Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Longitudinal Pipeline for Subjects with only 1 assessment
by Elijah Mak 30 May '14

30 May '14

Dear FS Experts, I am running a longitudinal analyses, and I'd like to use the Linear Mixed Effect framework as even subjects with only 1 time-point can be included into the model. How do I create the base for a subject with only 1 TP? Is this the correct approach? recon-all -base *[basename]* -tp [*subjectid] *-all ? I tried that, but I was met with the following error: ... mghRead(*subjectid*/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -436, rheno = -396 orig.nofix lhholes = 219, rhholes = 199 Loading mri/aseg.mgz Getting Brain Volume Statistics Darwin pspc112 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64 recon-all -s [*subjectid]* exited with ERRORS at Fri May 30 04:43:50 BST 2014 Thank you all. Best Regards, Elijah -- Elijah Mak, B.A. Doctoral Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

2 1

Extract peak voxel (vertex) coordinates from surfaces
by Milde, Christopher 30 May '14

30 May '14

Dear Freesurfers, I would be interested in figuring out the peak vertex of clusters based on coregistered functional FEAT data with the reconstructed anatomical surfaces. The FEAT preprocessing was run without smoothing and smoothing was applied after the feat2surf Does anyone know how to obtain the peak coordinate (preferentially on smoothwm surface) ? I need exact vertex indices for running mris_pmake Kindly regards, Christopher

1 0

Longitudinal recon-all –localGI after error on cross recon-all –localGI and optimal smoothing
by Knut J Bjuland 30 May '14

30 May '14

Hi Due to aberrantly high for a few of the subjects, I ran recon-all -autorecon2-wm -randomness -autorecon3 –hemi ?h before, calculating the localGI index. However, I intended to use these data in a longitudinal stream. These subject that were reprocessed using recon-all -autorecon2-wm -randomness -autorecon3 , and should I rerun the longitudinal stream for these subjects before doing I use recon-all –long id base_id –localGI? What are the optimal smoothing when using the linear mixed models? Best regards Knut J Bjuland

2 3

FDR correction in Matlab
by Nandita Vijayakumar 29 May '14

29 May '14

Hi FS team, I was wondering if you could help me with FDR correction for linear mixed models within Matlab. I have run FDR2 correction using the following command: *dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); *However, dvtx was empty, so I would like to try lme_mass_FDR instead. Could you please help me with the command for FDR correction, as well as how to visualise the corrected significance map in FreeSurfer? Thank you, Nandi Vijayakumar MPsych (Clinical Neuropsychology) / PhD Candidate ADAPT | Adolescent Development and Psychopathology Team Melbourne School of Psychological Sciences University of Melbourne Email: *n.vijayakumar(a)student.unimelb.edu.au <n.vijayakumar(a)student.unimelb.edu.au>*

2 1

Surface Label to Nifti File
by MCLAREN, Donald 29 May '14

29 May '14

I'm trying to convert a surface label to a nifti file to use with functional surface data that is already in nifti format. The ultimate goal is to be able to use the converted surface label as a seed in gPPI analyses that is run in MATLAB. I've been able to use volume based seeds for the MNI305 subcortical stream and carryout the analysis on the surfaces already. I'm just wanting to use cortical surface seeds now. I think I've got the code correct, but wanted to double check that I am using the correct command: mri_label2label -srclabel mylabel --s fsaverage --trglabel tmplabel --outmask test.nii --regmethod surface --hemi lh In this case, does the target surface matter? It seems to default to white? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

1 0

Tracula with multi-shell data
by Chris Watson 29 May '14

29 May '14

Dear Anastasia et al. I have data DTI that has multiple b-values. I worked around this by skipping '-tensor', and sym linking 'mean_fsumsamples.nii.gz' to 'dtifit_FA.nii.gz'. However, at the end of 'trac-path', there is an error thrown. Specifically when 'dmri_pathstats' is called, because it is looking for dtifit_{L1, L2, L3, V1, ...}. Do you have a workaround for this? Should I just run dtifit on the data? Also, merged_avg33_mni_bbr.nii.gz wasn't created, but I was able to create it (I copied the code from around line 400 of 'trac-paths'). When I view it with freeview, though, there is a light blue/greenish background. I assume those voxels are supposed to be 0's, but for some reason aren't here? Thanks, Chris

1 0

URGENT: Error in analyse
by Saloni Sharma 29 May '14

29 May '14

Dear Freesurfers, So I have followed all the instructions given on your website in order to use qdec. When i analyse the images only using a file group.levels that defines the two groups I'm comparing the analysis runs fine and gives me results, but when I add gender, for instance, as a discrete factor, it loads the data successfully but when I click analyse it shows the following error: Error in Analyze: Couldn't open file /tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/lh.thickness.fwhm10.fsaverage.mgh Please guide me as to what is going wrong and what I can do to fix it. I would appreciate a quick response as my thesis submission is due in two weeks and I cannot proceed until this problem is sorted. Thanks and regards, Saloni

6 13

asegstats2table Longitudinal data.
by Victor Montal Blancafort 29 May '14

29 May '14

FS experts, The aim of this mail is about some errors I had encountered when I try to generate a table from some *.stats files obtained after a longitudinal analysis. After running the command : *long_stats_slopes --qdec ./qdec/longi_presentacio.qdec.table.dat --stats aseg.stats --meas volume --do-avg --do-rate --do-pc1 --time years* (with no errors during the execution), I would like to extract and put together all the longitudinal aseg.stats files of rate and/or pc1 of my subjects. I had tried to run the command *asegstats2table --subjects $subjectes_table --statsfile=long.aseg.stats.volume-rate.dat --meas volume --tablefile aseg_stats_longi.txt* where $subjects is the list of subjects I want to focus. However, an error appears after running this command: *Parsing the .stats files* * Traceback (most recent call last):* * File "/usr/local/freesurfer/bin/asegstats2table", line 494, in <module>* * id_name_map, measurelist = parsed.parse(options.meas)* * File "/usr/local/freesurfer/bin/fsutils.py", line 117, in parse* * self.measurelist.append( float(strlst[self.measure_column_map[measure]] ))* * ValueError: could not convert string to float: Left-Cerebellum-White-Matter* I do not know if the problem is genereted on the long_stats_slopes command or during the asegstat2table execution. Thanks in advance for your attencion and help! Bests, Victor

2 1

FW: WG: WG: [Fwd: WG: missing temporal lobes], calculation CSF
by Mayer Kristina 29 May '14

29 May '14

Oh, I see. So in the calculation of total GM in aseg.stats does it include the hippocampus, although it is not showing on the masks for surface of GM or PIAL? I also tried to calculate total intracranial CSF (ventricles + outer liquor spaces). Is following calculation correct: e TIV - BrainSegNotVent = total intracranial CSF These calculations are voxels based. I rather prefer a surface based calculation of total intracranial CSF. Is this faisible with freesurfer? Thanks a lot! Cheers, Kristina -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 27, 2014 2:24 PM To: Mayer Kristina Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: WG: [Freesurfer] WG: [Fwd: WG: missing temporal lobes] 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 >>> >>> >>> > > > >

2 3

mris_convert to GIFTI misaligned in freeview
by Harms, Michael 29 May '14

29 May '14

4 3

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer