Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

Amygdala Segmentation T1.v20 Command
by Deng, Yushan Wisteria 07 Jan '20

07 Jan '20

Dear Freesurfer experts, Happy new year! I encountered an issue with the quantifyHAsubregions.sh command as I tried to extract amygdala subnuclei values from a previously segmented dataset. I tried both commands below, specifying the version (v20) and not: quantifyHAsubregions.sh amygNuc T1 All_Amyg [subjects_dir] quantifyHAsubregions.sh amygNuc T1.v20 All_Amyg [subjects_dir] The command did not run. No error message was given. It just skipped to a new command line. Please see attached for a screenshot. The recon was done in Freesurfer 5.3 and the sample size is very big (~1400). I wonder if that or anything else could be causing the problem. Any guidance is immensely appreciated! Thank you! Wisteria Wisteria Deng Clinical Research Coordinator Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2611 Charlestown, MA 02129 Phone: 617-643-4441

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Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?
by Mohammad Rashid 06 Jan '20

06 Jan '20

External Email - Use Caution Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! ________________________________ From: Mohammad Rashid <17mrr6(a)queensu.ca> Sent: Monday, January 6, 2020 12:04 PM To: Tim Schäfer <ts+ml(a)rcmd.org> Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated? Ah okay, I understand now, thank you very much for the help! In hindsight this was a stupid question. What you said makes things perfectly clear. Thanks again! ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Tim Schäfer <ts+ml(a)rcmd.org> Sent: Monday, January 6, 2020 3:29 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated? External Email - Use Caution In your command line: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` you run the command only for that single subject, 'subj507'. That is exactly what will happen, no command will be run for the other subjects, so their data remains unchanged. It has nothing to do with editing or not. If you want to run again for other subjects, you would have to run the recon-all command with their subject IDs (one command per subject). I hope I did not misunderstand your question? Tim > On January 4, 2020 at 6:09 PM Mohammad Rashid <17mrr6(a)queensu.ca> wrote: > > > External Email - Use Caution > > I recently ran this command: > `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having edited aseg.mgz (there was too much matter labelled as right hippocampus, so my edit was simply overwriting Right-Hippocampus voxels with Right-Cerebral-White-Matter ones). > > After the command's error-free completion, I checked the hippocampal volume measurements of all of the participants again using asegstats2table and found that they were all unchanged, except slight changes to subject subj507's measurements. > > So when instructed, does freesurfer only redo the reconstruction and recalculate stats only for those subjects that you've edited? If so, is there a way to have it recalculate every subject, not just those I've edited? > > Thank you in advance. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.… -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.…

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Re: [Freesurfer] Run Recon-all Parallel on Linux
by Frank Chau 06 Jan '20

06 Jan '20

External Email - Use Caution Dear Bruce, No, I want to run recon-all on 4-8 subjects at the same time. I could find detail tutorial on the Mac platform (Run: "ls *.nii | parallel --jobs 4 recon-all -s {.} -i {} -all -qcache", after installing Xcode and Homebrew.) But I couldn't find any similar information on the Linux platform. Regards Frank On Jan 3, 2020 11:15 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Frank do you mean completing a single recon faster? The easiest way to do that is to use the -openmp <N> flag, and set <N> to the number of threads/cores you want to use. Alternatively if you have enough RAM you can just run multiple recon-alls at the same time (which will give you a bigger effective speed increase) cheers Bruce On Fri, 3 Jan 2020, Frank Chau wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > > May I know how to run Recon-all in parallel on Linux? I have read some > source said that can use "gnu parallel" to complete it. But they do not > describe it in detail how to perform it. > > > Regards > > > Frank > > --------------------------- > > FRANK C Y CHAU > > > Research assistant > > Division of Neurology > > Department of Medicine > > > Tel: +852 6340 2553 > > Fax: 2872 5828 > > > E-mail : cyfrank(a)hku.hk > > > > Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, > Hong Kong > > >

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Question regarding T1 map from spoiled 3D GRE
by joe vanderlo 06 Jan '20

06 Jan '20

External Email - Use Caution Dear Freesurfer community, I computed T1 maps from Siemens VIBE (a spoiled 3D GRE variant; instead of Siemens FLASH (RF-Spoiled GRE)). I utilized mri_ms_fitparms to compute the T1 map (which looks ok) and compared the result to a T1 map (inline) from MP2RAGE. However, T1 values based on Siemens VIBE (FA: 4, 8, 13, 21, 34) are much lower than from MP2RAGE: (results from the same subject, same day/position/setup scan, same ROIs) WM/Corpus callosum: 652 ms (VIBE) vs 859 ms (MP2RAGE) Cerebellaer WM: 583 ms vs 834 ms --- GM/Cortex: 845 ms vs 1184 ms Deep/Inner GM: 780 ms vs 920 ms --- Liquor: 2222 or 3121 vs 2758 or 3652 ms Eye-Bulb: 112 vs 588 The literature suggests (mouse brain, 3T): Corpus callosum 1108±9 Internal capsule 913±16 Hippocampus 1310±15 Cortex 1246±28 (DOI: 10.1118/1.2968092) The literature suggests (rat brain, 3T): WM: 1084 or 1110 ms GM: 1820 or 1470 ms (DOI: 10.1002/mrm.20605) However, it appears that T1 values can be quite different (Fig. 3 from 10.1002/mrm.21313) #-----------# Therefore, I would like to ask: (1) Is it to be expected that T1 values differ dependent on the method used at same field strength and same scanner/setup? (2) Considering that mri_ms_fitparms has not option for B1 correction, can I "optimize" the maps in a different manner? Would it make sense to run N4B on the respective VIBE scans (before map computation) or maybe directly on the T1 map? (3) I would assume that the application of the VIBE sequence should be acceptable. Are there reasons not to believe so? Thanks in advance

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When rerunning recon-all from a later stage, are only edited participants' reconstructions recalculated?
by Mohammad Rashid 06 Jan '20

06 Jan '20

External Email - Use Caution I recently ran this command: `recon-all -autorecon2-noaseg -autorecon3 -subjid subj507` after having edited aseg.mgz (there was too much matter labelled as right hippocampus, so my edit was simply overwriting Right-Hippocampus voxels with Right-Cerebral-White-Matter ones). After the command's error-free completion, I checked the hippocampal volume measurements of all of the participants again using asegstats2table and found that they were all unchanged, except slight changes to subject subj507's measurements. So when instructed, does freesurfer only redo the reconstruction and recalculate stats only for those subjects that you've edited? If so, is there a way to have it recalculate every subject, not just those I've edited? Thank you in advance.

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Inflation cortical hemisphere to sphere in Freesurfer !?
by Fatemeh Ahmadi 05 Jan '20

05 Jan '20

External Email - Use Caution Dear experts,May I know the brain cortical hemisphere inflation method to the sphere in Freesurfer is a conformal mapping (such as Ricci flow)!? Regards & thanks

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Getting issue in running bt_recon
by sudhakar Mishra 04 Jan '20

04 Jan '20

External Email - Use Caution Hi, Please suggest something for the following error. Cannot allocate memory unsupported matlab format 839537524 (unknown) Best, Sudhakar Mishra Research Scholar Website <https://modelingemotion.wixsite.com/emotion> *सर्वद्वारेषु देहेऽस्मिन्प्रकाश उपजायते । ज्ञानं यदा तदा विद्याद्विवृद्धं सत्त्वमित्युत ॥* *श्रद्धावाँल्लभते ज्ञानं तत्परः संयतेन्द्रियः। ज्ञानं लब्ध्वा परां शान्तिमचिरेणाधिगच्छति।।* *योगश्चित्तवृत्तिनिरोधः*

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Surface file format differences
by Joshua Jacobs 03 Jan '20

03 Jan '20

External Email - Use Caution Hello, When working with the nightly development version of FreeSurfer recon-all (freesurfer-linux-centos6_x86_64-dev.tar.gz 23-Dec-2019 06:01) The surface file format differed by one character (\n) from previous versions. What makes me suspicious of this change is the difference between output and the fsaverage subject. See head -n 3 surf/rh.white for each below. recon-all output: ��created by root on Tue Dec 31 23:05:44 2019 ��YcR@��]�zk=�}��m�K�4�F��h��{yM��Ò��0@ �(��ě��̫�VY�vտ�1G�s��@t�4�*��>��C80�d?f��5��˿O+@�H&�f޿ˍ��ο�\i�.3��I� ^��dn��ٿp�7_��:�x��)��!�o�� fsaverage: ��created by greve on Thu Jul 19 12:52:07 2018 �A�3^�f�Bp�nA� This is the case for all sample data in the FS/subjects/ directory save for "bert". The data of which had been produced on 2019-12.21. Although I have not tried freeview on these files, it fails to open in the python library nibabel.freesurfer.io.load_geometry. Is this change intended? Thank You. Josh J.

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hardware upgrade affect Freesurfer?
by Dincer, Aylin 03 Jan '20

03 Jan '20

External Email - Use Caution Hi FreeSurfer Experts, Would upgrading computer hardware affect FreeSurfer output? We are using FreeSurfer version 5.3-HCP and we are considering upgrading our server. It will have the same operating system but different computer specs (memory, cpu, graphics, etc.). Thank you! Aylin -------------------- _____________________________ Aylin Dincer Senior Research Technician NeuroImaging Laboratories Imaging Core, Benzinger Lab 314-362-3629 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mis-registration question
by Nasiriavanaki, Zahra 03 Jan '20

03 Jan '20

Dear Freesurfers Hi I have a subject that the registration is not done correctly in two runs (run 12 and run 15) . The tkregister-sess values for this subject is shown below. Subject 1 10 0.2628 Subject 1 11 0.3038 Subject 1 12 0.7639 Subject 1 13 0.3364 Subject 1 14 0.3346 Subject 1 15 0.9361 Subject 1 16 0.2584 Subject 1 17 0.2488 I attached the screen shots from tkregister2 to this email. The functional data is only collected in a slab of parietal and occipital lobe. I appreciate if you let me know how to fix them. Thanks Mona [cid:6833a8d0-828b-4f31-9b61-2a4a1c3a670d][cid:7d39f7e2-609a-43a5-a964-dd95f8179c30] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Freesurfer January 2020