________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce Fischl [fis...@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 > 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> 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/ibea! 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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce > Fischl [fis...@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-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von > "Bruce Fischl [fis...@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.d...@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@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@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@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
