Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

bbregister and FLAIR
by Kayle Sawyer 27 May '14

27 May '14

Hello, We have been examining the pial surface adjustment with FLAIR scans, and the improvement is quite dramatic. There are MANY areas where the pial surface was clearly wrong and has been substantially improved, considerably reducing (often eliminating) the need for manual pial corrections. I suggest everyone who uses FreeSurfer surfaces acquire a FLAIR scan if they can (see attached for the sequence we’re using). However, for most of our participants, we have run into a serious problem with bbregister. We're running recon-all with two input volumes: -i MEMPRAGE_scan -FLAIR FLAIR_scan Recon-all completes successfully, however the results do not look good due to a bad 'bbregister' registration step. The MEMPRAGE and FLAIR runs were acquired within the same scanning session and they're very well registered to begin with. However, the 'bbregister' step seems to not work well, and they end up grossly misaligned. Here is an example (on the Martinos network): [kslays@ficus ~]$ source /usr/local/freesurfer/nmr-stable53-env; setenv SUBJECTS_DIR /autofs/space/ficus_004/users/SLOTS_subjects; cd $SUBJECTS_DIR; recon-all -all -subjid SLOTS007 \ -i $SUBJECTS_DIR/SLOTS007/3danat/006/MEMPRAGE_RMS.mgz \ -FLAIR $SUBJECTS_DIR/SLOTS007/flair/007/flair.mgz \ -FLAIRpial -mprage -3T -pctsurfcon -qcache -hippo-subfields Check input volume registration (looks good): tkregister2 --targ SLOTS007/mri/orig/001.mgz \ --mov SLOTS007/mri/orig/FLAIRraw.mgz \ --reg NULL --regheader Check bbregister output (looks bad): tkregister2 --mov SLOTS007/mri/orig/FLAIRraw.mgz \ --reg SLOTS007/mri/transforms/FLAIRraw.dat --surf How do we correct the bbregister step? Thanks in advance for your input. -Kayle P.S. If you would like to see other examples, feel free to look at other recons in the same directory. Here is an example where bbregister worked, and the pial corrections are dramatic: freeview -v SLOTS005/mri/FLAIR.mgz \ -f SLOTS005/surf/lh.white:edgecolor=yellow \ SLOTS005/surf/rh.white:edgecolor=yellow \ SLOTS005/surf/lh.pial:edgecolor=red \ SLOTS005/surf/rh.pial:edgecolor=red \ SLOTS005/surf/lh.woFLAIR.pial:edgecolor=green \ SLOTS005/surf/rh.woFLAIR.pial:edgecolor=green \ -ras -37 -46 -42 Kayle Sawyer, PhD Athinoula A. Martinos Center for Biomedical Imaging MGH East Campus, Charlestown Navy Yard Building 149, South Central 1113 - Seat F 149 13th Street Boston, MA 02129 OFFICE:(617) 726-8791 Laboratory of Neuropsychology Boston University School of Medicine L-815 72 E. Concord St Boston, MA 02118 OFFICE:(617) 638-4803 VA Boston Healthcare System Jamaica Plain 150 South Huntington Ave 151-A, D11-126 Boston, MA 02130 OFFICE:(857) 364-4003 FAX: (857) 364-5829

2 1

R: Re: R: Re: R: Re: Problem of size
by Andrea Tateo 27 May '14

27 May '14

Hi FreeSurfer expert, after that I have used the command "recon-all" I would like to obtain wm-lh and wm-rh information ( for example wm-lh-bankssts,wm-lh-caudalanteriorcingulate,wm-lh-caudalmiddlefrontal, ...). I have read that mri_aparc2aseg command can help me, but when I use it I have two problems: 1) When I use the command mri_aparc2aseg --s subject I obtain as output the image "aparc+aseg.mgz" which contains information only about cortical label. 2) When I use the command mri_aparc2aseg --s subject --a.2005 I get the following message: ERROR: Option --a2005 unknown Can you help me? Moreover, the recon-all output in directory /mri is: aparc.a2009s+aseg.mgz, aparc+aseg.mgz, aseg.auto.mgz, aseg.auto_noCCseg.label_intensities.txt , aseg.auto_noCCseg.mgz aseg.mgz, brain.finalsurfs.mgz, brainmask.auto.mgz, brainmask.mgz, brain.mgz, ctrl_pts.mgz, filled.mgz, lh.ribbon.mgz, mri_nu_correct.mni.log, norm.mgz, nu.mgz, nu_noneck.mgz, orig, orig.mgz, rawavg.mgz, rh.ribbon.mgz, ribbon.mgz, segment.dat , T1.mgz, talairach.label_intensities.txt , talairach.log, talairach_with_skull.log, transforms, wm.asegedit.mgz, wm.mgz, wmparc.mgz , wm.seg.mgz Do you think that the searched information is here? Thanks for your help. Best regards, Andrea

2 1

unpacking error
by Caroline Lewis 27 May '14

27 May '14

Hi, I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info however, when I try to run the next command to actually unpack the data: unpacksdcmdir -src 0008 -targ NIFTI -fsfast \ ? -run 7 3danat mgz 001.mgz \<<NIFTI>> I get the following error message: Missing name for redirect. Thanks, Caroline

2 5

"average" brain files
by Borzello, Mia 27 May '14

27 May '14

Hi Freesurfers, I was wondering if the SurferOutput files for the average subject's brain were somewhere tobe downloaded on the wiki or within the toolbox? Thanks, m

1 0

How to obtain stats on custom anatomical ROI in freeview/freesurfer
by Lucette Cysique 27 May '14

27 May '14

Dear Ruopeng and colleagues, I am interested in following same tracing protocol for the amygdala as in "Neuroimage. 2012 April 2; 60(2): 1226–1235: "A reliable protocol for the manual segmentation of the human amygdala and its subregions using ultra-high resolution MRI” I would like as they did use freeview because it has some versatility and resolution that other programs do not have. I have however one issue Once I have created my ROI in freeview it ends up being by default a .label file. I create my ROI using ROIs and edit ROI tools and simply save it. I have tried to use “mri_label2vol” to get my ROI file (e.g., right_amygdala.label) into a volume file from which I thought I could then compute stats using “mri_segstats” But it does not work, as it seems that the initial .label file does not have the current format? Or required info? My command line output that it cannot read my .label file Thanks for your assistance Lucette

2 1

High Intensity Spots and Surfacing Issues
by Jonathan Holt 27 May '14

27 May '14

Hi all, this is a recurring issue that I'm hoping I can find a solution to. Pictured is a brain with a particularly high intensity area that seems to defy surfacing. Is there a way to work around this? See attached image

2 4

Registration and Surface Flattening
by Caka 27 May '14

27 May '14

Thank you Bruce, I convert the fsaverage flat map into a ascii file, using: mris_convert -p lh.cortex.patch.flat lh.cortex.patch.flat.asc. Now I need to read these two files. (1) I used read_patch.m to read lh.cortex.patch.flat. But an error came out, it said ‘ Error using ==> read_patch at 28, could not open file …’. (2) I couldn’t find a read_patch_asc.m script in Freesurfer, as is suggested in https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35813.html (3) I found a read_asc.m instead, but when I used it to read the lh.cortex.patch.flat.asc, an error occurred: ‘Error using ==> fgets, Invalid file identifier. Use open to generate a valid file identifier’. Could you please give me some advices?Thank you very much! Best regards, Qiongmin ————————————————Original email--------------------------------------- Hi Qiongmin 1. I think this is a bug in the open GL code that is outside of our control. We will try to track it down 2. The flat maps aren't really any different than say the inflated fsaverage surface. If you can generate group (or individual maps) in fsaverage space you can display them on the flat maps. 3. The index of each vertex in the flattened space is stored in the patch files so you can always look up what vertex it was on inflated, sphere, etc... cheers Bruce On Mon, 26 May 2014, Caka wrote: > Dear Bruce, Doug and all, > Thanks for your suggestion, it helped a lot. > > (1) I load the fsaverage surface (lh.inflated) in tksurfer, and then load > the fsaverage patch (lh.cortex.patch.flat). The flat map was shown for > several seconds, and then ?an error occurred and tksurfer was shut down. The > terminal said: ?tksurfer.bin:tnl/t_vertex.c:407: update_input_ptrs: > Assertion ?a[j].inputstride == vptr-> stride? failed. Abort(core dumped)?. > ?Could you give me some advice? > I use a 'CentOS release 6.2' system. The freesurfer is > ?freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0?.? > > (2) Indeed, I want to flatten all cortical thickness surfaces of 140 > subjects onto the ?lh.cortex.patch.flat? of fsaverage. I just don?t > understand your idea how to do this. After I load ?lh.cortex.patch.flat? of > fsaverage, the tksurfer only shows this flat map (now it lasted for several > seconds and crashed), so how can I ' load whatever overlay you want in the > same way you would on the inflated surface?? > Does it mean that I load the individual flat map on the individual inflated > surface? But I haven?t got the individual flat map yet.? > > (3) I am wondering if there are some table recording the transformation > relationships between the fsaverage surface vertices and the flat map > vertices? If so, then I think all I need to do is extracting the cortical > thickness value of every vertex in individual inflated surface, and then > putting into the corresponding vertex in the flat map.? > > Thank you very much!? > > Best regards, > Qiongmin?

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Re: [Freesurfer] WG: WG: [Fwd: WG: missing temporal lobes]
by Bruce Fischl 27 May '14

27 May '14

Hi Kristina can you please post to the list so others can answer? If you add control points to the temporal WM where you are missing gm it should recover most if not all of it. Hippocampus is not neocortical and isn't supposed to be included. The surfaces are somewhat arbitrary there, and excluded from all subsequent calculations (like total cortical area/volume) cheers Bruce On Tue, 27 May 2014, Mayer Kristina wrote: > Dear Bruce > How can I get the Hippocampus and the missing parts of GM of the temporal lobe into the PIAL (sufrace mask)? How can I convince freesurfer those parts are belonging to gray matter? > > Cheers, > Kristina > ________________________________________ > Von: Mayer Kristina > Gesendet: Freitag, 23. Mai 2014 16:11 > An: Freesurfer support list; freesurfer-bounces(a)nmr.mgh.harvard.edu > Betreff: AW: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] > > ________________________________________ > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Gesendet: Freitag, 23. Mai 2014 14:52 > An: Freesurfer support list > Betreff: Re: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] > > Hi Kristina > > don't add CPs to the gray matter - that will mess everything up! > Bruce > On Fri, 23 > May 2014, Mayer Kristina wrote: > >> >> >> Dear Bruce >> My dataset is very young (around 2 years of age), I suppose the contrast >> and size is just different from the default-template of freesurfer. Is >> there a way to exchange the template (I am thinking of a probabilistic >> map) without creating an own atlas first? >> Attached you find screenshots of my work and the recon-log of the same >> subject. >> I first run all recon-all steps. Then I added CP where WM was missing. I >> also added CP in GM region where lost of GM was missing (temporal lobe) to >> get the pial right. Then I tried to remove the WM which came out too much, >> for I placed CP in GM regions. >> Is there another way for it? >> >> Best, >> Kristina >> >> log 0001339: >> Fri May 16 08:50:00 CEST 2014 >> FREESURFER_HOME /usr/local/freesurfer >> Actual FREESURFER_HOME /usr/local/freesurfer >> /media/n-NAS_MRI/freesurfer-subjects-dir/0001336 >> setenv SUBJECTS_DIR /media/n-NAS_MRI/freesurfer-subjects-dir >> -autorecon2-cp -autorecon3 -subjid 0001336 >> Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC >> 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> cputime unlimited >> filesize unlimited >> datasize unlimited >> stacksize 8192 kbytes >> coredumpsize 0 kbytes >> memoryuse unlimited >> vmemoryuse unlimited >> descriptors 1024 >> memorylocked 64 kbytes >> maxproc 1024 >> maxlocks unlimited >> maxsignal 514103 >> maxmessage 819200 >> maxnice 0 >> maxrtprio 0 >> maxrttime unlimited >> >> FSL_BIN=/usr/local/fsl/bin >> SSH_AGENT_PID=4883 >> XDG_SESSION_ID=35 >> HOSTNAME=cs2.kispi.int >> SELINUX_ROLE_REQUESTED= >> FS_OVERRIDE=0 >> GPG_AGENT_INFO=/home/maykr/.gnupg/S.gpg-agent:4883:1 >> GLADE_PIXMAP_PATH=: >> TERM=xterm-256color >> XDG_MENU_PREFIX=xfce- >> SHELL=/bin/bash >> HISTSIZE=1000 >> SSH_CLIENT=127.0.0.1 40762 22 >> FSLMULTIFILEQUIT=TRUE >> PERL5LIB=/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/freesurfer/mni/lib/perl5/5.8.5 >> SELINUX_USE_CURRENT_RANGE= >> WINDOWID=46782934 >> OS=Linux >> XAPPLRESDIR=/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/X11/app-defaults >> QT_GRAPHICSSYSTEM_CHECKED=1 >> http_proxy=http://proxy.uzh.ch:3128/ >> LOCAL_DIR=/usr/local/freesurfer/local >> USER=maykr >> LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: >> LD_LIBRARY_PATH=/opt/MATLAB/MATLAB_Compiler_Runtime/v715/sys/java/jre/glnxa64/jre/lib/amd64/server/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/bin/glnxa64/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/runtime/glnxa64/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/sys/java/jre/glnxa64/jre/lib/amd64/server/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/bin/glnxa64/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/runtime/glnxa64/:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/client:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/server:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/bin:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/os/glnxa64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/bin/glnxa64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/runtime/glnxa64:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/sys/java/jre/glnxa64/jre/lib/amd64/server/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/bin/glnxa64/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/runtime/glnxa64/:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/client:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/server:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/bin:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/os/glnxa64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/bin/glnxa64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/runtime/glnxa64:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/sys/java/jre/glnxa64/jre/lib/amd64/server/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/bin/glnxa64/:/opt/MATLAB/MATLAB_Compiler_Runtime/v715/runtime/glnxa64/:/media/n-NAS_MRI/Fontan/programs/ibe! a! > t/! >> MCR/v715 >> /sys/java/jre/glnxa64/jre/lib/amd64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/client:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/server:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/bin:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/sys/os/glnxa64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/bin/glnxa64:/media/n-NAS_MRI/Fontan/programs/ibeat/MCR/v715/runtime/glnxa64: >> FSFAST_HOME=/usr/local/freesurfer/fsfast >> GLADE_MODULE_PATH=: >> MNI_PERL5LIB=/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/freesurfer/mni/lib/perl5/5.8.5 >> FMRI_ANALYSIS_DIR=/usr/local/freesurfer/fsfast >> SSH_AUTH_SOCK=/home/maykr/.gnupg/S.gpg-agent.ssh >> FTP_PROXY=http://proxy.uzh.ch:3128/ >> ftp_proxy=http://proxy.uzh.ch:3128/ >> FSF_OUTPUT_FORMAT=nii >> SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/4872,unix/unix:/tmp/.ICE-unix/4872 >> MINC_BIN_DIR=/usr/local/freesurfer/mni/bin >> XDG_CONFIG_DIRS=/etc/xdg >> SUBJECTS_DIR=/media/n-NAS_MRI/freesurfer-subjects-dir >> DESKTOP_SESSION=xfce >> MAIL=/var/spool/mail/maykr >> NXSESSIONID=cs2.kispi.int-2000-678D3BAFF4D23A591199EAB35F8614B4 >> PATH=/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/media/n-NAS_MRI/Fontan/programs/ibeat:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/media/n-NAS_MRI/Fontan/programs/ibeat:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/media/n-NAS_MRI/Fontan/programs/ibeat:/media/n-NAS_MRI/Fontan/programs/ibeat/tools:/usr/local/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/maykr/.local/bin:/home/maykr/bin >> SHADOW_XAUTHORITY=/home/maykr/.nx/C-cs2.kispi.int-2000-678D3BAFF4D23A591199EAB35F8614B4/authority >> FSLMACHTYPE=linux_64-gcc4.8 >> PWD=/media/n-NAS_MRI/freesurfer-subjects-dir/0001336 >> FUNCTIONALS_DIR=/usr/local/freesurfer/sessions >> LANG=C >> KDE_IS_PRELINKED=1 >> FSLTCLSH=/usr/local/fsl/bin/fsltclsh >> KDEDIRS=/usr >> FSLMACHINELIST= >> MINC_LIB_DIR=/usr/local/freesurfer/mni/lib >> SELINUX_LEVEL_REQUESTED= >> FSLREMOTECALL= >> https_proxy=http://proxy.uzh.ch:3128/ >> FSLCONFDIR=/usr/local/fsl/config >> FSLWISH=/usr/local/fsl/bin/fslwish >> SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass >> SLAVE_PID=4068 >> HISTCONTROL=ignoredups >> SHLVL=7 >> HOME=/home/maykr >> IBEAT_HOME=/media/n-NAS_MRI/Fontan/programs/ibeat >> MNI_DIR=/usr/local/freesurfer/mni >> FREESURFER_HOME=/usr/local/freesurfer >> FSLDISPLAY=/usr/bin/display >> FSLCONVERT=/usr/bin/convert >> no_proxy= >> HTTP_PROXY=http://proxy.uzh.ch:3128/ >> LOGNAME=maykr >> FSLDIR=/usr/local/fsl >> DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-g9RDmq1Pw0,guid=f19916051f53a528d10b18f853638272 >> XDG_DATA_DIRS=/usr/local/share:/usr/share >> SSH_CONNECTION=127.0.0.1 40762 127.0.0.1 22 >> FIX_VERTEX_AREA= >> LESSOPEN=||/usr/bin/lesspipe.sh %s >> XDG_RUNTIME_DIR=/run/user/1019 >> DISPLAY=:2000.0 >> QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins >> GLADE_CATALOG_PATH=: >> FSLLOCKDIR= >> MNI_DATAPATH=/usr/local/freesurfer/mni/data >> FSLOUTPUTTYPE=NIFTI_GZ >> FSL_DIR=/usr/local/fsl >> COLORTERM=xfce4-terminal >> _=/usr/bin/tcsh >> HOSTTYPE=x86_64-linux >> VENDOR=unknown >> OSTYPE=linux >> MACHTYPE=x86_64 >> GROUP=ZfMRF >> HOST=cs2.kispi.int >> OMP_NUM_THREADS=1 >> REQUIRE_FS_MATCH=0 >> >> >> ________________________________________ >> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von "Bruce >> Fischl [fischl(a)nmr.mgh.harvard.edu] >> Gesendet: Donnerstag, 22. Mai 2014 14:10 >> An: Freesurfer support list >> Betreff: Re: [Freesurfer] missing temporal lobes >> >> Hi Kristina >> >> that shouldn't be needed. If you upload a dataset we will take a look >> >> cheers >> Bruce >> On >> Thu, 22 May 2014, Mayer Kristina wrote: >> >>> Hi there, >>> I tried to put more CP, so all the temporal lobe tissue is in the mask. >> This will end up in overestimation of white matter. So in a second step >> you will have to manually adjust WM mask. >>> In my dataset, after adjusting WM mask, WM ist still little bit >> oversetimated, but at least i am not missing tissue. >>> When you find a better option, I am glad to learn about. >>> Good luck! >>> >>> Best, Kristina >>> ________________________________________ >>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von >> "Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 22. Mai 2014 04:35 >>> An: Freesurfer support list >>> Betreff: Re: [Freesurfer] missing temporal lobes >>> >>> Hi Eileen >>> Does adding control points to both temporal lobes fix it? >>> Cheers >>> Bruce >>> >>>> On May 20, 2014, at 9:34 AM, "Daly, Eileen" <eileen.daly(a)kcl.ac.uk> wrote: >>>> >>>> Hello all, >>>> >>>> We are having trouble with the output after running recon-all -all >> -subjid subjectx on our scans. >>>> Registrations and skull striping look okay, but the white matter and >> pial surface segmentations leave outportions of the anterior temporal >> lobe. >>>> >>>> After adding control points to the left temporal lobe, we then ran >> recon-all -autorecon2 –cp -autorecon3 -subjid subjects. >>>> >>>> This made the the left lobe look better, but then we spotted new >> missing bits on the right side >>>> anterior temporal lobe. >>>> >>>> Any ideas on dealing with these missing temporal lobe issues? >>>> >>>> Thanks, >>>> >>>> Eileen Daly >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> 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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Re: [Freesurfer] Registration and Surface Flattening
by Caka 26 May '14

26 May '14

Dear Bruce, Doug and all, Thanks for your suggestion, it helped a lot. (1) I load the fsaverage surface (lh.inflated) in tksurfer, and then load the fsaverage patch (lh.cortex.patch.flat). The flat map was shown for several seconds, and then an error occurred and tksurfer was shut down. The terminal said: ‘tksurfer.bin:tnl/t_vertex.c:407: update_input_ptrs: Assertion ‘a[j].inputstride == vptr-> stride’ failed. Abort(core dumped)’. Could you give me some advice? I use a 'CentOS release 6.2' system. The freesurfer is ‘freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0’. (2) Indeed, I want to flatten all cortical thickness surfaces of 140 subjects onto the ‘lh.cortex.patch.flat’ of fsaverage. I just don’t understand your idea how to do this. After I load ‘lh.cortex.patch.flat’ of fsaverage, the tksurfer only shows this flat map (now it lasted for several seconds and crashed), so how can I ' load whatever overlay you want in the same way you would on the inflated surface’? Does it mean that I load the individual flat map on the individual inflated surface? But I haven’t got the individual flat map yet. (3) I am wondering if there are some table recording the transformation relationships between the fsaverage surface vertices and the flat map vertices? If so, then I think all I need to do is extracting the cortical thickness value of every vertex in individual inflated surface, and then putting into the corresponding vertex in the flat map. Thank you very much! Best regards, Qiongmin ------------------------------------------------------------------------------------------------------------------------------------------------- Load the fsaverage surface in tksurfer (say lh.inflated) then load the patch we distribute with fsaverage (I think it's called something like lh.cortex.patch.flat) with file->load patch. Then load whatever overlay you want in the same way you would on the inflated surface Cheers Bruce > On May 19, 2014, at 10:06 PM, Caka <qiongmin.ma(a)gmail.com> wrote: > > > Hi Doug, > Thanks for your suggestion on tksurfer, it works. > I would like to map all the subjects into a flat map because I am curious about the 2-D thickness patterns between different groups. I think there will be some distinctions. > But if I flatten fsaverage, how can I map everyone?s 3D surface onto the fsaverage?s 2D map? Is there a command? > > Best, > Qiongmin > > > > >> On 05/13/2014 11:19 PM, Caka wrote: >> Dear Doug and all, I have already done two things: (1) 'recon-all? to >> the segmentation for 140 subjects; (2) surface registration to >> fsaverage template for 1 subject using: mri_surf2surf --hemi lh >> --srcsubject sub001 --srcsurfval thickness --src_type curv >> --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I >> have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) >> Is this 'sub001-thickness-lh.mgz? a surface file or a volume file? How >> can I read it? I used ?freeview sub001-thickness-lh.mgz? to read it, >> but a dark scene was shown, nothing can be found. I also used >> ?mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz >> $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc?, an error occurred >> like ?ERROR: number of vertices in >> /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match >> surface (163842, 132230)?. > Try tksurfer fsaverage lh inflated -aparc -overlay > sub001-thickness-lh.mgz -fminmax .01 4 >> (2) After the registration, I want to flatten the surface of curvature >> or thickness into a full plane. The wiki says we should first specify >> 5 vertices and cut the whole area without the midline region, then >> ?kris_flatten? can be used. Indeed, this procedure requires quite a >> lot manually operation. I am wondering if there are some automatically >> commands that can do this flatten projects for 140 subject? Any reply >> would be really appreciated! Qiongmin >> _______________________________________________ Freesurfer mailing >> list Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > I don't think so, though I think bruce was working on something. You > could just flatten fsaverage and then map everyone to fsaverage (as you > have already done). Why do you want to map everyone to a flat map? > > doug > ______________________________

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modeling multiple scalars in F-contrasts
by L. Schweren 26 May '14

26 May '14

Dear Freesurfer experts, I am modelling multiple covariates (age, SES, nr of symptoms and nr of symptoms2) in one subject group. For the quadratic term I added a column in the fsgd-file. I want to visualize the effect of nr of symptoms, either their linear or their quadratic effects. I therefore made two contrasts: The effect of symptoms: 0 0 1 0 And the effect of symptoms2: 0 0 0 1 I would like to model these two effects together in one contrast (to get the results of both contrasts overlaid on top of each other, but in one mgh file). I tried the following contrast: 0 0 1 0 0 0 0 1 But the result is very different from the two individual contrasts. I get large (non-overlapping) clusters of significant effect in the two separate contrasts, but with the combined contrasts I get none. In the examples I found online for F-contrasts, they always add up to zero, as they are comparisons between groups. What would be the appropriate contrast if I want to visualize all regions with EITHER a linear OR a quadratic effect of symptoms? Thank you very much for your help! Best wishes, Lizanne

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