Freesurfer September 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
160 discussions

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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if: missing file name
by Yacila Isabela Deza Araujo 19 Sep '18

19 Sep '18

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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if:missing file name
by Yacila Isabela Deza Araujo 19 Sep '18

19 Sep '18

External Email - Use Caution Hello, I just started with Freesurfer and got the following error during the call of the command recon-all If: missing file name I should say that other commands work well. I looked for the error and it seems that it is a change in the script. I install Freesurfer in my Mac and did not change anything during installation. Why do I have this error then? Thanks a lot for your support, Yacila

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Question about register
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 registered my subjects to cvs_avg35_inMNI152 using mri_cvs_register. How can I transform the MNI coordinates back into the native space? Thanks!Qianwen

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Freesurfer September 2018