Freesurfer

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30076 discussions

How to automate recon-all command for multiple subjects
by Vivek Sharma 22 Nov '18

22 Nov '18

External Email - Use Caution Hi, I'm using freesurfer to generate head surfaces using MRI file. I want to execute recon-all command for number of subjects, but unable to run it. The script I'm using is: for i in `cat *subs.txt*` do recon-all -s $i -all -qcache done subs.txt contains the name of folder that contains .nii file. The scripts ends with the following error: ERROR: no run data found in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri. Make sure to have a volume called 001.mgz in /cblhome/vivek/freesurfer/subjects/sub-CC110033_T1w/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux cblhost 4.4.0-83-generic #106~14.04.1-Ubuntu SMP Mon Jun 26 18:10:19 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Please let me know how I can run recon-all for multiple subjects. Thank you. -- Vivek Sharma Mobile: +919953582034 Skype: vivek.sharma1015

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Corrupted T1 file (?) but segmentation look fine
by Anneliis Sartin-tarm 21 Nov '18

21 Nov '18

External Email - Use Caution Hello all, I have been running into a curious problem with a couple brains (8 out of 150 seem to have this problem) running through the recon-all pipeline. Upon loading brainmask.mgz, T1.mgz, and corresponding white matter and pial surfaces in Freeview, my colleague and I received an error that T1.mgz failed to load. Segmentation and parcellation seemed to run smoothly and accurately, however, the size of the T1.mgz file was 0. Assuming the file had been corrupted somehow (our server through which we run recon-all and store our data has tons of available memory), we reran the brains affected. Upon loading up the same re-run surfaces, T1.mgz loaded into the GUI as white, washed out voxels, displaying no brain at all. The size of this file is large, as well as all other surface and volume files. Curiously, the brainmask file seems normalized/stripped fine and surfaces displayed over the T1 look accurately segmented. I attached a screenshot displaying the T1.mgz file and surfaces that I'm referring to. I have a few concerns and questions. Because T1.mgz doesn't seem to be necessary for downstream manual editing and processing, can we proceed as normal, only displaying and using the brainmask file to make edits? Will our surface and volume metrics export properly without a usable T1 file? Lastly, any clues to how this might have occurred are welcomed. It seems like the mri_normalize step is the culprit, although the nu.mgz files corresponding to these brains seem normally sized. Best, Anneliis Sartin-Tarm Associate Research Specialist Neurocircuitry of Trauma and PTSD Study UW-Madison Dept. Psychiatry 608-262-6375

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faculty position at Stanford in Medical Imaging (fwd)
by Bruce Fischl 21 Nov '18

21 Nov '18

FYI ---------- Forwarded message ---------- Date: Wed, 21 Nov 2018 01:22:27 +0000 From: Jennifer A McNab <mcnabj(a)stanford.edu> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: faculty position at Stanford in Medical Imaging External Email - Use Caution Hi Bruce, The Radiological Sciences Lab in Stanford Radiology has an open faculty position, and we would appreciate your help distributing this information to suitable candidates. This is a broad area search for medical imaging, as described, so we encourage all strong applicants to apply. I would be happy to answer or redirect any questions regarding this position. Cheers, Jennifer _____________________________________ Jennifer A. McNab, Ph.D., Assistant Professor Radiology, Stanford University, Lucas P286 _____________________________________

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回复： ?????? ?????? Recon-all run error
by 1013364183 21 Nov '18

21 Nov '18

External Email - Use Caution Dear Bruce, I am sorry to let you wait so long, I have some troubles in transferring the data set, but it has been solved. Now I have sent the data set to ftp. I hope you can take the time to help us deal with the data set. We have already Running this data set for a long time but did not get results, the name of the data set is data_Yujunjie.zip,. The run command and the expert file are in the attachment. Express your heartfelt thanks again！ yours yujunjie ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月18日(星期天) 晚上11:15 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? ?????? Recon-all run error Instructions on how you can upload tarred and gzipped files here: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Sun, 18 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I am very sorry to bother you. We are currently experimenting with freesurfer, but I have > encountered a lot of problems during the experiment. We have three resolutions of data, the skull of > medium-resolution data can't be removed (neck can't be removed), and with high-resolution data, it > will report memory transfer errors. You said before that we can submit data sets to you, how should > we provide you with data sets? > > Thanks in advance > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??7??(??????) ????2:42 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] ?????? Recon-all run error > > does it occur if you run it outside of recon-all? Do you have enough free > ram? If so, you can filedrop us the dataset and we can try to replicate and > fit ix. > > On Tue, 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear Bruce, > > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > > don't think it's the reason for insufficient memory.. > > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > > version and set the expert file, this error will occur.Do I need to step through the instructions > to > > see the problem? How should this error be solved? > > > > Thanks in advance > > > > yours yujunjie > > > > ------------------ ???????? ------------------ > > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > > ????????: 2018??11??6??(??????) ????9:40 > > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > > ????: Re: [Freesurfer] Recon-all run error > > > > that certainly looks like something is running out of ram. Can you run > > the command that failed directly on the command line and see if it works? > > Was anything else running on the machine at the time? We do report total > > and free memory at the start of the recon in the recon-all.log file > > > > cheers > > Bruce > > On Tue, > > 6 Nov 2018, 1013364183 wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear FS, > > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > > mri_convert > > > command is executed. The specific errors are as follows: > > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > > mri_convert.bin "$@" > > > ERROR: converting to minc > > > We want to know if our high resolution image is too large for freesurfer to handle, or our > > computer > > > memory (64GB running memory) is limited. > > > > > > Thanks a lot in advance! > > > yours sincerely, > > > yu junjie > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'
by charujing123 21 Nov '18

21 Nov '18

External Email - Use Caution Hi, what is difference between 'lh_G_Ins_lg&S_cent_ins_volume' and 'lh_G_insular_short_volume'. Are these both insula? Thanks. Rujing 2018-11-21 charujing123

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nu_correct ERROR (FreeSurfer v6)
by Korom, Marta 20 Nov '18

20 Nov '18

External Email - Use Caution Dear FreeSurfer Developers, I have the most recent version of FreeSurfer installed on a MacOS Mojave (10.14) and as I was running recon-all, I received the following error message: "Assertion failed at line 742 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Darwin Martas-MacBook-Pro.local 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 recon-all -s plc0061 exited with ERRORS at Tue Nov 20 22:32:15 EST 2018" I reviewed many threads on the same error message, but none of them were solved. I have the same version of FreeSurfer on two other MacBooks (with older versions of iOS) and both work fine. I ran fixup_mni_paths as it was suggested on multiple threads and nu_correct, as well and I got the following message: "nu_correct nu_correct, version 1.12.0 Usage: nu_correct [-help] [options] in.mnc out.mnc" Any thoughts on what the problem might be and how it could be fixed? Could this be an iOS compatibility issue? Gratefully, Marta -- *Marta Korom | *PhD Candidate University of Delaware, Clinical Science e-mail: mkorom(a)udel.edu phone: 646 861 8461 http://www.abcintervention.org/

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differences between 'lh_G_front_middle_thickness' and 'lh_S_front_middle_thickness'
by charujing123 20 Nov '18

20 Nov '18

External Email - Use Caution Hi FS experts and users I found two middle frontal cortex in thickness, with different prefix. So what is the difference? Another question: Can I get the thickness of hippocampus and amygdala? Thanks. Rujing 2018-11-21 charujing123

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Bonferroni correction of 2spaces or 3spaces
by YAN Chao-Gan 20 Nov '18

20 Nov '18

External Email - Use Caution Dear freesurfer experts, I have a pretty naive question but would like to confirm. When we use --3spaces option in multiple comparison correction, does that mean we set the Cluster-wise threshold (cwp, not Cluster Defining Threshold or Cluster Forming Threshold) to 0.5/3=0.0167 for lh. Similar cwp at 0.0167 for rh and subcortical? In addition, if we use "--cortex" to restrict the calculation on cortex only, where can we find the corresponding mask or label file for cortex? Thanks, Chao-Gan -- Chao-Gan YAN, Ph.D. Professor, Principal Investigator Deputy Director, Magnetic Resonance Imaging Research Center Institute of Psychology, Chinese Academy of Sciences 16 Lincui Road, Chaoyang District, Beijing 100101, China - Initiator <http://rfmri.org/DPARSF>DPABI <http://rfmri.org/DPABI> <http://rfmri.org/DPARSF>, <http://dpabi.org>DPARSF <http://rfmri.org/DPARSF>, PRN <http://rfmri.org/PRN> and The R-fMRI Network <http://rfmri.org> (RFMRI.ORG <http://rfmri.org/>) http://rfmri.org/yan http://scholar.google.com/citations?user=lJQ9B58AAAAJ

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Re: [Freesurfer] License issue
by fsbuild 20 Nov '18

20 Nov '18

External Email - Use Caution Hi Sarah, I would just move that file aside (rename it to something that is not license.txt) and follow the instructions on the wiki to generate another license.txt file.  Then you could check it again with the previous commands. https://surfer.nmr.mgh.harvard.edu/fswiki/License - R. On Nov 20, 2018, at 18:30, Sarah Haigh <shaigh(a)unr.edu> wrote:        External Email - Use Caution        Hi,I ran the code and the license appeared, but no email address or numbers. These were the first few lines:FreeSurfer Software License Agreement ("Agreement")                    Version 1.0 (February 2011)Is this wrong? The rwx settings look correct.ThanksSarah On Nov 20, 2018, at 2:52 PM, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Hello Sarah,If you can bring up a terminal with your freesurfer environment set, then please try the following commands, i.e.,$ cd $FREESURFER_HOME$ cat $FS_LICENSE<output deleted>Without posting the contents of your license, I think the first line is an email address, followed by a line with several numbers, followed by 2 lines of text.$ ls -l $FS_LICENSE-rw-r--r--@ 1 userid  staff  57 Jan  9  2018 /Users/userid/license.txtthe rw-r-r privileges (644) mean its writeable only by you (which is fine).- R.- R.Sarah Haigh November 20, 2018 at 16:42External Email - Use Caution Yes, I set the FreeSurfer home environment and added the license file to that folder. It is Word readable.Sarah_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferGreve, Douglas N.,Ph.D. November 20, 2018 at 15:03did you put it in $FREESURFER_HOME/.license ? Is it world-readable?_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferSarah Haigh November 20, 2018 at 14:38External Email - Use Caution Hello Freesurfers,Can anyone help with a licensing issue I have? I downloaded Freesurfer the other day with a brand new license and got the following message: “ERROR: Invalid FreeSurfer license key was found in license file”. I tried getting a new license and even borrowed someone else’s license and they all came up with the same error. Any ideas?Thanks for your help.Sarah_____Assistant Professor,University of Nevada, Reno,Department of Psychology and Center for Integrative Neuroscience,1664 N. Virginia Street Reno, NV 89557-0296Carnegie Mellon University,Department of Psychology and Center for the Neural Basis of Cognition,5000 Forbes Avenue,Pittsburgh, PA 15213._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&amp;data=01%7C01%7Cshaigh%40unr..edu%7C16c5246a561d4631f7bc08d64f3ae949%7C523b4bfc0ebd4c03b2b96f6a17fd31d8%7C1&amp;sdata=W1G8vsv2ubqApboTTM9kTHllGoV%2Bc4aX9gC6sW2fTqI%3D&amp;reserved=0_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard..edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] License issue
by fsbuild 20 Nov '18

20 Nov '18

External Email - Use Caution Hello Sarah, If you can bring up a terminal with your freesurfer environment set, then please try the following commands, i.e., $ cd $FREESURFER_HOME $ cat $FS_LICENSE <output deleted> Without posting the contents of your license, I think the first line is an email address, followed by a line with several numbers, followed by 2 lines of text. $ ls -l $FS_LICENSE-rw-r--r--@ 1 userid  staff  57 Jan  9  2018 /Users/userid/license.txt the rw-r-r privileges (644) mean its writeable only by you (which is fine). - R. - R. Sarah Haigh November 20, 2018 at 16:42 External Email - Use Caution Yes, I set the FreeSurfer home environment and added the license file to that folder. It is Word readable. Sarah _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Greve, Douglas N.,Ph.D. November 20, 2018 at 15:03 did you put it in $FREESURFER_HOME/.license ? Is it world-readable? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Sarah Haigh November 20, 2018 at 14:38 External Email - Use Caution Hello Freesurfers, Can anyone help with a licensing issue I have? I downloaded Freesurfer the other day with a brand new license and got the following message: “ERROR: Invalid FreeSurfer license key was found in license file”. I tried getting a new license and even borrowed someone else’s license and they all came up with the same error. Any ideas? Thanks for your help. Sarah _____ Assistant Professor, University of Nevada, Reno, Department of Psychology and Center for Integrative Neuroscience, 1664 N. Virginia Street Reno, NV 89557-0296 Carnegie Mellon University, Department of Psychology and Center for the Neural Basis of Cognition, 5000 Forbes Avenue, Pittsburgh, PA 15213. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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