Freesurfer October 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
170 discussions

Optimal combination of MRI-sequences
by Erik Lindberg 18 Oct '16

18 Oct '16

Dear Freesufer experts, We are in the process of starting a large MRI project on normal aging and dementia. There has been a lot of discussions about what sequences to use. We are now thinking about combining several sequences. Is there an optimal combination of MRI sequences for Freesufer?

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Using "for" to run multiple subjects
by Farzaneh keyvanfard 18 Oct '16

18 Oct '16

Dear expert, I want to run recon-all for 100 subject simultaneously. I found the following link about it, but as I'm a beginner in this field, I don't understand how to use it. Would you please kindly give an example with a subject names, directory , etc. what should be written instead of * , or how could I define the number of subjects, ...? Thank you very much. https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/Two Best Regards F.Keyvanfard

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2 beginner questions
by Brad Matushewski 18 Oct '16

18 Oct '16

I am running Freesurfer on a Virtual machine on Windows 10. 1) I am having difficulty creating a shared drive between Windows and Freesufer / Linux. Has anyone had success with this? 2) I tried to install gedit. I went to the Ubuntu software centre and downloaded it. I then asked me for a password for authentication before I could install it. I never set up any such password...Where is this coming from and how do I proceed? 3) [Logo] Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447

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recon-all -s bert exited with errors
by Qinggang Yu 18 Oct '16

18 Oct '16

Hello FreeSurfer Developers, I was trying to run recon-all -all, and it failed roughly 30s after it started running, with the error message being: recon-all -s bert exited with errors. Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Platform: Red Hat Enterprise Linux Client Release 5.2 uname -a: Linux schizo.psych.med.umich.edu 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:32:05 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all.log: see attached Please let me know how I can fix this. Thank you very much! Best, Qinggang

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GLM on cortical and subcortical volume
by miracle ozzoude 18 Oct '16

18 Oct '16

Hello Expert, Is there are way to perform glm analysis on cortical and subcortical volumes. Thanks Best,. Paul

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mri_cvs_register quit for mris_resample: Command not found
by Cong 18 Oct '16

18 Oct '16

Dear freesufer experts I’m learning DTI image process according to steps in FsTutorial/ Diffusion_DtiIntegration. In Spatial Normalization I need create a .m3z morph file through mir_cvs_register. I used command mri_cvs_register --mov subjectname --template cvs_avg35. But it always stop for mris_resample: Command not found. I run freesurfer v5.3.0 in a MacBook Pro. Two log file in cvs folder are attached. Could you give me some advice? Thanks very much. Best Wishes Cong Chen

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mri_nu_correct crash
by Burkhard Maess 18 Oct '16

18 Oct '16

hello Freesurfer developers, during the recon-all (autorecon1) processing, it seems that the mne_nu_correct procedure does not always manage to finish successfully. I have searched the net, found a question in the mailing list, which seemed to be similar, but no answer (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html) Our status file shows, that we had sometimes runs which were completed without errors. Maybe, we should not have started the recon-all a second time. It would be very great if you could help with further hints. For instance, could we remove a file or several files to roll back to the situation when it worked? all the best, Burkhard ..................... FREESURFER_VERSION: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 Platform: ubuntu 16.04 (xfce) > uname -a Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Command: freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 -nuintensitycor-3T -subjid is09 -- Dr. Burkhard Maess Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess 'at' cbs.mpg.de, http://www.cbs.mpg.de

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Re: [Freesurfer] Problem in upload file through ftp
by Cong 17 Oct '16

17 Oct '16

Hi Bruce full session is listed. Thank you very much. Best Wishes Cong BrainwaverdeMacBook-Pro:~ Brainwaver$ ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 Name (surfer.nmr.mgh.harvard.edu:Brainwaver): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put /Users/Brainwaver/Desktop/Cong2Bruce.zip local: /Users/Brainwaver/Desktop/Cong2Bruce.zip remote: /Users/Brainwaver/Desktop/Cong2Bruce.zip 229 Entering Extended Passive Mode (|||37896|). 553 Could not create file. ftp> epsv EPSV/EPRT on IPv4 off. ftp> put /Users/Brainwaver/Desktop/Cong2Bruce.zip local: /Users/Brainwaver/Desktop/Cong2Bruce.zip remote: /Users/Brainwaver/Desktop/Cong2Bruce.zip 227 Entering Passive Mode (132,183,202,158,147,230). 553 Could not create file. ftp> > Date: Sun, 16 Oct 2016 16:04:12 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > Hi Cong > > can you send us your full session history - what exact commands did you > type and what was the screen output? > > cheers > Bruce > On Sun, 16 Oct 2016, Cong wrote: > >> Dear freesurfer experts? ? When I use command "put path/to/my/file?,?it?s >> always appear an error "229 Entering Extended Passive Mode (|||37867|). >> 553 Could not create file?, if I use epsv?command before put, then comes an >> error "227 Entering Passive Mode (132,183,202,158,147,237).?553 Could not >> create file?. Could you give me some advices? >> >> Best Wishes >> Cong Chen

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Generating aparc statistics that only correspond to a masked region
by Brandy Riedel 17 Oct '16

17 Oct '16

Hello Freesurfer's, I would like to generate the standard aparc.mgz statistics, but only for ROIs or for segments of an ROI that fall within the bounds of a mask. I've created the mask I want to use, have label files that correspond to the mask, have a masked version of the aparc.mgz, but I can't seem to figure out this final step. I was planning to use mris_anatomical_stats but none of the adjustments I've tried have yielded output different from the standard aparc stats. Any help would be appreciated! Thank you!

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S. Nigra
by Rockers, Elijah D. 17 Oct '16

17 Oct '16

Is it possible for freesurfer to parcellate the substantia nigra from a T1? -- Elijah Rockers Research Data Analyst Houston Methodist Research Institute O: 713-363-7729 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital 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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Freesurfer October 2016