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30132 discussions

Amygdala segmentation runtime error
by Emily K Clarke 11 Jan '18

11 Jan '18

Hi Freesurfer developers, I’m attempting to run the new amygdala segmentation command (segmentHA_T1.sh) using the developer version of Freesurfer 6.0. However, when I run my script I receive the following error — error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory I checked with our cluster administrator, and we do have the Matlab R2012 runtime installed. Does anyone have any insight into what could be causing this error? I’ve attached my full output as well as my script in case that’s any help! Thanks, Emily K. Clarke Duke University

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Description of a few files generated by
by Aaron Tanenbaum 11 Jan '18

11 Jan '18

I would like to get a clarification on what some the the files generated by FreeSurfer recon-all based on the URL https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles The web pages says the nu.mgz "This is a intensity normalized volume generated after correcting for non-uniformity in the orig.mgz". I just need a clarification the intensity normalized is just a global scaling and the correction for non-uniformity is the bias field correction. I was wondering if the orig.mgz is bias field corrected to generate the orig_nu.mgz and the intensity normalized to generate the nu.mgz. Finally what is the norm.mgz image. I cannot final details on how it is created.

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Re: [Freesurfer] reconstruction for very significant atrophy
by Rockers, Elijah D. 11 Jan '18

11 Jan '18

The entire result overlay appears shifted, yes. Put differently, we are seeing significant results in the regions just a bit superior to the regions we know to have atrophy. I am just wondering if there is something else I can check in the pipeline to make sure everything is lining up correctly before the glmfit analysis. Like just in case some of the subjects are not accurately registered into the common space used for the vertex-wise analysis. FYI we are comparing 8 diseased (nonfluent PPA) subjects to ~40 controls. I have manually checked the segmentations for all these images, and they are accurate. Thanks for your help, -Eli On Thu, 2018-01-11 at 11:43 -0500, freesurfer-request(a)nmr.mgh.harvard.edu wrote: Message: 3 Date: Thu, 11 Jan 2018 11:02:41 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] reconstruction for very significant atrophy To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1801111102310.32719(a)gate.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1801111102310.32719@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" do you mean that the entire surface is off by a fixed amount? On Thu, 11 Jan 2018, Rockers, Elijah D. wrote: Thanks Bruce. I went over some more images with our PI and he was mostly satisfied with the pial/white segmentations. The real problem here is that our results look correct, except for they seem to be translated vertically by a small amount, comparing with what we see on the MRIs. What can we check to make sure everything is lining up correctly? - Eli On Thu, 2018-01-11 at 08:08 -0500, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Message: 5 Date: Wed, 10 Jan 2018 20:26:11 +0000 From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> Subject: [Freesurfer] reconstruction for very significant atrophy To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <1515615971.3868.3.camel(a)houstonmethodist.org<mailto:1515615971.3868.3.camel@houstonmethodist.org>> Content-Type: text/plain; charset="utf-8" Hello, We have some images that reflect severe atrophy in some subjects, in which gray matter is virtually undetectable on the MRI in some regions. However, upon checking the segmentations visually, the whit e/pial surfaces are reflecting a significant cortical thickness in these areas. Is there perhaps any recon-all setting that might extend the white matter area out a little more agg ressively than it does with the default settings? Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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mri_glmfit ERROR: loading gamma0
by Gemma Salvadó Blasco 11 Jan '18

11 Jan '18

Hello Freesurfer developers, I'm make a statistical analysis between two groups. To do this, I followed the instructions of the Fs tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) but I'm having a problem at the last step of the process (mri_glmfit). I've checked that all the folders have the same number of folders and documents. Moreover, I've also checked, visually, all the thickness images but there is no problem there. However, when I run mri_glmfit command in the console appears: Loading gamma0 file MatrixRead( ) - file open failed No such file or directory ERROR: loading gamma0 FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c OS: ubuntu 16.04LTS I attach mri_glmfit.log Thank you very much in advance, Gemma -- *Gemma Salvadó Blasco*Neuroimage PhD Student *BarcelonaBeta* * Brain Research Center (BBRC) *gsalvado(a)barcelonabeta.org <enebot(a)fpmaragall.org> T. (+34) 902 33 15 33 <https://www.google.com/search?client=ubuntu&channel=fs&q=fundacio+pasqual+m…> C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Aquest missatge i els seus annexos poden contenir informació confidencial i exclusiva per al destinatari. El seu contingut no constitueix un compromís per part de l'emissor. Si rep aquest missatge per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent. Gràcies per la seva col·laboració. *Este mensaje y sus anexos pueden contener información confidencial y exclusiva para el destinatario. Su contenido no constituye un compromiso por parte del emisor. Si recibe este mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al remitente. **Gracias por su colaboración. *This message and attachments may contain confidential and exclusive information intended only for the individual named. The content of this message does not imply any commitment by the sender. If you have received this e-mail by mistake, please delete it before reading or distributing and notify the sender. Thank you for your cooperation. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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Re: [Freesurfer] reconstruction for very significant atrophy
by Rockers, Elijah D. 11 Jan '18

11 Jan '18

Thanks Bruce. I went over some more images with our PI and he was mostly satisfied with the pial/white segmentations. The real problem here is that our results look correct, except for they seem to be translated vertically by a small amount, comparing with what we see on the MRIs. What can we check to make sure everything is lining up correctly? - Eli On Thu, 2018-01-11 at 08:08 -0500, freesurfer-request(a)nmr.mgh.harvard.edu wrote: Message: 5 Date: Wed, 10 Jan 2018 20:26:11 +0000 From: "Rockers, Elijah D." <edrockers(a)houstonmethodist.org<mailto:edrockers@houstonmethodist.org>> Subject: [Freesurfer] reconstruction for very significant atrophy To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <1515615971.3868.3.camel(a)houstonmethodist.org<mailto:1515615971.3868.3.camel@houstonmethodist.org>> Content-Type: text/plain; charset="utf-8" Hello, We have some images that reflect severe atrophy in some subjects, in which gray matter is virtually undetectable on the MRI in some regions. However, upon checking the segmentations visually, the white/pial surfaces are reflecting a significant cortical thickness in these areas. Is there perhaps any recon-all setting that might extend the white matter area out a little more aggressively than it does with the default settings? Thanks, - Eli Houston Methodist. Leading Medicine. Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHo… and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMet…. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.ed… ------------------------------ Message: 6 Date: Wed, 10 Jan 2018 15:28:25 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] reconstruction for very significant atrophy To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1801101527330.32719(a)gate.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.20.1801101527330.32719@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Eli it's hard to say without looking at an image. Can you upload a subject and point us at a spot you think is incorrect? And do you really think the thickness should be 0 - there is no gray matter left at all? That seems unlikely.... cheers Bruce

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Amydala segmentation
by 郑凤莲 11 Jan '18

11 Jan '18

Hi FS experts, I ran "segmentHA_T1.sh 0010006 $SUBJECTS_DIR" for amydala segmentations. But there is only hippocampal subfields, no amydala segmentation .txt file in mri file. I ran ''recon-all'' in FS 6.0, and copy segmentHA_T1.sh and checkMCR to FREESURFER_HOME. Why there is no files of amydala? I am looking forward to your reply. Thank you very much. Sincerely, Zheng

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Errors while compiling FreeSurfer
by zuxfoucault Wong 11 Jan '18

11 Jan '18

Hi Freesurfers, Referring to https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-October/054329.…, I still got errors as following after compiling tcltktixblt via build_tcltktixblt.csh as the instruction in https://archive.fo/sNCX#selection-971.5-971.26 on ubuntu 16.04. /usr/bin/ld: IconLoaderTest.o: undefined reference to symbol 'Tcl_GetStringResult' /home/bc/software/environment/freesurfer_src/centos6-x86_64-packages/tcltktixblt/current/lib/ libtcl8.4.so: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status Makefile:947: recipe for target 'IconLoaderTest' failed make[2]: *** [IconLoaderTest] Error 1 make[2]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/vtkutils' Makefile:1256: recipe for target 'check-am' failed make[1]: *** [check-am] Error 2 make[1]: Leaving directory '/home/bc/software/environment/freesurfer_src/freesurfer/vtkutils' Makefile:1060: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1 Any suggestions? Thank you for your time! Best, Foucault

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Errors on compiling FreeSurfer
by zuxfoucault Wong 11 Jan '18

11 Jan '18

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Nonlinear CVS registration into average brain for coordinates
by Zhou, David Wei 10 Jan '18

10 Jan '18

Hi all, I have a data set of 14 subjects with intracranial (both cortical and subcortical) electrode implants, already recon'ed in Freesurfer, with an average brain + surface computed of these subjects. I would like to map each subject's electrode coordinates (a set of RAS points) into the average brain using a nonlinear transformation to account for individual deviations in surface topology. I'm trying to figure out the steps that must be taken to achieve this. With my average brain as a template, it seems like I would use mri_cvs_register to produce each subject warped onto the template. After generating those warps, how does one apply the same warp to a set of coordinates, for example to find out where my electrodes end up in the template brain? Which output file in .../cvs contains the data necessary to compute the coordinates in the template? I'd appreciate any instruction, thanks! David

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Re: [Freesurfer] hippocampal subfields in younger populations
by Iglesias Gonzalez, Eugenio 10 Jan '18

10 Jan '18

Dear Christian, They atlas is built using subfield segmentations on scans of older adult brains, but: 1. it’s also built with whole hippocampus segmentations of scans of subjects of a wider age range. 2. the deformation model should be able to account for large parts of the anatomical differences between subjects of different ages. > I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. I agree with this statement. I hope this helps! /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Christian Krog Tamnes <c.k.tamnes(a)psykologi.uio.no> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 10 January 2018 at 11:33 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] hippocampal subfields in younger populations Dear FreeSurfer and hippocampal subfield segmentation developers, I have noted that the FS6.0 hippocampal subfield segmentation procedure was developed using scans of older adult brains. Has the application of this method to kids, adolescents and/or young adults in any way been validated? Or do you have any thoughts regarding such use of the method? I would think this would be an issue for young kids that have markedly different brain volumes, but not for older kids and young adults that differ less dramatically from older adults. But I would greatly appreciate any input regarding this. Best regards, Christian

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