Freesurfer

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30070 discussions

mri_vol2surf error in FS6
by Fred Lado 05 Mar '17

05 Mar '17

Dear FreeSurfer Experts, I just installed FS6 and encountered the following error, which I can replicate by just entering “mri_vol2surf” on the command line: /Users/fred 3> mri_vol2surf 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 I am running Mac OS X El Capital 10.11.6, after searching the archives I also tried turning off SIP, which did not help. Any other advice? Thanks, Fred Fred Lado, MD PhD Director, Epilepsy - Central and Eastern Regions Northwell Health 917-608-1881 (mobile) 516-325-7000 (practice) 516-325-7001 (fax) flado(a)northwell.edu Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately.

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VISUALIZATION OF INTER-SUBJECT REGISTRATION
by Marco Martinolli 05 Mar '17

05 Mar '17

Dear Freesurfer users, I made a brain registration of several subjects to the template cvs_avg35_inMNI125 using mri_csv_register and now I would like to visualize the results of the alignment. I want to compare the surfaces of the subject before (subj/surf/lh.sphere) and after alignment (subj/surf/lh.cvs.to_cvs_avg35_inMNI125.sphere.reg) and of the template (cvs_avg35_inMNI125/surf/lh.sphere), overlayed with the curvature data (lh.curv) or the sulc data (lh.sulc).What is the best way to get this in FreeSurfer? I tried with Freeview, tksurfer and tkregister2 but I did not find anything that makes the comparison really practical and evident. Maybe there is a combination of flags/options that I do not know. By the way, an image like Figure 2 of Fischl's paper "High-Resolution Intersubject Averaging and a Coordinate System for the Cortical Surface", where the aligned sphere and the template sulci are overimposed, is what I am really looking for, so something like this would be very cool! Cheers,Marco

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panning Freeview on MacBook Pro
by me＠marychin.org 04 Mar '17

04 Mar '17

Hi, How do I pan on Freeview on a Mac please? Mine is an El Capitan, MacBook Pro (Early 2011). On https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsag… it reads: You can pan across the data, which is especially useful when zoomed in. To do so while in Navigate mode navigate.gif , Voxel Edit mode voxel_edit.gif , or Recon Edit mode recon_edit.gif click and hold the scroll button on the mouse while moving the image. Alternatively, you can use the arrow keys on the keyboard. When using the arrow keys, know that when you scroll up, down, right or left, the actual label moves around, not the screen. I have tried the touchpad, with and without cmd, alt, fn, shift, ctrl... Also tried the arrow keys. Thanks, mary

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ACPC alignment before or after running on Freesurfer?
by Lee Subin Kristine 03 Mar '17

03 Mar '17

Dear Freesurfer team, This may sound like a bit of a small question, but I could not find any exact answer elsewhere. Does the exact orientation of the input image have much effect on the accuracy of the segmentation in Freesurfer? It seems that some people apply ACPC alignment to the output of Freesurfer, so I am confused as to which order would be optimal. Thank you in advance, Kristine

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Reslice image
by John Anderson 03 Mar '17

03 Mar '17

Dear experts: I have nifti file with 96 slices. I want to re-slice it to form nifti file with 200 slice. Are there any tools in Freesurfer that can help to achieve this? Many thanks for any suggestion John

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Hippocampal overestimation 5.3 vs 6.0
by Dawn C. Matthews 03 Mar '17

03 Mar '17

Eugenio and Freesurfer team, Many thanks for responding to these questions. My question relates to hippocampal volume overestimation. I believe that a European team recently evaluated the performance of hippocampus segmentation using different automated segmentation methods including Freesurfer on more than 400 scans from several previous studies, and found that Freesurfer and FSL-FIRST may include tissue that is not part of the hippocampus. Liedlgruger et al, “Variability Issues in Automated Hippocampal Segmentation”, 2017, also reported that Freesurfer overestimated volumes vs. other methods tested. I wondered if version 6.0 addresses the overestimation issue? It appeared that the FS 6.0 release web page figure (which showed the hippocampal portion of an MRI at left, the 5.3 subfield segmentation in the middle, and the 6.0 subfield segmentation at right) showed that a portion of gray tissue superior to hippocampus was included in the 5.3 segmentation but not in the 6.0 version – was that an example of 5.3 overinclusion, addressed in 6.0? Thank you again for your help and for the team’s continued advances. Dawn

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Re: [Freesurfer] FreeSurfer v6.0 in an AWS cloud configuration (hipposubfield/brainstem failures)
by randrews＠admdx.com 03 Mar '17

03 Mar '17

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LGI: "Error using freesurfer_read_surf (line 90) could not open surface file lh.pial."
by Louise Baruël Johansen 03 Mar '17

03 Mar '17

Hi FreeSurfer developers, I’m trying to compute the gyrification index using the command: recon-all -s subject1 -localGI But I get the following error message when trying different subjects and with different versions of matlab: (the left hemisphere - not the right - invokes the error) —— FREESURFER_READ_SURF [v 1.2 ] Error using freesurfer_read_surf (line 90) could not open surface file lh.pial. Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); ERROR: find_corresponding_center_FSformat did not complete successfully! Linux big22 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux ---- I can’t find a solution to this error on the mailing list… FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thanks, Louise

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to evaluate volume and thickness of the amygdala using asegstats2table
by Gwang-Won Kim 02 Mar '17

02 Mar '17

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Re: [Freesurfer] wm.mgz manual editing
by Antonin Skoch 02 Mar '17

02 Mar '17

Dear Eli, I have looked at your data. Due to the fact that the white matter does have intensity well below 110 in the large portion of white matter area under your problematic spot, I think that instead of editing wm.mgz the better way in your case would be to add some control points to the white matter surrounding region 112,49,128. Btw, it seems that the white matter has generally very inhomogeneus signal intensity. Does not the image originate from the subjects with some kind of severe pathology of white matter? What is the large hypointense spot centered at 102,64,126? This causes large hole in wm.mgz But there are other hypointensities, for example at 96,77,151. Does not your problematic spot correspond to some pathology? Regards, Antonin Bruce, Main problem area that I can see is at coordinates [104,42,124].My first attempt, I don't think I had the recon editing box checked when I was editing the white matter, but I used a brush value of 255. My second attempt I painted over the same voxels but with the recon editing box checked. Both times, after saving wm.mgz I ran the following command: "recon-all -autorecon2-wm -autorecon3 -subjid my_subject -sd `pwd`" Only thing different from the guide is I specify a different subject directory. Below are download links for the important files, let me know if you would like to look at anything else. If you look at wm.mgz along with the rh.white, you can see the surface doesn't appear to acknowledge my edit. 001.mgz: https://1drv.ms/u/s!AoOsIIayCH7qlxLBNvCT4JCvM1Kc recon-all.logs.tar.gz: https://1drv.ms/u/s!AoOsIIayCH7qlxRGOWpUCttk5Zji brainmask+surf+wm.tar.gz https://1drv.ms/u/s!AoOsIIayCH7qlxbDSS54gfHkq2M3 Thanks tremendously for your time, Eli > ------------------------------ > > Message: 4 > Date: Wed, 1 Mar 2017 16:39:33 -0500 (EST) > From: Bruce Fischl <fis...(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm.mgz manual editing > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > > <https://urldefense.proofpoint.com/v2/url?u=http-3A__alpine.LRH.2.20.1703011… > > > Content-Type: text/plain; charset="utf-8" > > Hi Eli > > hmm, maybe you should just upload the subject and email us the voxel > coords you are talking about? > > Also, in general it is hard for us to help you unless you include more > information. What exact command did you run? What was the screen output? > What was in the recon-all.log? > > cheers > Bruce > > > On Wed, 1 > Mar 2017, Rockers, Elijah D. wrote: > > > Couple of questions: > > > > 1) > > > > I edited wm.mgz following the instructions in the wiki guide, but it did > > not change anything after reconstruction. I am still using 5.3 right > > now, so maybe the guide is wrong for me. What is the brush value > > supposed to be? I used 255 but it did not extend the white matter > > surface to include my edits. I checked to make sure they saved > > correctly, they did, but the surface didn't change. Any ideas? > > > > 2) > > > > The reason I am editing wm.mgz is to try to include some cortex that was > > left out of the pial surface. I don't suppose there's any way to fix > > this without editing wm.mgz? Because the white matter surface actually > > looks fine the way it is. > > > > Thanks, > > Eli > > > > Houston Methodist. Leading Medicine. > >

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