Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

WM editing and longitudinal processing v5.3.0
by Ed Gronenschild 05 Feb '14

05 Feb '14

Hi, From what I can read in the wiki about wm editing, I understand that edited wm voxels have values of either 255 (added) or 1 (removed) and no other values. These are stored in the file wm.mgz. Is that correct? Before processing a lot of data I want to be sure that running recon-all with the option autorecon2-wm will recognize these voxels, also during longitudinal processing. Can you confirm this. FreeSurfer v5.3.0 Mac OSX10.6 Kind regards, Ed

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3D thickness scale
by Jonathan Holt 05 Feb '14

05 Feb '14

Hi all, I’ve pulled up a 3D inflated thickness figure by loading the following into freeview lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 I’m wondering how the colors correspond to thickness and whether or not I can generate a scale to help interpret the figure. best, Jon

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hippocampus misestimation
by Adam Mezher 05 Feb '14

05 Feb '14

Hi all, I was curious to know if anyone has been able to use edits to correct hippocampal under- or over-estimation. I've experienced a number of cases in which about half of the left hippocampus is labeled as ctx-lh-unknown or Left-Cerebral-White-Matter (for reference, I'm using FreeSurfer version 5.1 for these projects). If anyone has any suggestions to correct this error, it would be much appreciated. Thank you, Adam *Adam MezherStaff Research Associate IICenter for Imaging of Neurodegenerative DiseasesSan Francisco VA Medical Center4150 Clement St. (114M)San Francisco, CA 94121Tel: 415-221-4810 Ext. 4629 Fax: 415-668-2864*

2 1

mri_convert fails
by Douglas Wojcik 05 Feb '14

05 Feb '14

Good morning; I am new to freesurfer, and I am having issues getting my dataset imported; Any help will be greatly appreciated; I am running: [root@satellite cd_files]# uname -a Linux satellite 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux I have copied the dicom files into the following directories: [root@satellite cd_files]#pwd /opt/local/freesurfer/subjects/cd_files [root@satellite cd_files]# ls Autorun.inf Cache DICOM DICOMDIR Reports Viewer ViewImages.cmd I try to import the images, & and it looks like it is missing some metadata: [root@satellite freesurfer]# recon-all -s 20442 -i /opt/local/freesurfer/subjects/cd_files/DICOMDIR Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /opt/local/freesurfer/subjects Actual FREESURFER_HOME /opt/local/freesurfer Linux satellite 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /opt/local/freesurfer/subjects/20442 mri_convert /opt/local/freesurfer/subjects/cd_files/DICOMDIR /opt/local/freesurfer/subjects/20442/mri/orig/001.mgz mri_convert /opt/local/freesurfer/subjects/cd_files/DICOMDIR /opt/local/freesurfer/subjects/20442/mri/orig/001.mgz WARNING: searching dicom file /opt/local/freesurfer/subjects/cd_files/DICOMDIR for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /opt/local/freesurfer/subjects/cd_files/DICOMDIR... WARNING: searching dicom file /opt/local/freesurfer/subjects/cd_files/DICOMDIR for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. Starting DICOMRead2() dcmfile = /opt/local/freesurfer/subjects/cd_files/DICOMDIR dcmdir = /opt/local/freesurfer/subjects/cd_files WARNING: tag ImageNumber not found in /opt/local/freesurfer/subjects/cd_files/DICOMDIR WARNING: tag SeriesNumber not found in /opt/local/freesurfer/subjects/cd_files/DICOMDIR WARNING: tag image orientation not found in /opt/local/freesurfer/subjects/cd_files/DICOMDIR Ref Series No = 21729 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu Linux satellite 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 20442 exited with ERRORS at Wed Feb 5 08:50:54 CST 2014 For more details, see the log file /opt/local/freesurfer/subjects/20442/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I don't know that this is a bug, or just a low-compliance set of dicom files; Unable to find a similiar issue in the archives... Any suggestions would be greatly appreciated, and Many Thanks in Advance; Douglas

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Freeview
by Saurabh Thakur 05 Feb '14

05 Feb '14

Hi Freesurfer experts, I got to know about freeview. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewGeneralUsag… and went to test it.... but getting error : *saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeviewfreeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory* can anyone help me in this regards, Thanks in advance. cheers Saurabh Thakur,

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Re: [Freesurfer] Installation error
by Saurabh Thakur 05 Feb '14

05 Feb '14

Hi, I have got all the files necessary. as per your instructions. as well as environment is also set. //===================================================================// freesurfer-Linux-centos4-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 /home/saurabh/Desktop/saurabh_freesurfer MNI_DIR /usr/local/freesurfer/mni saurabh@saurabh-Dell-System-XPS-L502X:~$ ls -l /usr/local/freesurfer total 376 -rw-r--r-- 1 root root 3302 Mar 1 2013 ASegStatsLUT.txt -rw-r--r-- 1 root root 728 Mar 1 2013 AUTHORS drwxr-xr-x 7 root root 4096 Mar 1 2013 average drwxr-xr-x 2 root root 36864 Mar 1 2013 bin -rw-r--r-- 1 root root 43 Mar 1 2013 build-stamp.txt drwxr-xr-x 3 root root 4096 Mar 1 2013 data -rw-r--r-- 1 root root 47514 Mar 1 2013 DefectLUT.txt drwxr-xr-x 3 root root 4096 Mar 1 2013 diffusion drwxr-xr-x 3 root root 4096 Mar 1 2013 docs -rw-r--r-- 1 root root 84833 Mar 1 2013 FreeSurferColorLUT.txt -rwxr-xr-x 1 root root 16760 Mar 1 2013 FreeSurferEnv.csh -rwxr-xr-x 1 root root 16846 Mar 1 2013 FreeSurferEnv.sh drwxr-xr-x 2 root root 4096 Mar 1 2013 fsafd drwxr-xr-x 5 root root 4096 Mar 1 2013 fsfast drwxr-xr-x 12 root root 4096 Mar 1 2013 lib -rw-r--r-- 1 root root 10297 Mar 1 2013 LICENSE drwxr-xr-x 3 root root 4096 Mar 1 2013 matlab drwxr-xr-x 8 root root 4096 Feb 21 2010 mni -rw-r--r-- 1 root root 4793 Mar 1 2013 NOTICE -rw-r--r-- 1 root root 635 Mar 1 2013 README -rw-r--r-- 1 root root 28445 Mar 1 2013 SegmentNoLUT.txt drwxr-xr-x 2 root root 4096 Mar 1 2013 sessions -rwxr-xr-x 1 root root 1303 Mar 1 2013 SetUpFreeSurfer.csh -rwxr-xr-x 1 root root 1293 Mar 1 2013 SetUpFreeSurfer.sh -rw-r--r-- 1 root root 4104 Mar 1 2013 Simple_surface_labels2009.txt drwxr-xr-x 14 root root 4096 Mar 1 2013 subjects -rw-r--r-- 1 root root 1681 Mar 1 2013 tkmeditParcColorsCMA drwxr-xr-x 2 root root 4096 Mar 1 2013 tktools drwxr-xr-x 35 root root 4096 Mar 1 2013 trctrain -rw-r--r-- 1 root root 50 Mar 1 2013 VERSION -rw-r--r-- 1 root root 25944 Mar 1 2013 WMParcStatsLUT.txt saurabh@saurabh-Dell-System-XPS-L502X:~$ ls -l /usr/local/freesurfer/tktools/ total 71772 -rwxr-xr-x 1 root root 46572 Mar 1 2013 fsgdfPlot.tcl -rw-r--r-- 1 root root 6180 Mar 1 2013 license.cortechs.txt -rwxr-xr-x 1 root root 17992 Mar 1 2013 tkanalyse.tcl -rwxr-xr-x 1 root root 722 Mar 1 2013 tkm_common.tcl -rwxr-xr-x 1 root root 1591 Mar 1 2013 tkm_dialog.tcl -rwxr-xr-x 1 root root 102 Mar 1 2013 tkmedit -rwxr-xr-x 1 root root 19541885 Feb 4 18:52 tkmedit.bin -rwxr-xr-x 1 root root 154763 Mar 1 2013 tkmedit.tcl -rwxr-xr-x 1 root root 40941 Mar 1 2013 tkm_functional.tcl -rwxr-xr-x 1 root root 2805 Mar 1 2013 tkm_graph.tcl -rwxr-xr-x 1 root root 47324 Mar 1 2013 tkm_wrappers.tcl -rwxr-xr-x 1 root root 106 Mar 1 2013 tkregister -rwxr-xr-x 1 root root 106 Mar 1 2013 tkregister2 -rwxr-xr-x 1 root root 16911243 Mar 1 2013 tkregister2.bin -rwxr-xr-x 1 root root 16792599 Mar 1 2013 tkregister2_cmdl -rwxr-xr-x 1 root root 27967 Mar 1 2013 tkregister2.tcl -rwxr-xr-x 1 root root 27967 Mar 1 2013 tkregister.tcl -rwxr-xr-x 1 root root 103 Mar 1 2013 tksurfer -rwxr-xr-x 1 root root 19578559 Feb 4 18:52 tksurfer.bin -rwxr-xr-x 1 root root 200280 Mar 1 2013 tksurfer.tcl -rwxr-xr-x 1 root root 56875 Mar 1 2013 tkUtils.tcl saurabh@saurabh-Dell-System-XPS-L502X:~$ tkedit subject1 orig.mgz tkedit: command not found saurabh@saurabh-Dell-System-XPS-L502X:~$ //==========================================================// cheers Saurabh Thakur, On Tue, Feb 4, 2014 at 6:11 PM, Markus Gschwind <markus.gschwind(a)gmail.com>wrote: > Hi Saurabh, > > Did you download the file again? You also can download old versions here: > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ > so we are sure that there is not anything missing in your freesurfer > folder. > Can you write into the terminal: > ls -l /usr/local/freesurfer > > For your info: I get this: > > ~$ ls -l /usr/local/freesurfer >> total 372 >> -rw-r--r-- 1 root root 3302 May 14 2013 ASegStatsLUT.txt >> -rw-r--r-- 1 root root 728 May 14 2013 AUTHORS >> drwxr-xr-x 7 root root 4096 May 14 2013 average >> drwxr-xr-x 2 root root 32768 May 14 2013 bin >> -rw-r--r-- 1 root root 50 May 14 2013 build-stamp.txt >> drwxr-xr-x 3 root root 4096 May 14 2013 data >> -rw-r--r-- 1 root root 47514 May 14 2013 DefectLUT.txt >> drwxr-xr-x 3 root root 4096 May 14 2013 diffusion >> drwxr-xr-x 3 root root 4096 May 14 2013 docs >> -rw-r--r-- 1 root root 84833 May 14 2013 FreeSurferColorLUT.txt >> -rwxr-xr-x 1 root root 16760 May 14 2013 FreeSurferEnv.csh >> -rwxr-xr-x 1 root root 16846 May 14 2013 FreeSurferEnv.sh >> drwxr-xr-x 2 root root 4096 May 14 2013 fsafd >> drwxr-xr-x 5 root root 4096 May 14 2013 fsfast >> drwxr-xr-x 12 root root 4096 May 14 2013 lib >> -rw-r--r-- 1 root root 10297 May 14 2013 LICENSE >> drwxr-xr-x 3 root root 4096 May 14 2013 matlab >> drwxr-xr-x 9 root root 4096 Nov 1 2007 mni >> -rw-r--r-- 1 root root 4793 May 14 2013 NOTICE >> -rw-r--r-- 1 root root 635 May 14 2013 README >> -rw-r--r-- 1 root root 28445 May 14 2013 SegmentNoLUT.txt >> drwxr-xr-x 2 root root 4096 May 14 2013 sessions >> -rwxr-xr-x 1 root root 1352 May 14 2013 SetUpFreeSurfer.csh >> -rwxr-xr-x 1 root root 1342 May 14 2013 SetUpFreeSurfer.sh >> -rw-r--r-- 1 root root 4104 May 14 2013 Simple_surface_labels2009.txt >> drwxr-xr-x 15 root root 4096 Jan 28 16:24 subjects >> -rw-r--r-- 1 root root 1681 May 14 2013 tkmeditParcColorsCMA >> drwxr-xr-x 2 root root 4096 May 14 2013 tktools >> drwxr-xr-x 35 root root 4096 May 14 2013 trctrain >> -rw-r--r-- 1 root root 52 May 14 2013 VERSION >> -rw-r--r-- 1 root root 25944 May 14 2013 WMParcStatsLUT.txt >> > > As you see there is also tktools. > > What does it say if you type: > ls -l /usr/local/freesurfer/tktools/ > > > This is my version: > > ~$ ls -l /usr/local/freesurfer/tktools/ >> total 93888 >> -rwxr-xr-x 1 root root 46572 May 14 2013 fsgdfPlot.tcl >> -rw-r--r-- 1 root root 6180 May 14 2013 license.cortechs.txt >> -rwxr-xr-x 1 root root 17992 May 14 2013 tkanalyse.tcl >> -rwxr-xr-x 1 root root 722 May 14 2013 tkm_common.tcl >> -rwxr-xr-x 1 root root 1591 May 14 2013 tkm_dialog.tcl >> -rwxr-xr-x 1 root root 102 May 14 2013 tkmedit >> -rwxr-xr-x 1 root root 25409422 May 14 2013 tkmedit.bin >> -rwxr-xr-x 1 root root 154763 May 14 2013 tkmedit.tcl >> -rwxr-xr-x 1 root root 40941 May 14 2013 tkm_functional.tcl >> -rwxr-xr-x 1 root root 2805 May 14 2013 tkm_graph.tcl >> -rwxr-xr-x 1 root root 47324 May 14 2013 tkm_wrappers.tcl >> -rwxr-xr-x 1 root root 106 May 14 2013 tkregister >> -rwxr-xr-x 1 root root 106 May 14 2013 tkregister2 >> -rwxr-xr-x 1 root root 22267238 May 14 2013 tkregister2.bin >> -rwxr-xr-x 1 root root 22105890 May 14 2013 tkregister2_cmdl >> -rwxr-xr-x 1 root root 27967 May 14 2013 tkregister2.tcl >> -rwxr-xr-x 1 root root 27967 May 14 2013 tkregister.tcl >> -rwxr-xr-x 1 root root 103 May 14 2013 tksurfer >> -rwxr-xr-x 1 root root 25685088 May 14 2013 tksurfer.bin >> -rwxr-xr-x 1 root root 200280 May 14 2013 tksurfer.tcl >> -rwxr-xr-x 1 root root 56875 May 14 2013 tkUtils.tcl >> > > Hope this helps, > M > > > > 2014-02-04 Saurabh Thakur <srbhthkr(a)gmail.com>: > > Hi, >> >> I am using laptop with 8Gb RAM, >> i7 Core processor, >> and >> enough HDD.... >> >> still i m getting same erro ( */usr/local/freesurfer/tktools/tkmedit.bin: >> Command not found*. ) because i m working on laptop...? >> >> or >> >> "recon-all --help " is working but *tkmedit is not working* >> >> Hope to get response asap. >> >> Thanks in advance. >> >> >> Saurabh Thakur, >> >> >> On Tue, Feb 4, 2014 at 2:09 PM, Markus Gschwind < >> markus.gschwind(a)gmail.com> wrote: >> >>> Hi Saurabh, >>> >>> I recently installed FS un ubuntu 12.04, and it was not difficult. >>> >>> I would recommend that you again download the file from here >>> http://surfer.nmr.mgh.harvard.edu/fswiki/Download (I took the Centos4 >>> file) >>> >>> to make sure that it is complete. >>> >>> Than you "untar" the file at any given place (most people recomment >>> /usr/local/ but you need to do it in "sudo" mode). >>> >>> Then make sure that you put the license file at the right place ( >>> http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall) >>> >>> and adapt the configuration file ( >>> http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration) >>> >>> I used bash and it worked well. >>> >>> Take care that you have writing permission on the folders you want to >>> use ($SUBJECT_DIR). >>> For that reason I copied the folder "bert" to my home folder in order to >>> be able to run the installation test as recommended here: >>> http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer >>> >>> Hope that helps! >>> Cheers, >>> Markus >>> >>> 2014-02-04 Saurabh Thakur <srbhthkr(a)gmail.com>: >>> >>>> Hello everyone, >>>> >>>> Can u anyone help me in simplest and best way to install freesurfer on >>>> >>>> *i m not able to run command : * >>>> >>>> >>>> >>>> *1. tkmedit 2. tksurfer.System specification: * >>>> >>>> Dell laptop >>>> Ubuntu 12.04 LTS >>>> RAM 8Gb >>>> Graphics cards: Nvidia cards 1 Gb >>>> >>>> Thanks in advance. >>>> >>>> Saurabh Thakur, >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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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autorecon2 error
by Gabriel Gonzalez Escamilla 05 Feb '14

05 Feb '14

2 1

from label to mask diffusion space
by Garikoitz Lerma-Usabiaga 05 Feb '14

05 Feb '14

Hi Doug, I've been reading the list and I ended with 4 steps to move from a label to a mask in diffusion space (below). Is this correct? Is there any other more straightforward way? It should end with a binary mask in diffusion space (I am using the anatorig2diff.bbr.dat created in the Tracula process). tkregister2 --mov mri/rawavg.mgz --targ mri/aseg.mgz --regheader --reg mri/rawreg.dat --noedit Create volume (it does it in LPS ): mri_label2vol --label label/lh.th13labels-001.label --temp mri/rawavg.mgz --reg mri/rawreg.dat --fillthresh .5 --o mri/fromlabel_lh.th13labels-001.nii Move volume to anatorig (LIA) : mri_vol2vol --mov mri/fromlabel_lh.th13labels-001.nii --targ /mri/brainmask.mgz --regheader --o mri/anatorig_lh.th13labels-001.nii --no-save-reg Move to diffusion space (LAS): mri_vol2vol --mov dmri/dtifit_FA.nii.gz --targ /mri/anatorig_lh.th13labels-001.nii --inv --interp nearest --o mri/diff_fromlabel_lh.th13labels-001.nii --reg dmri/xfms/anatorig2diff.bbr.dat --no-save-reg thanks! Gari

2 2

mris_divide_parcellation replication
by Christian Brodbeck 05 Feb '14

05 Feb '14

Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085) I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L4…) but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian

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Re: [Freesurfer] High resolution GM/WM segmentation
by Megha K. 04 Feb '14

04 Feb '14

Dear Nick and the Freesurfer team, We are following the pipeline “HiResRecon” to process our 0.7mm isotropic data. The pipeline completed without error but we cannot visualize the Grey/White matter segmentation using "-surfs”. The error messages is shown below: TM:~ Timwang$ tkmedit hires_3 brainmask.mgz -surfs Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. Converting main surface: 100% done. Converting main surface: 100% done. Converting pial surface: 100% done. tkmedit.bin(7641,0xa0a8d1a8) malloc: *** mach_vm_map(size=8388608) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug We would greatly appreciate your help on how we can visualize the GM/WM segmentation result of the HiResRecon pipeline. Many thanks, Megha Kaushik Save Sight Institute Sydney, Australia >

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Freesurfer February 2014