Freesurfer March 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
84 discussions

editing pre-existing annotations
by Eric Feczko 09 Nov '06

09 Nov '06

Hey, Is there a way to add structures/labels to a pre-existing annotation file? I sampled an annotated atlas onto a subjects surface. But when I load the annotation and try to create a new label, I can't export the edited annotation without eliminating the new label. I tried to create a new color lookup table with the new structure included, and I can load the table in tksurfer just fine. However, when I also try to import the pre-existing annotation(in order to edit it), the color table existing in the annotation overrides the color lookup table I load. If it try to load the table after importing the annotation, the new structure/label does not show up in the label window. If anyone can help me with this issue, that would be great, thanks! -Eric

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Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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retinotopy and FsFast
by Jane Aspell 17 May '06

17 May '06

Hi Thanks for all your previous help with freesurfer. I am trying to use FsFast to do retinotopy analysis and have been following the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I come undone at the stage of running the actual analysis, where the command should be: >sfa-sess -s avdk -a rtopy what does 'avdk' refer to? when i run it i get: ERROR: could not find session avdk when i try it with the arguments: >sfa-sess -analysis rtopy -sf sessid which is similar to the arguments needed for 'selxavg-sess' i get a similar error of not been able to find my (particular subject's) session. i believe i have set up the all the directory structures etc correctly for the sessions format as previous steps worked fine. any ideas what's going wrong? thanks Jane Aspell

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Re: [Freesurfer] Re: mk-fieldsign problems
by Jane Aspell 03 May '06

03 May '06

Hi I would be really grateful if someone could help me with the problems I am having with mk-fieldsign. Even after installing a new version of freesurfer and making various changes to libraries etc. when i run: "paint-sess -sf sessid -a rtopy -hemi rh" i get the error below: tksurfer: run tcl script: mk-fieldsign.tcl couldn't read file "mk-fieldsign.tcl": no such file or directory even though mk-fieldsign.tcl is in the same directory as tksurfer.tcl (which works fine). i am running Red Hat Linux release 9 (Shrike) and installed from freesurfer-Linux-rh9-v2.2.tar.gz any idea what to do? thanks again for your help! Jane In message <1134599450.17318.34.camel(a)minerva.nmr.mgh.harvard.edu> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > Jane, > > Concerning the libraries libitk3.2.so and libitcl3.2.so, Freesurfer does > not use these libraries any more (I think the older -20040218 release > did, however). > > Do you have the environment variable ITCL_LIBRARY defined in your > startup .cshrc file? You can test if it is set by typing (in csh or > tcsh): > > env|grep ITCL > > If it is set (which it might be, from your older freesurfer > installation), then it should be deleted or commented-out from > your .cshrc (or possibly it was placed in your > $FREESURFER_HOME/SetUpFreeSurfer.csh file). > > You can also just type this: > > unsetenv ITCL_LIBRARY > > and then try tkmedit. > > If this is not the problem, can you tell me which OS you are running? > Type: > > cat /etc/redhat-release > > and > > uname -a > > A last ditch effort is to install the itcl libs, from this site: > > http://rpmfind.net/linux/rpm2html/search.php?query=itcl > > But this should not be necessary, as tkmedit that you have does not use > this library (I am truly puzzled why 'ldd' shows that it needs these > libs). > > Thanks, > > Nick > > > On Mon, 2005-12-12 at 11:40 +0000, Jane Aspell wrote: > > hi nick > > > > when i type >ldd `which tkmedit` i get the ouput pasted below this email. > > libitk3.2.so and libitcl3.2.so are not found - could be the problem? > > > > uncommenting 'source ${FSL_DIR}/etc/fslconf/fsl.csh' in FreeSurferEnv.csh > > (and typing 'unsetenv TCLLIBPATH') had no effect. > > > > an earlier version of freesurfer(freesurfer-20040218) didn't give me any of > > these problems and tkmedit etc worked fine. > > > > also, does ANYONE know how to interpret the colour coding (for fovea/vertical > > meridian etc) produced by the FsFast retinotopy analysis?! > > > > thanks again! > > > > jane > > > > > > >ldd `which tkmedit` > > libtix8.1.8.3.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.3.so (0x40017000) > > libtk8.4.so => /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtk8.4.so > > (0x40051000) > > libtcl8.4.so => > > /home/jaspell/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x40111000) > > libglut.so.3 => /usr/lib/libglut.so.3 (0x401ba000) > > libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x401ef000) > > libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x401f8000) > > libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x40210000) > > libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000) > > libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000) > > libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x402ab000) > > libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x402ef000) > > libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x403ce000) > > libtiff.so.3 => /usr/lib/libtiff.so.3 (0x403ed000) > > libcrypt.so.1 => /lib/libcrypt.so.1 (0x4042e000) > > libz.so.1 => /usr/lib/libz.so.1 (0x4045b000) > > libm.so.6 => /lib/tls/libm.so.6 (0x40469000) > > libpthread.so.0 => /lib/tls/libpthread.so.0 (0x4048b000) > > libc.so.6 => /lib/tls/libc.so.6 (0x42000000) > > libitk3.2.so => not found > > libitcl3.2.so => not found > > libdl.so.2 => /lib/libdl.so.2 (0x4049a000) > > libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x4049e000) > > libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x404f0000) > > libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x404ff000) > > libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x405b2000) > > /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) > > > > > > > > In message <1133802940.21136.14.camel(a)minerva.nmr.mgh.harvard.edu> Nick > > Schmansky <nicks(a)nmr.mgh.harvard.edu> writes: > > > Jane, > > > > > > This is an unusual error, since tkmedit and tksurfer do not use the ITK > > > library. To figure out how libitk3.2.so is being referenced, can you > > > send me the output of this command: > > > > > > ldd `which tkmedit` > > > > > > I suspect there is some conflict between the FSL setup and Freesurfer, > > > as FSL does use ITK, and Freesurfer does not, but performs the FSL setup > > > (as a convenience to MGH-NMR users). Along this line, one option is to > > > edit the file FreeSurferEnv.csh (found in your $FREESURFER_HOME) and > > > comment-out this line: > > > > > > source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > like this: > > > > > > # source ${FSL_DIR}/etc/fslconf/fsl.csh > > > > > > Another option is to type this after sourcing the freesurfer setup file: > > > > > > unsetenv TCLLIBPATH > > > > > > This last option is just a guess at a fix though. > > > > > > Nick > > > > > > > > > On Mon, 2005-12-05 at 15:37 +0000, Jane Aspell wrote: > > > > hi > > > > > > > > i installed a newer version of freesurfer (using download > > > > freesurfer-Linux-rh9-v2.2.tar.gz) but when i try and run tkmedit or tksurfer i > > > > get the error: > > > > > > > > "error while loading shared libraries: libitk3.2.so: cannot open shared object > > > > file: No such file or directory" > > > > > > > > this is my output when i source SetUpFreeSurfer.csh: > > > > > > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > > FREESURFER_HOME /home/jaspell/freesurfer > > > > FSFAST_HOME /home/jaspell/freesurfer/fsfast > > > > SUBJECTS_DIR /home/jaspell/freesurfer/subjects > > > > FUNCTIONALS_DIR /home/jaspell/freesurfer/sessions > > > > MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > > > > MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > > > TCLLIBPATH /home/jaspell/freesurfer/lib/tcltktixblt/lib > > > > FSL_DIR /usr/local/fsl > > > > > > > > and these are the contents of /home/jaspell/freesurfer/lib/tcltktixblt/lib: > > > > > > > > blt2.4/ libBLTlite24.a libtclstub8.4.a libtk8.4.so* > > > > tix8.1/ > > > > libBLT24.a* libBLTlite.2.4.dylib* libtix8.1.8.3.so libtk.so.0* > > > > tixConfig.sh > > > > libBLT.2.4.dylib* libBLTlite.a libtix8.1.8.4.so libtkstub8.4.a > > > > tk8.4/ > > > > libBLT.2.dylib* libtcl8.4.so* libtixsam8.1.8.4.so tcl8.4/ > > > > tkConfig.sh > > > > libBLT.a* libtcl.so.0* libtix.so.0 tclConfig.sh > > > > > > > > > > > > any idea how to fix it? > > > > > > > > i don't suppose there's a way of updating an old version of freesurfer without > > > > reinstalling the entire (new version) package? > > > > > > > > thanks! > > > > > > > > jane > > > > > > > > > > > > > > > > > > > > In message <Pine.LNX.4.62.0512021326490.5676(a)icebox.nmr.mgh.harvard.edu> Doug > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > > > > > > That's a pretty old version. Can you download and install a new version? > > > > > > > > > > I actually don't know that much about the interpretation of the color > > > > > wheel. Maybe Nouchine or Sari can help with this. > > > > > > > > > > doug > > > > > > > > > > > > > > > On Fri, 2 Dec 2005, Jane Aspell wrote: > > > > > > > > > > > hi again > > > > > > > > > > > > i'm still really stuck with my retinotopy analysis as i'm not sure if my > > > > > > version of paint-sess $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp $ > > > > > > FAST Version 20031218) has a bug in it (it doesn't make the field sign > > map). i > > > > > > originally downloaded freesurfer-20040218-Linux.tar.gz (for RedHat 9). > > > > > > > > > > > > also, can someone also confrim the colour coding is: red=upper field/fovea, > > > > > > blue=horizontal meridian/parafovea, green=lower visual field/periphery? > > > > > > > > > > > > i can't work out what the overlay threshold settings should be in > > tksurfer to > > > > > > correctly display the colours to code the retinotopy, is there some > > rationale > > > > > > for choosing them? > > > > > > > > > > > > thanks a lot for your help! > > > > > > > > > > > > Jane > > > > > > > > > > > > > > > > > > In message > > <Pine.LNX.4.62.0511280225500.19611(a)icebox.nmr.mgh.harvard.edu> Doug > > > > > > Greve <greve(a)nmr.mgh.harvard.edu> writes: > > > > > >> > > > > > >> What version of freesurfer (and paint-sess) are you using? This was a > > > > > >> problem in some versions about 6 mo ago, but I thought I fixed them > > > > > >> all. > > > > > >> > > > > > >> doug > > > > > >> > > > > > >> > > > > > >> > > > > > >> On Thu, 24 Nov 2005, Jane Aspell wrote: > > > > > >> > > > > > >>> hi again > > > > > >>> I have been proceeding with the retinotopy analysis using FsFast, > > > > > > following the > > > > > >>> instructions at: > > > > > >>> > > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > > > > > >>> and i believe i have successfully overlaid the results on my surfaces and > > > > > > now > > > > > >>> have two questions: > > > > > >>> > > > > > >>> i wasn't able to create the fieldsign with 'paint-sess' because it > > > > > > couldn't find > > > > > >>> tksurfer.new. when i run 'surf-sess' i use the flag -old which forces it > > > > > > to use > > > > > >>> tksurfer.old but this doesn't work in the former case. how can i make > > > > > >>> 'paint-sess' use tksurfer.old and thus create the fieldsign? > > > > > >>> > > > > > >>> there are no instructions on how to relate the colours seen when viewing > > > > > > eccen > > > > > >>> and polar to the location of the ring and wedge. is there a map somewhere > > > > > > that > > > > > >>> can be loaded that tells me what order the colours run from fovea to > > > > > > periphery > > > > > >>> and from vertical to horizontal meridian etc.? > > > > > >>> > > > > > >>> thanks again for your help! > > > > > >>> > > > > > >>> jane > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >> > > > > > >> -- > > > > > >> Douglas N. Greve, Ph.D. > > > > > >> MGH-NMR Center > > > > > >> greve(a)nmr.mgh.harvard.edu > > > > > >> Phone Number: 617-724-2358 > > > > > >> Fax: 617-726-7422 > > > > > >> > > > > > > > > > > > > > > > > > > > > > > -- > > > > > Douglas N. Greve, Ph.D. > > > > > MGH-NMR Center > > > > > greve(a)nmr.mgh.harvard.edu > > > > > Phone Number: 617-724-2358 > > > > > Fax: 617-726-7422 > > > > > > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > >

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segmentation fault for: mris_convert
by Dahlia Sharon 14 Apr '06

14 Apr '06

Hi, I'm trying to use mris_convert and am getting a segmentation fault error. The precise steps are pasted below. Can anyone figure out why this is happening now? Thanks! Dahlia. mirabai:dahlia[81] setenv SUBJECTS_DIR ~/structurals/ mirabai:dahlia[82] nmrenv -------- freesurfer-Linux-centos4-stable-v3.0.1c-20060329 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable FSFAST_HOME /usr/local/freesurfer/stable/fsfast SUBJECTS_DIR /homes/6/dahlia/structurals/ FUNCTIONALS_DIR /usr/local/freesurfer/stable/sessions MINC_BIN_DIR /usr/local/freesurfer/stable/mni/bin MINC_LIB_DIR /usr/local/freesurfer/stable/mni/lib PERL5LIB /usr/local/freesurfer/stable/mni/lib/perl5/5.8.0 GSL_DIR /usr/local/freesurfer/stable/lib/gsl QTDIR /usr/local/freesurfer/stable/lib/qt TCLLIBPATH /usr/local/freesurfer/stable/lib/tcltktixblt/lib FSL_DIR /usr/local/freesurfer/stable/fsl [mirabai:~] (nmr-std-env) cd structurals/subj06_bay2/surf/ [mirabai:surf] (nmr-std-env) mris_convert rh.occip.patch.flat rh.occip.patch.flat.asc Segmentation fault [mirabai:surf] (nmr-std-env)

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Short Course in fMRI
by Doug Greve 10 Apr '06

10 Apr '06

Mark Vangel and I are offering a short course in the statistical signal processing of fMRI. October 31 (Mon) & November 1 (Tue), 2005 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.php doug

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RE: [Freesurfer] how to register subcortical segmentation with theoriginal image
by Durastanti, Valentina (NIH/NINDS) [F] 01 Apr '06

01 Apr '06

Hi, I'm trying to run -autorcon1 of a subject who has 3 mgz images but always came out an error about the motion correction. So I tried run the step using just 1 image and it has gone fine! Have you any suggestion about the reason? The images look good! Thanks Valentina

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new to Freesurfer
by Chacko Cherian 01 Apr '06

01 Apr '06

Hello there, I am a Graduate research assistant at a Neuroimage analysis lab.I am starting to use Freesurfer for image analysis at our labs.Could you please let me know about any prerequisites which I would need before starting to use this tool.(I presume Tcl would be gud to know).Your advice will help me a long way in my work Thanks in advance Take care Chacko Cherian. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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RE: [Freesurfer] lh.curv versus lh.curv.pial
by Durastanti, Valentina (NIH/NINDS) [F] 30 Mar '06

30 Mar '06

thanks Valentina -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, March 30, 2006 12:44 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] lh.curv versus lh.curv.pial depends on what kind of machine, but yes it can take that long (sorry) Bruce On Thu, 30 Mar 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > > Hi, > I've a question: I'm running the autorecon2 of some subjects and I > realized that they take more than 24 hours to finish it. Is it possible? > I know that the step can take upwards of 15 hours but I was wondering if > it is too much! > > Thanks > > Valentina > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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RE: [Freesurfer] lh.curv versus lh.curv.pial
by Durastanti, Valentina (NIH/NINDS) [F] 30 Mar '06

30 Mar '06

Hi, I've a question: I'm running the autorecon2 of some subjects and I realized that they take more than 24 hours to finish it. Is it possible? I know that the step can take upwards of 15 hours but I was wondering if it is too much! Thanks Valentina

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Freesurfer March 2006