Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Troubles to determine the type of recon editing needed
by Diamond, Bram Ryder 20 Sep '18

20 Sep '18

Hi Matthieu, I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm surprised FreeSurfer did as well as it did. As for the recon editing - I would recommend editing the wm.mgz to more accurately represent the wm from slice 84 to 39. You can take a look at the white matter edits tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0> for details on how to do that. Then run the following command (substituting <subj_id> for your subject's id): recon-all -autorecon2-wm -autorecon3 -subjid <subj_id> The surface reconstruction may also benefit from labeling the right lateral ventricle in the wm.mgz (as an intensity of 250) - but I'm not certain since you didn't send us the surfaces for the left hemisphere. Before you do that, edit the wm.mgz as explained in the tutorial and tell us how that goes. All the best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598

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Error running recon-all
by Mark Wagshul 20 Sep '18

20 Sep '18

External Email - Use Caution Hi. I am getting the following error trying to run recon-all (with Version 6.0), it is failing while running the routine mri_nu_correct.mni: Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /public/apps/freesurfer/6.0.0/mni/bin/nu_correct line 37. I am guessing that this has to do with the setup of the environment variables, but not sure what needs fixing. Any advice would be much appreciated, thanks. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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freeview automated screenshots using color wheel scale & qt library issues
by Emil H.J. Nijhuis 20 Sep '18

20 Sep '18

External Email - Use Caution Hi, I am attempting to generate automated screenshots with freeview version 3.July 2018 and I noticed that when applying the color wheel option for a surface overlay the coloring would be wrongly applied and I would need to enter the configuration window to fix/refresh the overlay coloring. Is there any way to enforce a refresh for overlays using the command line? Also is there a way to save/load custom color scales with the command line? I tried to use the latest developmental freeview.bin, however it gives me the error: version 'qt_5' not found; for 4 existing qt libraries which are softlinked to a newer versions (qt 5.5) in my system. Do you have any advice to achieve automated screenshots with freeview? With kind regards, Emil Nijhuis

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mris_fill ERROR: dyld: lazy symbol binding failed:
by 岡留敏樹 20 Sep '18

20 Sep '18

External Email - Use Caution Hello freesurfer experts, when trying to run ‘ft_prepare_mesh’ command from fieldtrip with MATLAB R2018a, I run into an error. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mris_fill -c -r 1 /Users/okadometoshiki/Desktop/SubjectUCI29/freesurfer/surf/lh.pial /private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz: Aborted reading filled volume... gunzip: can't stat: /private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz (/private/var/folders/cc/fv5fk09d3hj5g5kx7dg7pqq80000gn/T/tp0a8d7856_136c_4156_bf73_d23f64bbf687_pial.filled.mgz.gz): No such file or directory ERROR: problem reading fname I’m running this on a iMac, macOS High Sierra 10.13.6, with freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. From past archives, I think this is because of SIP. So I disabled SIP of OSX, but I run into same errors. I tried different subjects, which caused similar errors. Any ideas would be greatly appreciated, thank you! ======== Toshiki Okadome

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Step of coordinates transforming
by 薛倩雯 19 Sep '18

19 Sep '18

External Email - Use Caution Dear Freesurfer experts, I need to transform a bunch of MNI coordinates of fiber tracts to native space. I have already done the follow steps: (1)intra-subject registration (register the individual's low-b diffusion to T1images using bbregister ) (2)inter-subject registration (register the individual's T1 image to cvs_avg35_inMNI152 template) How can I transform the MNI coordinates back into the native space? Thanks!Qianwen

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Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault
by Matthew Grecsek 19 Sep '18

19 Sep '18

External Email - Use Caution Yes, a part of the brain appears missing. See attached screenshot. I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags. ------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700 Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks! a.y

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Urgent help with preprocessing pipeline
by Martin Juneja 19 Sep '18

19 Sep '18

External Email - Use Caution Hi, I am using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version of FreeSurfer. I used cross-sectional pipeline to identify ROIs (from Desikan atlas) with significant difference in cortical volume (CV) between controls and *patients (subjects 1-40, baseline)*, say I get ROIs: R1, R2 and R3. I am using these ROIs (R1, R2 and R3) for further analysis to determine the effect of two treatments: *T1 (placebo) (for subjects 1 to 20) and T2 (active) (for subjects 21 to 40)*, compared to their corresponding baseline. I compared CV of these ROIs (R1, R2 and R3): *T1 vs. baseline and T2 vs. baseline* using both cross-sectional as well as longitudinal pipeline. *Using cross-sectional pipeline:* I found there is significant improvement in CV (p = 0.019) for these ROIs for treatment T2 compared to baseline and no change for placebo treatment T1. *Using longitudinal pipeline: *There is little improvement in CV (p = 0.2) for these ROIs for treatment T2 compared to baseline and no change for placebo treatment T1. I was wondering why I am getting results so different between these pipelines, and which pipeline suits better in such comparison when my ROIs are identified using cross-sectional pipeline, but further analysis of these ROIs involved longitudinal comparison. I would really appreciate any help (as early as possible). Thank you so much !

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Using freesurfer without intensity normalization
by Raquib Ridwan 19 Sep '18

19 Sep '18

External Email - Use Caution Hi, I would like to know if intensity normalization(not bias field correction) so that white-matter is ~110 and gm is ~60 is necessary for freesurfer segmentation. Will intensity normalization using other methods still work for freesurfer segmentation?

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Re: [Freesurfer] if: missing file name
by Yacila Isabela Deza Araujo 19 Sep '18

19 Sep '18

External Email - Use Caution Hello, Please, find in the attachment the capture of the terminal output. It is basically the same that I get when I run it from the freesurfer/subjects directory. I also need to say that the problem is only with this Mac. It runs without any problem in a Linux computer. Thanks a lot for your support Yacila > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Sep 2018 15:35:08 +0000 > From: Yacila Isabela Deza Araujo > <yacila_isabela.deza_araujo(a)tu-dresden.de> > Subject: [Freesurfer] if: missing file name > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <DC2EE6A5-D782-4874-B1CC-B864B0FC84EF(a)msx.tu-dresden.de> > Content-Type: text/plain; charset="us-ascii" > > External Email - Use Caution > > Dear Freesurfer experts, > > Please find in the attachment a file with the errors I get when I try to follow the examples of recon-all > > Thanks a lot for your support, > > Yacila >

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Freesurfer 6.0 - Tracula - Segmentation fault
by Matthew Grecsek 19 Sep '18

19 Sep '18

External Email - Use Caution I ran standard recon-all on a single subject and then trac-all -prep. The process ran for approximately 1 hour and exited with errors: Segmentation fault. This is my first time testing Tracula, so user error likely. Here are the final lines from the console and trac-all.log attached: INFO: Distances between consecutive points in test subject's space are 9 13 13 12 WARN: Could not find satisfactory control point fit - try 912 Finding center streamline INFO: Step is 5 voxels WARN: Turning off deviation check for center streamline INFO: Step is 5 voxels WARN: Turning off FA check for center streamline INFO: Step is 5 voxels WARN: Turning off overlap check for center streamline INFO: Step is 5 voxels INFO: Length of center streamline is 114 voxels Selecting 5 points on center streamline INFO: Minimum allowable distance between dominant points is 15 INFO: Minimum allowable curvature at a dominant point is 0.0447089 INFO: Points where local peeks in curvature occur are 67 116 39 (curv = 0.0963721) 77 75 87 (curv = 0.114559) 75 76 95 (curv = 0.0564307) 69 74 105 (curv = 0.126918) 74 67 115 (curv = 0.0809615) INFO: Intermediate dominant points are 67 135 33 67 116 39 75 82 76 69 74 105 74 49 116 INFO: Final dominant points are 67 135 33 67 116 39 77 75 88 69 74 105 74 49 116 WARN: Defaulting to equidistant control points INFO: Selected control points are 67 135 33 68 108 46 75 83 75 69 74 105 74 49 116 INFO: Distances between consecutive points are 30 39 32 28 INFO: Selected control points in test subject's space are 56 58 -8 56 46 -3 58 35 9 55 30 22 57 19 26 INFO: Distances between consecutive points in test subject's space are 13 16 14 12 WARN: Could not find satisfactory control point fit - try 913 Writing output files to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_* Writing spline volume to /Users/Matthew/Downloads/matt/matt3/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz Segmentation fault Darwin Matthews-MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Sep 17 16:26:23 EDT 2018 Thanks, -Matt

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