_avi.log is as follows: *** dyld: Symbol not found: ___keymgr_global Referenced from: /Applications/freesurfer/bin/gauss_4dfp Expected in: /usr/lib/libSystem.B.dylib in /Applications/freesurfer/bin/gauss_4dfp Abort ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 ERROR: mpr2mni305 execution aborted *** to be clear, this - /usr/lib/libSystem.B.dylib exists exactly where is was expected... the input image, orig.mgz, looks fine and is in 1 mm res... so im having trouble getting to the bottom of the error. thanks in advance, Shachar

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Project Effect Size onto Desikan-Killiany Atlas
by Taralee Hamner 24 Dec '18

24 Dec '18

External Email - Use Caution Hi all, We would like to project effect sizes on the FS average brain using Desikan-Killiany Atlas. We will then manually color code regions based on the effect size range. However, our command line is not loading the Desikan-Killiany Atlas. (Tksurfer fsaverage lh inflated -annotation aparc). See picture below. [image: Screen Shot 2018-12-11 at 10.35.40 AM.png] Please advise on 1) how to load the atlas on the FS average brain and 2) if it would be better to manually color code regions based on effect size or project the raw effect size data on the brain. I hope everyone is having a happy holiday season. Best, Taralee

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Finding the surface vertex for a voxel in the cortex
by ts+ml＠rcmd.org 24 Dec '18

24 Dec '18

External Email - Use Caution Dear FreeSurfer experts, given a voxel in the cortex of the fsaverage subject, I would like to find the vertex on the surface that corresponds to the voxel (e.g., if volume data would be projected to the surface). I found the documentation at http://freesurfer.net/fswiki/CoordinateSystems, which helped me a lot, but it would be great if someone could comment on whether or not what I'm doing is correct: This seems to be use case 4 on the page (bottom), so I would: 1) get the affine matrix by running: mri_info --vox2ras-tkr $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz 2) Apply the matrix to my voxel x, y, z to get the coords At this point I'm not sure how to get the vertex. Should I just compute the distance from the coords to all vertices and pick the one with minimal Euclidian distance? Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] mpr2mni305 failed, during recon-all {Disarmed}
by fsbuild 23 Dec '18

23 Dec '18

External Email - Use Caution Hello, I have not tried it, but it would not surprise me to see incomplete library references when running the old freesurfer 5 binaries on the latest version of Mac OS, i.e., Mac OS 10.14 (Mojave) I would try to use the rev 6 release binaries for MacOS from, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall I have built the latest development branch of freesurfer on Mac OS 10.14, but please be aware this has not been tested like the previous rev 6 release.  (I used the makefile.wiki to build it which you can download from https://surfer.nmr.mgh.harvard.edu/fswiki/CMake) - R. On Dec 23, 2018, at 10:00, Shachar Gal <gal.shachar(a)gmail.com> wrote:        External Email - Use Caution        Sorry, out of the office for the day. I'll get back to you about it tomorrowShacharOn Sun, Dec 23, 2018, 16:56 Glasser, Matthew <glasserm(a)wustl.edu> wrote:        External Email - Use Caution        Is that FreeSurfer 5.3?Matt.From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.com>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Sunday, December 23, 2018 at 8:35 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: Re: [Freesurfer] mpr2mni305 failed, during recon-all        External Email - Use Caution        this is my Freesurfer version - freesurfer-i386-apple-darwin10.8.0-stable5-20130513and I think the update to macOS Mojave was after successfully running the pipeline.you think this could be the issue? should I just upgrade my freesurfer?thanksOn Sun, 23 Dec 2018 at 16:28, Glasser, Matthew <glasserm(a)wustl.edu> wrote:        External Email - Use Caution        Which version of FreeSurfer is this and did you do some OS upgrade in between?Matt.From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.com>Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Date: Sunday, December 23, 2018 at 8:24 AMTo: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] mpr2mni305 failed, during recon-all        External Email - Use Caution        hello,I'm running the hcp's FreeSurfer pipeline, and for some reason, after working successfully several times, on different subjects, im getting this error:***/Users/georgieboy/Research/Piano/test/222/222/mri\n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \nERROR: mpr2mni305 failed, see transforms/talairach_avi.logDarwin medical613-6.tau.ac.il 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct  5 19:41:49 PDT 2018; root:xnu-4903..221.2~2/RELEASE_X86_64 x86_64recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018***the information in the talairach_avi.log is as follows:***dyld: Symbol not found: ___keymgr_global  Referenced from: /Applications/freesurfer/bin/gauss_4dfp  Expected in: /usr/lib/libSystem.B.dylib in /Applications/freesurfer/bin/gauss_4dfpAbortERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134ERROR: mpr2mni305 execution aborted***to be clear, this -  /usr/lib/libSystem.B.dylib exists exactly where is was expected...the input image, orig.mgz, looks fine and is in 1 mm res...so im having trouble getting to the bottom of the error.thanks in advance,Shachar The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard..eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Error saving NPC results
by Daniel Leopold 23 Dec '18

23 Dec '18

External Email - Use Caution Dear Freesurfer Community, Drs. Winkler, Greve, Fischl, et al. *My apologies if this reposts, but this is my first time emailing the listserv, and I'm not sure if my earlier email went through* Could anyone help me understand which palm options are needed in order to produce tfce and clustere NPC results that are fwe-corrected across contrasts (i.e., npc_fisher_cfwep_)? I'm analyzing area and thickness and have four one-tailed contrasts of interest (e.g., C1+, C1-, C2+, C2-). Currently, I am only able to get the "output'_dpv_npc_fisher_cfwep_c[1234]" results, but the palm log ends abruptly after saving these files and does not save the _tfce_ or _clustere_ versions: Saving p-values for NPC between modalities (uncorrected and corrected within contrasts). Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c1 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c1 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c2 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c2 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c3 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c3 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c4 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c4 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c4 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c4 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c4 Saving p-values for NPC between modalities (corrected across contrasts). Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c1 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c2 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c3 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c4 >> The error log contains the following text, and my efforts to read through these source files have been in vain: {^HCell contents reference from a non-cell array object. Error in palm_saveall (line 1043) distmax(:,j) = plm.Tclumax{m}{c}; Error in palm_core (line 2489) palm_saveall(plm,opts); Error in palm (line 81) palm_core(varargin{:}); }^H ^G I have essentially permuted the various -corr(con/mod) and -npc(con/mod) options, as well as various combinations of -T & -C {z}, -Tuni & -Cuni {z}, and -Tnpc & -Cnpc {z}, using a small number of permutations to assess the number of output maps and whether jobs finish appropriately. Here's an example of one of the palm commands that resulted in these output and error logs (with line-breaks for legibility): fsl_sub -l $logdir palm -designperinput -i {area_dir}/292_${hemi}.area_stack.mgh -d {design_dir}/wordadhd_npc_areatotal.mat -t {design_dir}/wordadhd_npc_areatotal.con -i {thickness_dir}/292_${hemi}.thickness_stack.mgh -d {design_dir}/wordadhd_npc_thickmean.mat -t {design_dir}/wordadhd_npc_thickmean.con -m {base_dir}/palm/input/${hemi}mask.mgz -s ${surf_dir}/${hemi}.white ${surf_dir}/${hemi}.white.avg.area.mgh -o wordadhd_npc_${hemi} -eb ${EB} -corrcon -corrmod -logp -ise -npc -T -C 1.64485 -n 5 If knowing versions helps at all: PALM alpha109 MATLAB 8.3.0.532 (R2014a) FreeSurfer 5.3.0 FSL 5.0.8 Any advice you could provide on this particular error, why my input doesn't produce the tfce_npc_fisher_cfwep or clustere__npc_fisher_cfwep results, or other problem-solving suggestions would be greatly appreciated! With gratitude, Dan

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Re: [Freesurfer] Freesurfer from source library dependencies dead link
by fsbuild 22 Dec '18

22 Dec '18

External Email - Use Caution Hello Joseph, You can also try doing the cmake build via makefile.wiki found under the section, "Complete Cmake Build with makefile wrapper” on the page  ttps://surfer.nmr.mgh.harvard.edu/fswiki/CMake That will try and use curl to download 3rd party packages as part of doing the build. - R. On Dec 22, 2018, at 05:26, ts+ml(a)rcmd.org wrote:       External Email - Use Caution        Please see this recent email from the list archives, I think it is what you are looking for:TimHello Joseph,Try this link for the 3rd party libs (to use with the cmake build)http://surfer.nmr.mgh.harvard.edu/pub/data/fspackages/prebuilt/- robOn Sep 20, 2018, at 8:39 PM, Moon,> wrote:       External Email - Use CautionHi,I’m trying to build Freesurfer according to the instructions athttp://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_lin…, the FTP link to prebuilt 3rd party libraries seems to be down. The directory “ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt” is no longer being hosted.Please let me know if I misunderstood something!On December 21, 2018 at 5:23 PM "King, Maximilian" <maximilian_king(a)brown.edu> wrote:       External Email - Use Caution        Hi Freesurfer folks!I am attempting to build freesurfer from source for our HPC center here atBrown University, but are running into a snag. Looks like the documentationpoints to a dead link for Step 3 of the freesurfer_linux_developers_page<https://surfer.nmr.mgh.harvard.edu/fswi… are required to get the prebuilt bundle of 3rd party dependancies using:wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x…, the command fails as the directory does not exist.$ wgetftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/cento… 11:07:49--ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt… ‘centos6-x86_64-packages..tar.gz’Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)...132.183.240.105Connecting to surfer.nmr.mgh.harvard.edu(surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21...connected.Logging in as anonymous ... Logged in!==> SYST ... done.    ==> PWD ... done.==> TYPE I ... done.  ==> CWD (1)/pub/dist/fs_supportlibs/prebuilt/centos6_x86_64 ...No such directory ‘pub/dist/fs_supportlibs/prebuilt/centos6_x86_64’.Any chance I could get the updated path for these dependencies? Happyholidays!Cheers,Max-- *Maximilian King, MSc*HPC Application ScientistCenter for Computation and VisualizationBrown University Computing and Information Systems180 George St, Providence, RI 02906, USATel: +1 (401) 863-7448*maximilian_king(a)brown.edu* <maximilian_king@brown.edu>*http://ccv.brown.edu* <http://ccv.brown.edu/>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ERROR: QdecDataTable::GetFactor: '' is not in datatable!
by vittal korann 22 Dec '18

22 Dec '18

External Email - Use Caution Hi Freesurfer people, I'm running the QDEC on schizophrenia and controls group. Some mystery error is occurring frequently. Due to this error, I'm not able to work properly. Below is the error message in italic. Continuous Factors: Mean: StdDev: ------------------- ----- ------- Left-Lateral-Ventricle 7816.020 3727.173 Left-Inf-Lat-Vent 350.121 226.504 Left-Cerebellum-White-Matter 14621.627 2633.306 Left-Cerebellum-Cortex 53209.396 5898.023 Left-Thalamus-Proper 7482.565 1232.123 Left-Caudate 3331.808 532.262 Left-Putamen 4709.175 830.860 Left-Pallidum 1924.535 309.669 3rd-Ventricle 1229.524 408.770 4th-Ventricle 1853.426 553.034 Brain-Stem 21725.101 3957.940 Left-Hippocampus 4050.520 498.924 Left-Amygdala 1659.871 274.044 CSF 1028.790 239.493 Left-Accumbens-area 562.265 116.404 Left-VentralDC 4657.927 1037.213 Left-choroid-plexus 523.561 212.131 Right-Lateral-Ventricle 7118.300 3678.386 Right-Inf-Lat-Vent 420.917 194.063 Right-Cerebellum-White-Matter 13789.140 2276.811 Right-Cerebellum-Cortex 54513.076 5816.474 Right-Thalamus-Proper 7526.933 1477.932 Right-Caudate 3401.037 590.197 Right-Putamen 4702.361 823.977 Right-Pallidum 1860.576 304.344 Right-Hippocampus 4039.939 594.601 Right-Amygdala 1760.872 282.234 Right-Accumbens-area 522.139 114.505 Right-VentralDC 4428.377 1022.441 Right-choroid-plexus 522.657 222.093 WM-hypointensities 1709.401 4648.253 Optic-Chiasm 196.811 55.050 CC_Posterior 946.755 142.995 CC_Mid_Posterior 528.413 272.659 CC_Central 533.220 241.533 CC_Mid_Anterior 591.063 215.231 CC_Anterior 858.551 158.497 BrainSegVol 1099482.415 99478.583 BrainSegVolNotVent 1079167.296 97450.382 BrainSegVolNotVentSurf 1078648.495 97590.844 lhCortexVol 226023.502 21598.352 rhCortexVol 224689.284 22938.042 CortexVol 450712.786 43902.643 lhCerebralWhiteMatterVol 216638.257 23876.074 rhCerebralWhiteMatterVol 216556.639 24674.208 CerebralWhiteMatterVol 433296.898 48337.532 SubCortGrayVol 58400.254 6862.247 TotalGrayVol 618102.046 55580.442 SupraTentorialVol 961614.009 89842.372 SupraTentorialVolNotVent 945356.847 88183.050 SupraTentorialVolNotVentVox 942566.063 88006.239 MaskVol 1523295.056 188225.886 BrainSegVol-to-eTIV 0.792 0.054 MaskVol-to-eTIV 1.097 0.132 lhSurfaceHoles 31.176 21.318 rhSurfaceHoles 27.803 17.941 SurfaceHoles 58.979 37.649 EstimatedTotalIntraCranialVol 1394219.483 146922.169 demean_ICV -0.000 1.000 Age 30.711 6.309 scanner 0.134 0.342 Number of subjects: 142 Number of factors: 63 (2 discrete, 61 continuous) Number of classes: 4 Number of regressors: 248 Data table loading completed successfully. SUBJECTS_DIR is '/usr/local/freesurfer/subjects' *ERROR: QdecDataTable::GetFactor: '' is not in datatable!* *ERROR: QdecGlmDesign::Create: bad factor!* I'm using linux gedit for creating qde.dat file. Is it because of gedit or something else creating the problem while copying from libre to gedit. How can I overcome this error? This is repeatedly happening and also testing my patience. Would be great if someone helps me to get rid of this error ..!! * Thanks & regards* *Vittal*

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