Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

Dear freesurfer users
by 주요한 12 Jan '18

12 Jan '18

Dear all, I’m a beginner in FreeSurfer. Actually I tried to get an information for cerebellum volume. Thus I installed the FreeSurfer and typed recon-all ~ ... After the processing, I got an information from aseg.stats in the stats folder. The information is here. # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 8186 8459.1 Left-Lateral-Ventricle 39.5864 11.4363 22.0000 93.0000 71.0000 2 5 141 190.2 Left-Inf-Lat-Vent 56.3475 10.4033 34.0000 78.0000 44.0000 3 7 12336 13138.8 Left-Cerebellum-White-Matter 87.7091 6.0827 35.0000 103.0000 68.0000 4 8 55173 55127.2 Left-Cerebellum-Cortex 66.0291 11.1028 8.0000 95.0000 87.0000 (I guess the information is..) The volume of Left cerebellum-white-matter : 13138.8 mm3 The volume of left cerebellum-cortex : 55127.2 mm3 However, as you know I’m only a beginner. Thus I guess the information is as that, but I cannot sure. Would you let me know - is this correct information or not? If it is not, please let me know how to get the information for cerebellum volume. Thank you. Best Regards John.

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making masks with subfields etc
by Erik O'Hanlon 12 Jan '18

12 Jan '18

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why freesurfer is not able to segment frontal cortex
by Vidhu Agrawal 12 Jan '18

12 Jan '18

Respected Sir Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_middle.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_operacula.nii --match 1106 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_orbital.nii --match 1107 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_inf_triangula.nii --match 1108 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_middle.nii --match 1109 mri_binarize --i aseg.mgz --o ctx-lh-g_frontal_superior.nii --match 1110 but it is not segmenting any region Looking forward for your reply. Thanking you With regards vidhu agarwal

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Recon-all Hires Segmentation Failure
by Giovana dos Santos Cover 12 Jan '18

12 Jan '18

Dear Freesurfer Developers, I am trying to segment the grey matter and pial surface using the FreeSurfer command recon-all with the hires flag. But even though there is no error while executing my code, when I analyze the output surfaces, the segmentation is missing some areas in the brain (I attached an image to show these brain regions). My command is: recon-all -all -s $SUBJ -hires -i $IMAGE -expert $EXPERT_FILE My expert file contains: mri_em_register -p .5 mris_fix_topology -s 50 mris_inflate -n 100 Does anyone have any thoughts on how to troubleshoot my problem? Thanks in advance, Gio. 1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2. u-name -a: Linux ubuntu 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux [cid:b5b990e1-aacc-4a2f-a73e-0d92496f8736]

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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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Freesurfer January 2018