Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

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

Registration and Surafce Flattening
by Caka 28 May '14

28 May '14

Hi Bruce, Yes I am trying to do some quantitative analysis rather than just displaying the patches. The only way I know for getting the vertex indices and the coordinations is reading it into matlab. (1) flat = read_patch(‘lh.cortex.patch.flat’); This command worked today! I rebooted my system. (2) patch = read_asc(‘lh.cortex.patch.flat.asc’); This command still couldn’t work. The error information is: ??? Error using ==> reshape To RESHAPE the number of elements must not change. Error in ==> read_asc at 39 v = reshape(v, [4 S(2)])’ ; Thanks very much! Qiongmin --------------------- Original email ----------------------- Hi Qiongmin why are you trying to read the patches into matlab? Also, can you send us your full matlab command that generated the error? Sounds like you passed the incorrect file name cheers Bruce On Tue, 27 May 2014, Caka wrote: > 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 suggestedin?https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/m… > tml > (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? > > >

1 0

Qdec factor.levels loading error
by Yu(余)Qijing(奇静) 28 May '14

28 May '14

Dear Freesurfers, I am experiencing the following problem when I load the qdec.table.dat file in qdec: Loading data table /Volumes/fMRI/Scanner_Data/qdec/qdec.table.dat... QdecDataTable::Load: will attempt to open as Mac text file... Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 89 Reading discrete factor levels from config file /Volumes/fMRI/Scanner_Data/qdec/gender.levels ?? done. ERROR: /Volumes/fMRI/Scanner_Data/qdec/gender.levels is invalid. Must have at least two levels. The discrete factor is gender. I tried adding a new line at the end of both qdec.table.dat and gender.levels files, but still have the problem. I attached the gender.levels. I created both .dat and .levels files in excel, and saved as delimited txt, then forced the extension to be .levels and .dat. Did I do anything wrong when creating them? Also I noticed "QdecDataTable::Load: will attempt to open as Mac text file...", could this mean the error may be from qdec.table.dat file? Thank you very much! All the best, QJ

2 2

recon -all with .nii input problems with perl version 5.18
by Samuel Thorpe 28 May '14

28 May '14

Hello, I recently upgraded from Ubuntu 13.10 to 14.04, and I started getting a new error message while running "recon-all" with .nii file inputs (details below). From the error message I believe the problem might be that Ubuntu 14.04 ships with perl version 5.18 (as opposed to 5.14 for previous versions), and the Ubuntu 14.04 Perl manpage (http://manpages.ubuntu.com/manpages/trusty/man1/perl5120delta.1.html) specifically lists "shellwords.pl" as a newly deprecated library. My naive instinct was to install perl version 5.14 using perlbrew, and switch to it whenever a new shell is launched by editing my .bashrc file, by adding the lines "source ~/perl5/perlbrew/etc/bashrc" "perlbrew switch perl-5.14.4" When I do this my shell recognizes perl-5.14.4 as the active version, but freesurfer does not. This makes me worry it won't be such a simple fix. Any Ideas as to the best way to handle this? Am I on the right track? Many Thanks! -Samuel Thorpe bugr related info: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer SUBJECTS_DIR: /usr/local/freesurfer/subjects "which recon-all" gives "/usr/local/freesurfer/bin/recon-all" Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: jessie/sid Kernel info: Linux 3.8.0-32-generic x86_64 Linux OS: Ubuntu 14.04 LTS "Trusty Tahr" example commands executed: --------------------------------------------------------------------- subject: "bert", "bert_nii" after converting "/usr/local/freesurfer/subjects/bert/mri/orig/001.mgz" to .nii using "mri_convert" (operation successful), I attempt, "recon-all -i /usr/local/freesurfer/subjects/bert/mri/orig/001.nii -s bert_nii -all" error message: --------------------------------------------------------------------- "Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/mritotal line 460." /usr/local/freesurfer/subjects/bert_nii/script/recon-all.log attached

2 1

dt_recon error
by Weber, Wade (weberw) 28 May '14

28 May '14

Hi all, I have been trying to work with DTI data in FreeSurfer for the first time. We acquire our data on a 4T Varian and reconstruct into AFNI format (BRIK/HEAD files). I set up the bval and bvec files successfully and ran the "dt_recon" script. It seemed to run fine until I got an fslregister error saying "G-W contrast is negative but expecting positive." It says to try running with the "--T1" flag. The problem is that I'm not sure which line I put the flag into. I tried re-running the dt_recon line again with the --T1 flag, but it did not work. I know I may not be giving enough information, so if anyone needs more information, just let me know what you want to know. Thanks in advance! Wade Weber University of Cincinnati

2 4

mri_vol2vol error "--o: command not found"
by Ben Mooneyham 28 May '14

28 May '14

Hi all, I'm trying to transform a mean functional image into subject (T1) space using mri_vol2vol. Originally, my code worked successfully, but in attempts to re-run the procedure, both on the same data and on additional data, I've encountered an error in which the log reports an "ERROR: Option unknown" and also "--o: command not found." I am hoping to resolve this issue; does anyone see where my issue is arising from? This is especially strange given that I've gotten it to work before, and I don't think I made any changes to the script besides changing the directory locations for different subjects' data. Here is the mri_vol2vol command as I currently have it: mri_vol2vol --reg ${iSub}_bbregister.dat --mov ${iSub}_Tempfiltered_mean.nii --targ ${DataDir}/S1/${iSub}/${iSub}_brainmask.gcuts.nii \ --o ${iSub}_mean_epi_inT1.nii The cd is ${DataDir}/S1/${iSub} , which contains the ${iSub}_bbregister.dat , ${iSub}_Tempfiltered_mean.nii , and ${iSub}_brainmask.gcuts.nii files. Thanks for your help, Ben Mooneyham -- Graduate Student UCSB - Department of Psychological & Brain Sciences Building 429 Room 102 (210) 912-6076 bwmooneyham(a)gmail.com

2 1

extract mean thickness, surface area of ROI
by sabin khadka 28 May '14

28 May '14

Hi all, I want to extract mean cortical thickness, surface area of an ROI I created with some clusters that showed some group difference. I already have the ROIs I need. What is the easiest way to extract mean values of ROI from all the subjects? Thanks, Sabin

2 1

vtk scalars to freesurfer annot
by Ronald Pierson 28 May '14

28 May '14

Does anybody know a straightforward way to take a labeled vtk image and create a freesurfer image with the accompanying annotation file? Or is there a way to create an annotation file from the list of vertices and labels? Ronald Pierson

1 0

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