Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30076 discussions

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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Re: [Freesurfer] Quantifying volumes
by Damien MARIE 17 Oct '16

17 Oct '16

Hi, Just adding a word about the e-mail of ma colleague Josue. What he meant is that he extracted volumes for exactly the same ROI (a merging of destrieux labels of Hechl’s gyrus, Heschl's sulcus and planum temporale) using 1- a .curv file of this ROI, mri_binarize and mri_segstats or 2- a .label file of this ROI and mris_anatomical_stats. We get a different volume output (ratio of difference between the 2 methods = approx. 2.5, similar to mean thickness I would say…), so we would like to understand what is happening exactly. Using the method 1, it’s actually a surface measurement we get no? Would that be possible to convert a .cuvr file to a .label file ? Thank you and best, Damien Josue Luiz Dalboni Da Rocha Wed, 12 Oct 2016 07:26:32 -0700 Dear Doug, Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats . Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491 Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much? Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...(a)nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes I would binarize the curv file with mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh Then compute the volume with mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote: > Dear Douglas, > > I have a ".curv" file that contains the curvature information inside an > automatically delineated ROI and 0 everywhere else. > I would like to calculate the volume of this ROI, > > Can I extract statistics directly from the ".curv" file? > > Best regards, > Josue > ________________________________________ > From: freesurfer-boun...(a)nmr.mgh.harvard.edu > <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...(a)nmr.mgh.harvard.edu> > Sent: Tuesday, October 4, 2016 9:41 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Quantifying volumes > > What is the nature of the segmentation? Is it just a binary (1=in, > 0=out) segmentation? And what file format? In general we don't use .w > anymore, but it can be converted into something else. > > doug > > > On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote: >> Dear Douglas, >> >> >> I have a segmented gyrus curvature file (.curv or .w) and I would like >> to calculate the volume (and other statistics) of this gyrus. >> >> >> I currently only know mris_anatomical_stats to perform that, but >> requiring a '.label' file. >> >> >> Can I extract statistics directly from the ".curv" file? >> >> >> Or can I convert directly from .curv to .label in order to extract >> these statistics? >> >> >> As another option, is it feasible to convert the '.curv' file to nifti >> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to >> label (mri_cor2label)? >> >> >> What does the output nifti file from 'mri_surf2vol' contain? Does it >> contain the complete volume behind the surface? Or does it only >> contain the surface over the 3D space? >> >> >> Thank you very much in advance for your help! >> >> >> Best regards, >> >> Josue >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Job offer: research-fellow position in Japan
by Jarek Rokicki 17 Oct '16

17 Oct '16

A research-fellow post is available at the Integrative Brain Imaging Center, National Center of Neurology and Psychiatry. We are looking for a candidate with expertise in MRI, fMRI, PET (optional) image analysis and with a strong publication record. You are expected to take a lead or co-author role in publishing existing datasets within the lab, as well as acquiring new data, data analysis and novel algorithm development. *Your responsibilities will include:* 1. Analysis of behavioral and neuroimaging data 2. Presentations at national and international meetings 3. Manuscript preparation for publication *Required skills:* 1. A doctoral degree and publication record in cognitive science, neuroscience, computer science or related field 2. An independent, target-driven attitude 3. Matlab or Python or C++ programming skills 4. Familiarity with Unix based operating systems 5. At least 3 month experience of living abroad 6. Basic background in statistics 7. Experience with FSL, or SPM, or conn, or AFNI, R, SPSS 8. Fluency in English – written and oral 9. Japanese is not necessary, but beneficial *About the post:* 1. One year contract, extensible up to 3 years 2. Salary is based on a per hour basis: 1 hour = from 1840 to 2652 yen depending on experience and qualifications (in case of medical license holder 2800 yen). Additionally, travel allowance and other bonuses are offered. 3. Working hours: up to 31 hours/week (+ up to 200 hours of paid overtime/year) 4. Social insurance, unemployment insurance, accident insurance are covered by the Center 5. A dorm room is available for singles *To apply, please send the following documents:* 1. CV (with picture) 2. List of publications and international conferences attended 3. Summary of major research achievements and future research objectives (up to 400 words) 4. Reference from your direct supervisor or your current workplace (reference should be addressed to the President of National Center of Neurology and Psychiatry) For more details on the Center, please go to: http://www.ncnp.go.jp/ibic/ english/index.html Interested parties should email all necessary papers to matsudah(a)ncnp.go.jp <matsudah(a)ncno.go.jp> 宜しくお願い致します。 Sincerely, Jarek Rokicki, Ph.D. Integrative Brain Imaging Center (IBIC) National Center of Neurology and Psychiatry (NCNP) *4-1-1 Ogawahigashi-chyo, Kodaira, Tokyo 187-8551 Japan* TEL: +81-80-6628-5709 国立精神・神経医療研究センター脳病態統合イメージングセンター(IBIC) 臨床脳画像研究部画像情報解析研究室 *〒187-8551 東京都小平市小川東町4-1-1*

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