Freesurfer

freesurfer@nmr.mgh.harvard.edu

8 participants
30091 discussions

surface area mesurment and qatools
by Knut J Bjuland 11 Mar '13

11 Mar '13

Hi What would be the best way to measure cortical surface either the white surface area or pial surface? Is the total surface area calculated by mris_anatomical the same pial surface? When using QA tool which article should I cite? Knut J

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Re: [Freesurfer] Time
by Douglas N Greve 11 Mar '13

11 Mar '13

You cannot give recon-all a folder as input. It must be an image file. If you have multiple files, you need multiple -i flags. doug On 03/07/2013 03:48 PM, Valtina Pouegue wrote: > Hi, > Here it is > [esther@IP132-207-67-224 ~]$ recon-all -i > /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 13B > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects > Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer > Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 > UTC 2012 x86_64 x86_64 x86_64 GNU/Linux > /home/esther/Freesurfer/freesurfer/subjects/13B > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz > corRead(): can't open file > /home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13B... > > VP -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Permission denied - could not open lh.BA3b.thresh.label
by preciado＠nmr.mgh.harvard.edu 11 Mar '13

11 Mar '13

Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Definition of anatomical regions
by akshay pai 11 Mar '13

11 Mar '13

Hi, I have been working on a DBM based method to obtain longitudinal atrophy on some brain data. To quantify ROI, i use aseg.mgz. Several papers talk about Whole Brain, ventricular atrophy but do not actually define what substructures they use? It will be great if somebody can help me get the actual definition of whole brain and ventricles. For ex: WM Hypointensities are part of whole brain?, Since they increase in volume. Thank you , Akshay University of Copehagen

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Re: [Freesurfer] Segfault on first test
by Nick Schmansky 10 Mar '13

10 Mar '13

Marcos, Our Centos 4_x86_64 build machine uses kernel v2.6.9-89.33.1, and the Centos 6_x86_64 machine uses v2.6.32-279.22.1. Before trying an earlier Fedora, can you try setting this in your tcsh prior to setting-up freesurfer and running tkmedit? set anyerror there was a bug in tcsh 6.17.06 but i think it was fixed in 6.18. 'set anyerror' was the workaround. Nick On Sat, 2013-03-09 at 21:15 -0300, Marcos Martins da Silva wrote: > Hi, Nick. Thank you for your fast answer. > My tcsh is version 6.18.00-3 (64 bit). > All are servers here are Fedora. But this machine I am using (a laptop > for tests) is using the newest version. Perhaps, I can try with a > previous version. What is the kernel version CentOS 4 or 6 uses? > > Em Sáb, 2013-03-09 às 18:18 -0500, Nick Schmansky escreveu: > > Marcos, > > > > Does mri_convert work? What version of tcsh was installed? Maybe you > > can try the freesurfer centos4_x86_64 distribution? We havent tested on > > Fedora 18 so we havent seen this before. > > > > Nick > > > > > > On Sat, 2013-03-09 at 16:11 -0300, Marcos Martins da Silva wrote: > > > I did and got the following to test freesurfer installation according > > > to freesurfer website directions: > > > [marcos@alien ~]$ tkmedit bert orig.mgz > > > > > > > > > =================================== > > > ERROR: A segfault has occurred. This is not your fault, > > > : but is most likely an unrecoverable error and has > > > : made the program unstable. > > > : > > > : Please send the contents of the file .xdebug_tkmedit > > > : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu > > > : > > > : Now exiting... > > > : > > > ___________________________________ > > > the contents of .xdebug_tkmedit: > > > tkmedit started: Sat Mar 9 14:16:07 2013 > > > > > > /usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz > > > > > > $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 > > > $ > > > Set user home dir to /home/marcos > > > Set subject home dir to /usr/local/freesurfer/subjects/bert > > > > > > Segfault > > > Importing volume with MRIread > > > xDebug stack (length: 5) > > > 04: Volm_ImportData( this=0x27f84ab0, > > > isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) > > > 04: Importing volume with MRIread > > > 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) > > > 03: Reading data into volume > > > 02: ParseCmdLineArgs( argc=3, > > > argv=/usr/local/freesurfer/tktools/tkmedit.bin ) > > > 02: Loading volume orig.mgz > > > 01: main() > > > 01: Parsing command line arguments > > > 00: > > > 00: > > > > > > ___________________________________ > > > running bugr I got: > > > FREESURFER_HOME: /usr/local/freesurfer > > > > > > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > > > > > > RedHat release: Fedora release 18 (Spherical Cow) > > > > > > Kernel info: Linux 3.8.1-201.fc18.x86_64 x86_64 > > > > > > > > > ___________________________________ > > > Additional environment info: > > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 -------- > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME /usr/local/freesurfer > > > FSFAST_HOME /usr/local/freesurfer/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR /usr/local/freesurfer/subjects > > > MNI_DIR /usr/local/freesurfer/mni > > > > > > ___________________________________ > > > [marcos@alien ~]$ which tkmedit > > > /usr/local/freesurfer/bin/tkmedit > > > ___________________________________ > > > > > > I did the installation according website. My only additional step was > > > to install tcsh because when I tried tkmedit it returned: > > > bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: > > > File or directory not found. > > > > > > My machine is an Alienware MX17R2 with 8GB RAM and Intel(R) Core(TM) > > > i5 CPU M 520 @ 2.40GHz (Quadcore) > > > My video from lspci is Advanced Micro Devices [AMD] nee ATI Broadway > > > XT [Mobility Radeon HD 5800 Series] and I am using native drivers > > > instead of AMD proprietary driver > > > > > > thank you for your support > > > > > > _______________________________________________ > > > 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. >

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Segfault on first test
by Marcos Martins da Silva 09 Mar '13

09 Mar '13

I did and got the following to test freesurfer installation according to freesurfer website directions: [marcos@alien ~]$ tkmedit bert orig.mgz =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... : ___________________________________ the contents of .xdebug_tkmedit: tkmedit started: Sat Mar 9 14:16:07 2013 /usr/local/freesurfer/tktools/tkmedit.bin bert orig.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /home/marcos Set subject home dir to /usr/local/freesurfer/subjects/bert Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27f84ab0, isSource=/usr/local/freesurfer/subjects/bert/mri/orig.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=orig.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=3, argv=/usr/local/freesurfer/tktools/tkmedit.bin ) 02: Loading volume orig.mgz 01: main() 01: Parsing command line arguments 00: 00: ___________________________________ running bugr I got: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 RedHat release: Fedora release 18 (Spherical Cow) Kernel info: Linux 3.8.1-201.fc18.x86_64 x86_64 ___________________________________ Additional environment info: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni ___________________________________ [marcos@alien ~]$ which tkmedit /usr/local/freesurfer/bin/tkmedit ___________________________________ I did the installation according website. My only additional step was to install tcsh because when I tried tkmedit it returned: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: File or directory not found. My machine is an Alienware MX17R2 with 8GB RAM and Intel(R) Core(TM) i5 CPU M 520 @ 2.40GHz (Quadcore) My video from lspci is Advanced Micro Devices [AMD] nee ATI Broadway XT [Mobility Radeon HD 5800 Series] and I am using native drivers instead of AMD proprietary driver thank you for your support

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Converting structural masks back to native space
by Tal, Assaf 08 Mar '13

08 Mar '13

Dear FreeSurfer community, I am trying to obtain subcortical segmentation masks for a group of healthy volunteers using FreeSurfer v5.1 running on Ubuntu 12.10. I need the masks to be in the native space of the original 1mm^3-isotropic 256*256*160 T1-weighted images. I found a helpful link which seems to answer my need: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Running it seems to produce good results when overlaid on top of the original images. However, I couldn't find any mention in either the newsgroups or the wiki as to whether this affects the subcortical masks in any (significant?) way. What sort of differences should I expect between the masks in the "freesurfer space" and the ones converted back to native space? Are there any structures or artifacts I should mindful of? Thank you! Assaf PS Just to make things concrete, assuming I have a patient called Sam, then, after running recon-all, I typed in: cd $SUBJECTS_DIR/Sam/mri mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz e.g., for cerebral WM: mri_extract_label aseg-in-rawavg.mgz 2 41 cerebralWMNative.mgh mri_convert cerebralWMNative.mgh cerebralWMNative.img (this last step is used to create ANALYZE format images which is the format my code is already structured to read out)

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Re: [Freesurfer] Viewing volumes and surfaces in Native Space
by Douglas N Greve 08 Mar '13

08 Mar '13

Tim, what were your vol2vol, surf2surf, and freeview commandlines? doug On 03/08/2013 11:10 AM, Timothy Brown wrote: > Hi Doug, > > Thank you for your reply. > > I tried FreeView and have attached screenshots of results. > > freeview_native_brain.jpg - snapshot of native brain > > freeview_aseg.jpg - aseg.mgz added. This appears to correspond with > native brain > > freeview_aseg_in_raw.jpg - aseg_in_raw shown. This is quite similar > to aseg.mgz. Slightly different, as I'd expect, corresponds well to > native brain. > > freeview_native_brain_lh_pial.jpg - The pial (left) surface is shown. > This is the FreeSurfer output, ie not reoriented. It corresponds well > to aseg.mgz and native brain > > freeview_native_brain_lh_pial_native.jpg - The pial (left) surface > that I created using register.dat and mri_surf2surf is shown. This > does not correspond to the native brain. > > I wonder if there are some FreeView options that I should be using? > > Best regards, > -Tim > > > > On Thu, 7 Mar 2013, Douglas N Greve wrote: > >> Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit >> rigid and expects things to be a certain way (ie, not in native space). >> Try using freeview instead. >> doug >> >> On 03/07/2013 03:19 PM, Timothy Brown wrote: >>> Dear FreeSurfer users, >>> >>> I wish to view volumes and surfaces in native space. >>> >>> I used the information at: >>> >>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>> >>> to convert volumes. >>> >>> I then used: >>> >>> tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg >>> register.dat >>> cp register.dat ../surf/ >>> mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native >>> --tval-xyz --hemi lh --s 1158119_3_6 >>> >>> When I use tkmedit to view the surfaces and volumes, the surface that >>> I thought would be in native space does not seem to correspond with >>> the "native space" volumes. (graphic attached) >>> >>> Can you let me know the steps/procedure to do this? >>> >>> Many thanks, >>> >>> -Tim >>> >>> Timothy Brown email: timothy(a)cis.jhu.edu >>> Computational Anatomist phone: 410.516.7551 >>> Center for Imaging Science fax: 410.516.4557 >>> Johns Hopkins University >>> 301 Clark Hall >>> 3400 N. Charles Street >>> Baltimore, MD 21218 >>> >>> >>> _______________________________________________ >>> 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 >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: 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. >> > > Timothy Brown email: timothy(a)cis.jhu.edu > Computational Anatomist phone: 410.516.7551 > Center for Imaging Science fax: 410.516.4557 > Johns Hopkins University > 301 Clark Hall > 3400 N. Charles Street > Baltimore, MD 21218 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 3

cortical thickness of ROIs derived from VBM results
by ZhiLiangLong 08 Mar '13

08 Mar '13

Hi all: I got some regions of interest showing significant diffencese in VBM between two groups. Now, i attemp to compare cortical thickness of these ROIs. However, i don't know how to map the ROIs to cortical surface and extract cortical thickness values? I need help.

2 1

roi analysis on longit. processed data
by Andreas Werner 08 Mar '13

08 Mar '13

2 1

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