Freesurfer February 2021

freesurfer@nmr.mgh.harvard.edu

98 participants
118 discussions

Regarding recon-all's -T2pial option
by S.R. Poortman 09 Feb '21

09 Feb '21

External Email - Use Caution Dear sir/madam, Being interested in improving the pial surface construction in our datasets (acquired at 3 Tesla), I have been considering the addition of the T2-weighted image from our studies' protocol to our recon-all run. However, looking at its acquisition parameters, I'm sure as to whether making use of this T2-weighted image would benefit pial surface construction. First, some parameters: T1-weighted image: 3D sagittal spoiled-gradient FFE TR/TE: 10.02/4.6 FA: 8 Slices: 200 .75x.75x.8 mm³ T2-weighted image: Dual Echo - TSE clinical scan transversal T2-weighted TR/TE: 600/80 FA: 90 17 slices of 5 mm slicegap: 1.2 mm And our initial recon-all run, without the T2-weighted image: recon-all -all -i sub -subjid subid -3T -hires -expert expert.opts The recon-all run I had in mind with the T2-weighted image added: recon-all -all -i sub -subjid subid -3T -hires -expert expert.opts -T2/path/to/T2 -T2pial expert.opts content: mris_inflate -n 50 Now, my question is, would a T2-weighted image acquired at the abovementioned parameters actually do the pial surface construction any good when included to a recon-all -hires run on submillimeter T1-weighted images like ours? Or, would it perhaps worsen pial surface construction, even (owing to, for example, the low resolution of the T2-weighted image)? I have tested this on one of our subjects, which had a lot of dura included to the pial surface in the recon-all run without the addition of the T2-weighted image. After running recon-all on this subject again, this time with the T2-weighted image included and -T2pial turned on, (slightly) less dura was included to the pial surface (i.e., improvement; top two images for comparison example), but now it also seemed to exclude some parts of the cortex on other spots (bottom two images for comparison example), as well. [cid:196242f0-e97c-43e8-b940-8843db62ab07] [cid:737f0df8-9a94-4b61-ac9f-a403d5389acf] dura inclusion comparison left: without -T2 and -T2pial right: with -T2 and -T2pial and: [cid:afefd874-e994-4b34-87fd-cef34040bdce] [cid:d7047b7f-d15f-424d-8f5e-1c9602a3f298] pial surface quality comparison in sulcus left: without -T2 and -T2pial right: with -T2 and -T2pial I would greatly appreciate FreeSurfer experts' advice on this. Thank you very much for your time! Kind regards, Simon Poortman (Erasmus MC, Rotterdam)

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beta coefficients
by Marina Fernández 09 Feb '21

09 Feb '21

External Email - Use Caution Dear experts, In addition to t and p-value, I would like to report the beta coefficient of the fixed effects in the following regression equation for the vertex showing the max statistic within the cluster that survived multiple comparison correction: y = β0 + β1*sex + β2*age + β3*(sex+age) + e I know that beta.mgh contains the beta estimates corresponding to the intercepts of male and female and the slopes of age for each sex. However, what I need is the beta corresponding to the intercept (β0), and the beta for the slope of sex (β1), age (β2) and sex*age interaction (β3). I also need the residual variance of the model (e), but rvar.mgh contains 4 values, 2 for the intercepts and another two for the slopes. I would really appreciate if you could help me to obtain this information. Thanks a lot in advance Marina

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Issues using curl for FreeSurfer tutorial data
by Karten, Jordan 09 Feb '21

09 Feb '21

Hi FreeSurfer Community, I was wondering if anyone else has been receiving the error "curl: (23) Failed writing body (8192 != 16384)" when attempting to download the data for tutorials, and if anyone had a solution that worked? I tried to find a fix online, but this issue seems to have many causes. Thanks for any help! All the best, Jordan

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Re: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release
by fsbuild 09 Feb '21

09 Feb '21

External Email - Use Caution I have another library change you can try for freesurfer 6.  I will send it to your private email shortly. - R. On Feb 8, 2021, at 06:14, Costanza Parodi <costanza.bianca.parodi(a)gmail.com> wrote:        External Email - Use Caution        no difference has been detected  in the files but the same error comes up.  Error opening file dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib  Expected in: /usr/lib/libSystem.B.dylibI would like to avoid disabling the SIP. Any other suggestions? Does the v7 have the same bug?On 6 Feb 2021, at 00:15, fsbuild <fsbuild(a)contbay.com> wrote:If you followed the directions for the 6.0.0 patch, then you replaced the copy of libgomp.1.dylib inside the freesurfer application bundle with the updated version from the patch archive under,./Freeview.app/Contents/Frameworks/libgomp.1.dylibBut there is another copy of libgomp under,./lib/gcc/lib/libgomp.1.dylibIn the original 6.0.0 download, those 2 copies of libgomp are identical (or unpatched).So you could try using the patched version of libgomp.1.dylib to replace the copy under ./lib/gcc/lib as well.You could move it aside and replace it with something like,$ sudo cd <base path>/freesurfer/lib/gcc/lib$ sudo mv  libgomp.1.dylib  OLD_libgomp.1.dylib$ sudo cp -p  -f  ../.../../Freeview.app/Contents/Frameworks/libgomp.1.dylib  .$ sudo diff  libgomp.1.dylib  ../../../Freeview.app/Contents/Frameworks/libgomp.1.dylib… no diff results should be reported ...Then try running your command again.- R.On Feb 5, 2021, at 12:37, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote:Yes, this probably has to do with SIP being enabled, which blocks libraries stored in /usr. This was a pretty common issue that people had with v6. You can try disabling SIP via MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1uG6UXYVIX4Qv9ThgW7BBFXpQkpCa09pA5EP47j…; on behalf of Costanza Parodi <costanza.bianca.parodi@gmail.com>Date: Friday, February 5, 2021 at 9:30 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release        External Email - Use Caution        Hello Freesurfer Developers, I was attempting to use the mri_cvs_register command ( mri_cvs_register -- mov subjid  -- mni) and I received this error: asegfname asegUsing m3z type morph files.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 Abort I resolved the issue by downloading the Freeview_6.0.0_MacOS patch, but a new error came up :  Error opening file dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib  Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address  Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib  Expected in: /usr/lib/libSystem.B.dylib I did not find similar errors in the archive. Should I disable SIP? Could you help me trouble-shoot this error? My freesurfer is installed on an external hard disk and I am processing my subjects on my Mac desktop.  1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c2) MacOs High Sierra version 10.13.63)Darwin MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 18 21:21:34 PDT 2020; root:xnu-4570.71.82.5~1/RELEASE_X86_64 x86_644)Xquartz 2.7..11       _______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/12n5HE8E0nxxKBXpiKD0HN8y_lOSwlBdKZ9IxF… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Post-doctoral position / tenure-track potential / neuroimaging
by Marcin Szwed 09 Feb '21

09 Feb '21

External Email - Use Caution Post-doctoral position / tenure-track potential / neuroimaging MRI neuroimaging of the impact of air pollution on school age children. https://secure-web.cisco.com/1o-JZUmYuwXe-IsNnj3tFSchXCuQr6gLv3C1rCZMjHdnFk… A postdoctoral position is available in the Neurosmog project in the Szwed lab in the department of Psychology at the Jagiellonian University in Kraków, Poland, to work on the impact of ambient air pollution on the developing brain in school-age children. The successful candidate is expected to take the role the associate leader in the ongoing collection and the planned analysis of the rich Neurosmog neuroimaging data (task and RS- fMRI, DWI, structural, myelin mapping). The Neurosmog project endeavours to investigate the effects of air pollution on behavioural and neural changes in school-age children. It combines four scientific teams in the fields of pollution assessment, child psychology, neuroimaging and epidemiology with the common goal of determining the impact of ambient air pollution on the developing brain in school age children. It uses MRI imaging and in-depth psychological testing of 300 cases of an ADHD group and 500 cases of a control group selected from the general population. Data collection has already began, and its end is foreseen in July 2022. This post is fully funded by a 3.5M EUR grant awarded by the Foundation for Polish Science (Fundacja na rzecz Nauki Polskiej, FNP) The candidate is expected to take the role the associate leader of a large-scale neuroimaging project with an enormous relevance to urgent public health issues. The position is initially for 33 months, and can be extended and converted into a tenure-track position on the condition of receiving external funding. The Institute of Psychology will support and encourage this extension. It will also cover the cost of the necessary advanced degree (Habilitation) required for career advancement. The candidates’ job will be to: • supervise ongoing MRI data collection • With the help of the projects’ data manager/programmer and a PhD student, and in liaison with the epidemiology/child psychology groups, and plan, build and execute MRI data analysis • Present and publish project results • Plan an expansion of the neuroimaging data analysis by using the vast amount of unique data gathered under Neurosmog. Options include, but are not limited to fields such as green space research, socioeconomic research, ADHD research, or similar • In the last year of the postdoc contract, apply for new funding schemes The candidate will be based in Institute of Psychology at Jagiellonian University in Kraków, Poland. JU Institute of Psychology, ranked number one in Poland for psychological research. Located in a newly renovated building in the very heart of Kraków, a vibrant city famous for its architecture, culture and quality of life, the Institute is a renowned centre of excellence and hosts research teams working on themes ranging from neuroimaging and neuroplasticity to health and social psychology. Applicants must have a PhD (or equivalent) degree in psychology, neuroscience, or a related field including, computer science, applied mathematics, biology etc., obtained not earlier than in 2012 (extensions possible for parental leave). Previous experience in MRI imaging is indispensable. Experiences with neuroimaging packages (SPM, FSL, Freesurfer and similar), structural MRI and DTI or large-scale MRI datasets will be a plus, but are not obligatory. Terms of employment: The position is initially available for is initially for 33 months (until end of December 2023). Salary for this position will be approximately 7300 PLN (Net) - for candidates who obtained their PhD after 2015, and approximately 8500 PLN (Net) - for candidates who obtained their PhD between 2012 and 2015. Both are sufficient for a high standard life in Kraków, where living costs are substantially lower than the EU average. The position can be extended on the condition of receiving external funding. The candidate will be expected to apply for Polish and international tenure-track funding schemes such as the NAWA Chair Programme the NCN/Max Planck Dioscuri Programme (before beginning of the contract), and the NCN funding schemes (OPUS, SONATA, SONATA BIS, during his/her postdoc contract). Benefits include health coverage (NFZ) for the candidate and his/her family, summer and winter holiday benefit for children and teenagers, childcare subsidy and sport and leisure activities/subsidies. The NeuroSmog project provides ample research funding for equipment, database access, software, conferences and collaborative travel. To apply send a CV including a list of publications, research experience and scientific interests, and email addresses of two science or professional mentors for possible references to: m.szwed(a)uj.edu.pl Enquiries are welcome, and should be sent to the same email address Deadline for application is 26.02.2021. Starting date is April 2021 but can be postponed in exceptional cases

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Workshop on Artificial Intelligence in NMR/MRI and Neuroscience
by Nicola Toschi 08 Feb '21

08 Feb '21

External Email - Use Caution Dear Freesurfer users, I hope this message is not out of place in this list. If it is, please ignore! I am writing to let you know about a high-level workshop we have organized titled "/The promises and Dark Sides of Artificial Intelligence in NMR, MRI and Neuroscience/", which is now online at https://secure-web.cisco.com/16ixw_i6BPFmKCirvs3yOpFZBsOe6rAcNXR8zplPC_9eTp… (complete info are available on the website). We are particularly glad to have recruited _eminent speakers both from the scientific field and from Industry_ (e.g. Philips, Siemens, Amazon Web Services etc.) and to have been able to include talks on e.g. regulatory and ethical aspects as well as sections on e_xplainability, clinical applications and precision medicine_. The format is both asynchronous (until *March 31st*) and synchronous (*live *session on Feb *19th, 2021*). ** The registration *deadline *is *Feb 14th. *The workshop also carries 30 ECM credits.* * In the hope that this initiative may be of interest for you, your group (Empirical Inference) and Institute (MPI for Intelligent Systems), I would be most grateful if you could relay this scientific and educational resource among your local community as well as professional networks. Please, do not hesitate to contact me for more information. Best Regards, Nicola Toschi PS below you can find some social media posts of this annoucement for fast sharing: Twitter: https://secure-web.cisco.com/19wfe8NTs6BcghR1QgJE7XIPjlhtSJM-4phbv197Rde3id… Facebook: https://secure-web.cisco.com/1OFTx4jTf9EvgHOq_35AESclP5jtClp-vlijK5-rZTcxRq… Instagram: https://secure-web.cisco.com/1USByxHXPJfIKKfcItZcYfTBdK3Fp7j9UmzaXhDIGQ1q1K… LinkedIn: https://secure-web.cisco.com/1viCIXQ0B_0IOfzus-8CBV-CbnJCh0nGG_2mS547pV27-8… -- Prof. Nicola Toschi Associate Professor of Medical Physics Medical Physics Section - Department of Biomedicine and Prevention University of Rome "Tor Vergata" Via Montpellier 1 - 00133 Rome (IT) toschi(a)med.uniroma2.it Research Staff, Associate Investigator A.A. Martinos Center for Biomedical Imaging - Harvard Medical School/MGH 149 13th street, 02129 Boston (MA), USA nicola(a)nmr.mgh.harvard.edu -- This email has been checked for viruses by Avast antivirus software. https://secure-web.cisco.com/1jkaGBfKYYGqr5hk9GieAti-oND1hcigV7en69WTwpsQZb…

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Number of threads in mri_em_register
by gunes 08 Feb '21

08 Feb '21

External Email - Use Caution Dear freesurfer developers, I'm using freesurfer v5.3.0 and having problems with the number of threads opened by `mri_em_register`. It automatically opens up as many threads as there are in the system, but I need to limit that. I have seen this post with the same problem: https://secure-web.cisco.com/19w3ZWmagO9QFaobk1ln0Z4sQQWaHjFCCO6n7ZqpGmL6VZ… In the end, it seems to be solved by setting OMP_NUM_THREADS to 1 in the mri_em_register script, but it is a binary file. I don't know how to set it. Kind regards, Gunes

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Can't find longHippoSubfieldsT1.sh
by Xin Qi 08 Feb '21

08 Feb '21

External Email - Use Caution Dear Freesurfer Community, I ran the Freesurfer longitudinal pipeline for my subjects (1.5T, T1_data, 6 timepoints each). Now I want to continue with the longitudinal segmentation of hippocampal subfields:https://secure-web.cisco.com/1GVcN-oB6m3ReFE6G1f2L7PU8wxxvY2rraj4… However, when I want to run the command: longHippoSubfieldsT1.sh <baseID> I get the error message "bash: longHippoSubfieldsT1.sh: command not found" First thing I did, was checking the Freesurfer folder for the longHippo..sh file. I am using FS 7.0 but the file is not available. *So my questions: where can I get the file longHippoSubfieldsT1.sh or what else can I do to proceed with the HC subfield segmentation?* Thanks a lot for your support and looking forward to your reply. Best Xin

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Re: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release
by fsbuild 08 Feb '21

08 Feb '21

External Email - Use Caution If you followed the directions for the 6.0.0 patch, then you replaced the copy of libgomp.1.dylib inside the freesurfer application bundle with the updated version from the patch archive under, ../Freeview.app/Contents/Frameworks/libgomp.1.dylib But there is another copy of libgomp under, ../lib/gcc/lib/libgomp.1.dylib In the original 6.0.0 download, those 2 copies of libgomp are identical (or unpatched). So you could try using the patched version of libgomp.1.dylib to replace the copy under ./lib/gcc/lib as well. You could move it aside and replace it with something like, $ sudo cd <base path>/freesurfer/lib/gcc/lib$ sudo mv  libgomp.1.dylib  OLD_libgomp.1.dylib$ sudo cp -p  -f  ../../../Freeview.app/Contents/Frameworks/libgomp.1.dylib  .$ sudo diff  libgomp.1.dylib  ../../../Freeview.app/Contents/Frameworks/libgomp.1.dylib… no diff results should be reported ... Then try running your command again. - R. On Feb 5, 2021, at 12:37, Hoopes, Andrew <AHOOPES(a)mgh.harvard.edu> wrote:Yes, this probably has to do with SIP being enabled, which blocks libraries stored in /usr. This was a pretty common issue that people had with v6. You can try disabling SIP via http://secure-web.cisco.com/1MdCcIwOcu00nJ… <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Costanza Parodi <costanza.bianca.parodi@gmail.com>Date: Friday, February 5, 2021 at 9:30 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release        External Email - Use Caution        Hello Freesurfer Developers, I was attempting to use the mri_cvs_register command ( mri_cvs_register -- mov subjid  -- mni) and I received this error: asegfname asegUsing m3z type morph files.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 Abort I resolved the issue by downloading the Freeview_6.0.0_MacOS patch, but a new error came up :  Error opening file dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address  Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib  Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address  Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib  Expected in: /usr/lib/libSystem.B.dylib I did not find similar errors in the archive. Should I disable SIP? Could you help me trouble-shoot this error? My freesurfer is installed on an external hard disk and I am processing my subjects on my Mac desktop.  1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c2) MacOs High Sierra version 10.13.63)Darwin MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 18 21:21:34 PDT 2020; root:xnu-4570.71.82.5~1/RELEASE_X86_64 x86_644)Xquartz 2.7.11       _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Freesurfer VirtualBox password
by fsbuild 05 Feb '21

05 Feb '21

External Email - Use Caution I will send the info to your email shortly. -R. Gabriel Mackie (gmac8922(a)gmail.com) February 4, 2021 at 08:45 Hello FreeSurfer Developers, I am attempting to start Ubuntu via VirtualBox on Windows 10, but Ubunturequests a login password for the "Developer" account, while installationguide assumes automatic login. Can I ask for the password or is there any other way to successfully startUbuntu? For the installation and setup, I followed  the Windows VM Install & Setup,using the virtual disk image of the VM Ubuntu_710_clone_2.7z (downloaded onFeb 2, 2021). Thank you for your help,Gabriel _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/11fpBMUrpoysPqdTkQrMml3xZbiQJpf9qM8PCjT_C4Ok17…

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Freesurfer February 2021