Freesurfer

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30135 discussions

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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I: R: R: R: Re: To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 16 Feb '16

16 Feb '16

1 0

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

16 Feb '16

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? Preemptive thanks, Brendan Grafe ----------------------------- 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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tkregister visualization issue
by Philip Brandner 16 Feb '16

16 Feb '16

Dear Freesurfer team, I encountered a visualization error with tkregister-sess after trying to look at the overlays of my 1st level analysis in a standard fMRI block designed localizer. tkregister loads without errors (menu plus window) but only very faint and small colored dots are visible, no inflated hemisphere as a surface no significant overlay of the contrast, nothing. It might seem like a specific problem with my setup, because from another computer in the lab the surface is visible (but no overlay). *Here is the terminal output during tkregiter-sess:* -bash-3.2$ tksurfer-sess -s NC211pre/ -analysis face.object.sm5.lh -c face-vs-object Surface fsaverage lh Map Surface fsaverage lh $Id: tksurfer-sess,v 1.16.2.2 2012/11/19 22:35:56 greve Exp $ Linux wiener 2.6.18-407.el5 #1 SMP Fri Oct 16 12:04:40 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux Tue Feb 9 11:51:24 EST 2016 /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/bin/tksurfer list face-vs-object con/map face-vs-object /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii maplist /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii mri_concat /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/face-vs-object/sig.nii --o /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii cd /Freiwald/cpressl/imaging/tle setenv SUBJECTS_DIR /Freiwald/cpressl/imaging/tle/ tksurfer fsaverage lh inflated -overlay /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii -label-outline -colscalebarflag 1 -annot aparc -fthresh 2 -fmid 3.00000000000000000000 -fslope .50000000000000000000 Contrasts 0 face-vs-object setting colscalebarflag to 1 setting fthresh to 2.0000 setting fmid to 3.0000 setting fslope to 0.5000 subject is fsaverage hemi is lh surface is inflated surfer: current subjects dir: /Freiwald/cpressl/imaging/tle/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Freiwald/cpressl/imaging/tle checking for nofix files in 'inflated' Reading image info (/Freiwald/cpressl/imaging/tle//fsaverage) Reading /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz surfer: Reading header info from /Freiwald/cpressl/imaging/tle//fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 tkmedit: Trying to open /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.dat surfer: Interpreting overlay volume /Freiwald/cpressl/imaging/tle/NC211pre/bold/face.object.sm5.lh/tksconcat.nii as encoded scalar volume. surfer: curvature read: min=-0.673989 max=0.540227 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 13887 vertices did not have an annotation! surfer: double buffered window surfer: tkoInitWindow(fsaverage) surfer: using interface /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tksurfer.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_common.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkm_wrappers.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/lib/tcl/fsgdfPlot.tcl Reading /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % Please let me know if you have encountered this before and whether you might have a solution for this issue. Best regards, Philip Brandner

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