Freesurfer

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16 participants
30098 discussions

Fwd: 3D viewing ROIs by Freeview
by Faeze Vedaei 18 Feb '16

18 Feb '16

Hello Freesurfer experts, I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D brain map in Freeview? In advance, I would appreciate your time and consideration. Regards, Faezeh Vedaei

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stable6
by Grafe,Brendan P. (BIDMC - Neurology) 18 Feb '16

18 Feb '16

Hello all, I have been slowly processing a longitudinal dataset off and on again since last August, sourcing /usr/local/freesurfer/nmr-stable6-env. Does this represent v.6.0-beta or v.6.0 in development? We were initially interested in applying the hippocampal subfield segmentation functionality on (1mm) T1 MPRAGE acquisitions and have found varying reproducibility, and questionable segmentation, of certain scans. I was aware that these volumetric measurements were to be interpreted with caution, but I'm separately wondering if the data I have processed in this environment can be trusted in analysis of cortical thickness change or if reprocessing with a previous version would be advised. -Brendan ----------------------------- Brendan P. Grafe MSc Clinical Research Assistant Berenson-Allen Center for Noninvasive Brain Stimulation Beth Israel Deaconess Medical Center 330 Brookline Avenue Boston, MA 02215 Tel: 617-667-0256 Fax: 617-975-5322 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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pial edits in subject with severe atrophy
by Corinna Bauer 18 Feb '16

18 Feb '16

Dear Experts, I have a subject with severe atrophy in bilateral frontal and parietal regions and after many rounds of edits to the brainmask, wm.mgz, and control points, these regions are still left uncaptured. Is there a way to edit the pial surface to include these grey matter regions? I am hesitant to draw them in via the wm surface since there is no definite WM present. I do have a FLAIR also on this subject. I've attached a couple examples. Thanks! Corinna

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Help - Surface extraction to Matlab
by Ittai Shamir 18 Feb '16

18 Feb '16

Hello, My name is Ittai and I am currently working on my M.Sc. in the department of Neurobiology in Tel Aviv University. I am a new FreeSurfer user. My question regarding the software is- After successfully running my data (T1 image - MPRAGE) through FS, I would like to extract both cortical surfaces (adjacent to pia and white matter) to Matlab. Is there a simple method of extracting these surface data to Matlab? or converting them to a format that is compatible with Matlab? I would greatly appreciate any help in this matter. Thanks in advance, Ittai Shamir

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infant data recon-all error
by 葉丁瑞 18 Feb '16

18 Feb '16

Dear Freesurfer experts, I'm involved in the infant research (less than 1 year of age). I tried running the recon-all command, however it fails and I got the error below at the end. Could anybody please let me know how to fix it? other error message please see attached file below. --- #@# Talairach Wed Feb 17 16:07:00 CST 2016 /Volumes/YangLab/S001/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n /Volumes/YangLab/S001/mri /Applications/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Darwin MRI2deiMac.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 Wed Feb 17 16:07:21 CST 2016 tmpdir is transforms/tmp.talairach.45862 /Volumes/YangLab/S001/mri mri_convert orig_nu.mgz transforms/tmp.talairach.45862/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.45862/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=10.34, TE=5.09, TI=0.00, flip angle=12.00 i_ras = (-1, 1.32713e-08, 0) j_ras = (-7.45058e-09, -7.45058e-09, -1) k_ras = (-5.82077e-09, 1, 0) writing to transforms/tmp.talairach.45862/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /Applications/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.45862/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /Applications/freesurfer/mni/bin/../lib/mni_autoreg /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Applications/freesurfer/mni/lib/../Library/Perl/Updates/5.10.0 /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at /Applications/freesurfer/mni/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log Darwin MRI2deiMac.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64 recon-all -s S001 exited with ERRORS at Wed Feb 17 16:07:23 CST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- *thank you,* *Yeh Ting-Jui*

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repost: more on comparing runs on the same scan
by Krieger, Donald N. 17 Feb '16

17 Feb '16

Hi everyone, I'm reposting this from 2 days ago. Please excuse if someone responded and I missed it. We have been able to establish that we are getting identical results when running recon-all -all on the same scan on different machine for the following: All .mgz files in directories mri, mri/orig, and mri/transforms, by comparing using mri_diff ... All of the .label and .annot files in directory label with md5sum ... Many of the files in directory surf with mris_diff. We continue to see differences in the label/BA*.annot files and in about 20 of the files in surf including [lr]h.inflated|orig|pial . We do see identity for lh.area.pial but not for lh.pial for instance. I've attached the output of our test routine. Your thoughts would be welcome on this pesky question. Best - Don

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-qcache of v5.0 data with newer versions
by Daniel Ferreira 17 Feb '16

17 Feb '16

Dear experts, Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been recon-all -all with FS 5.0.0? Thanks Dani

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Freesurfer version 6.0
by Barbara Kreilkamp 17 Feb '16

17 Feb '16

Dear Freesurfer experts, How may I get Freesurfer v 6 ? Thank you very much, Best wishes, Barbara

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Hippocampal subfield segmentation in FS 6.0
by Sarah Lancaster 17 Feb '16

17 Feb '16

Hi all, We are running hippocampal subfield segmentations on about 300 subjects. We initially ran recon-all using FreeSurfer 5.3, but we used the new FreeSurfer 6.0 method for the hippocampal subfields. Will this cause problems in our analysis? Should we run them through recon-all again with 6.0? Thanks, Sarah Sarah Lancaster Research Assistant Duke-UNC Brain Imaging and Analysis Center Mental Illness Research, Education and Clinical Center Durham VA Medical Center sarah.lancaster(a)dm.duke.edu 919-286-0411 x7660

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R: Re: v.6.0 Permissions Error
by Grafe,Brendan P. (BIDMC - Neurology) 17 Feb '16

17 Feb '16

Hello Doug, I tried rerunning the -base creation step without any luck. It appears that this process is reliant on the removed file: ERROR: cannot find /usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca -Brendan ------------------------------ Message: 21 Date: Tue, 16 Feb 2016 16:40:43 -0500 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] v.6.0 Permissions Error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <56C3975B.60401(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed ok, try now On 02/16/2016 04:38 PM, Grafe,Brendan P. (BIDMC - Neurology) wrote: > > Hello all, > > I am in the middle of a FreeSurfer v.6.0 longitudinal analysis, > running on the Martinos cluster, and I received an error today during > the (-base) template creation step regarding a file > that the pipeline calls upon: > > GCAread(/usr/local/freesurfer/stable6/average/RB_all_2016-02-11.gca): > could not open file > > I noticed that permissions access to this file are limited at present > to the greve group and that the file was last modified earlier today. > I'm unfamiliar with this component's functionality, but am assuming > access to it is necessary for template creation. Would this simply be > the issue? ----------------------------- Brendan P. Grafe MSc Clinical Research Assistant Berenson-Allen Center for Noninvasive Brain Stimulation Beth Israel Deaconess Medical Center 330 Brookline Avenue Boston, MA 02215 Tel: 617-667-0256 Fax: 617-975-5322 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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