Re: [Freesurfer] Re: MINC toolkit
Hi After having major hard drive problems i've lost the minc tools that i had installed at /usr/pubsw/packages/mni/current/lib so i need to download the minc tools again. I've been trying to download them from: https://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads but when i click on the link for MINC tools I get: "The requested URL /pub/dist/fs_supportlibs/mni-prebuilt/mni-1.4_rh9.tar.gz was not found on this server." Is there somewhere else I can get the tools from? I know they now come packaged with the full freesurfer program but I don't want to download the whole thing as I've downloaded 3 versions of freesurfer already! thanks! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: 2005 versions of freesurfer
Thanks for the new link. Since my hard drive failure many of the freesurfer programs work, complaining of missing libraries, eg "tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory" which I suspect were lost from the /usr directories when my hard drive failed. I thought that reinstalling freesurfer might fix these problems but I don't want to install the newest release as I am mid-study. Can I get the older releases (last year's) from a website? I can't find them on your wiki. thanks a lot! Jane In message <[EMAIL PROTECTED]> "Nick Schmansky" <[EMAIL PROTECTED]> writes: > Sorry, broken link in the wiki (fixed now). > > Use: > > https://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/binaries/rh9/mni-1.4_rh9.tar.gz > > > Hi > > > > After having major hard drive problems i've lost the minc tools that i had > > installed at /usr/pubsw/packages/mni/current/lib so i need to download > > the minc > > tools again. I've been trying to download them from: > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/MiscellaneousDownloads > > > > but when i click on the link for MINC tools I get: > > > > "The requested URL > > /pub/dist/fs_supportlibs/mni-prebuilt/mni-1.4_rh9.tar.gz was > > not found on this server." > > > > Is there somewhere else I can get the tools from? I know they now come > > packaged > > with the full freesurfer program but I don't want to download the whole > > thing as > > I've downloaded 3 versions of freesurfer already! > > > > thanks! > > > > Jane > > > > > > -- > > Dr Jane Aspell > > Department of Experimental Psychology, University of Oxford, > > South Parks Road, Oxford, OX1 3UD > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multiple simultaneous overlays
hi i need to view several overlays simultaneously (to see where my activation lies relative to retinotopic map overlays) on a surface. is there no way of doing this with freesurfer? its seems like a function that a lot of users would need. in one posting regarding this you suggested loading the overlays into matlab using load_wfile, combine them, then write them out using write_wfile...are these actual programs? where would i get them from and do i need any additional matlab programs for this to work? and how does the combining stage work - are there any further instructions on this? many thanks! Jane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multiple simultaneous overlays
hi i need to view several overlays simultaneously (to see where my activation lies relative to retinotopic map overlays) on a surface. is there no way of doing this with freesurfer? its seems like a function that a lot of users would need. in one posting regarding this you suggested loading the overlays into matlab using load_wfile, combine them, then write them out using write_wfile...are these actual programs? where would i get them from and do i need any additional matlab programs for this to work? and how does the combining stage work - are there any further instructions on this? many thanks! Jane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multiple simultaneous overlays
hi i need to view several overlays simultaneously (to see where my activation lies relative to retinotopic map overlays) on a surface. is there no way of doing this with freesurfer? its seems like a function that a lot of users would need. in one posting regarding this you suggested loading the overlays into matlab using load_wfile, combine them, then write them out using write_wfile...are these actual programs? where would i get them from and do i need any additional matlab programs for this to work? and how does the combining stage work - are there any further instructions on this? many thanks! Jane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Multiple simultaneous overlays
hi i need to view several overlays simultaneously (to see where my activation lies relative to retinotopic map overlays) on a surface. is there no way of doing this with freesurfer? its seems like a function that a lot of users would need. in one posting regarding this you suggested loading the overlays into matlab using load_wfile, combine them, then write them out using write_wfile...are these actual programs? where would i get them from and do i need any additional matlab programs for this to work? and how does the combining stage work - are there any further instructions on this? many thanks! Jane ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_surface error
Hi I have been trying to run make_average_surface but get the error below. Any idea what the problem is? Many thanks, Jane Aspell >make_average_surface --subjects jane kader anna make_average_surface input subjects: jane kader anna output subject: average mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_sulc No such file or directory mris_average_curvature... processing subject jane... processing subject kader... processing subject anna... MRISwriteCurvature: could not open ../average/surf/lh.avg_curv No such file or directory mris_make_average_surface... reading vertex positions from orig... processing subject jane... The following must be revisited** Segmentation fault PS the version info for the program i have is: ProgramName: mris_make_average_surface ProgramArguments: -all-info ProgramVersio n: $Name: $ TimeStamp: 05/11/07-11:44:07-GMT CVS: $Id: mris_make_average_surfac e.c,v 1.9 2004/01/29 14:59:12 tosa Platform: Linux PlatformVersion: 2.4.20-20.9 CompilerName: GCC CompilerVers ion: 29600 -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] retinotopy and FsFast
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy and FsFast
Ok, thanks. It seems that the problem with finding the session came about because I was running 'sfa-sess' from the 'MYSTUDY' study directory when it seems i should have run it from the 'session parent' directory. cheers, Jane In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> writes: > > that's a bug in the wiki, "-s avdk" should not appear there. Rather, it > should be "-s yoursession" or "-sf sessidfile". If it cannot find the > sessions, then something is not set up correctly. Can you double check > that the sessions in the sessidfile are in the current directory? > > > Jane Aspell wrote: > > >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 > > > > > > > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy and FsFast
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 -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> writes: > > that's a bug in the wiki, "-s avdk" should not appear there. Rather, it > should be "-s yoursession" or "-sf sessidfile". If it cannot find the > sessions, then something is not set up correctly. Can you double check > that the sessions in the sessidfile are in the current directory? > > > Jane Aspell wrote: > > >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 > > > > > > > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy and FsFast
Thanks. My colours don't seem to correspond very well though - ie i see red in dorsal occipital cortex when it should be blue, reversing doesn't help. (And btw if freesurfer only uses 3 colours for polar presumably there will be no difference for right and left hemispheres?). Could the creation of 'polar' be going wrong because the fieldsign creation didn't work? I have made an occipital patch so that can't be the problem. when i run: tksurfer -dorothy rh inflated -tcl mk-fieldsign.tcl i get errors like '% can't read "name": no such variable% and 'can't read "env(MRI_DIR)": no such variable% i have previously run 'source Setupfreesurfer so i don't know why this is happening. thanks for your help Jane Re: [Freesurfer] retinotopy and FsFast Stephanie McMains Thu, 24 Nov 2005 11:51:14 -0800 The eccen should go fovea=red, parafoveal=blue, and periphery = green. If they aren't going in that order, reverse the overlay. the polar angle should be, blue for horizontal meridian, green for lower visual field and red for upper visual field. Making the fs map will also fail if you don't have a occipital patch made. Thought that might be your trouble. Stephanie McMains On Nov 24, 2005, at 12:09 PM, 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 In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> writes: > > you should be running everything fromt the study dir. Often, your study > dir is also the parent to the sessions. When it is not, then you need to > supply a -d sesspar or -df sessparfile > > doug > > > Jane Aspell wrote: > > >Ok, thanks. > >It seems that the problem with finding the session came about because I was > >running 'sfa-sess' from the 'MYSTUDY' study directory when it seems i should > >have run it from the 'session parent' directory. > >cheers, > >Jane > > > > > >In message <[EMAIL PROTECTED]> Doug Greve > ><[EMAIL PROTECTED]> writes: > > > > > >>that's a bug in the wiki, "-s avdk" should not appear there. Rather, it > >>should be "-s yoursession" or "-sf sessidfile". If it cannot find the > >>sessions, then something is not set up correctly. Can you double check > >>that the sessions in the sessidfile are in the current directory? > >> > >> > >>Jane Aspell wrote: > >> > >> > >> > >>>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&#x
Re: [Freesurfer] retinotopy and FsFast
hi doug i'm not sure how to find out what the version of freesurfer is as the -all-info command doesn't work on csurf. however, the installation tar file i originally downloaded was called: freesurfer-20040218-Linux.tar.gz (for RedHat 9) my paint-sess log says the version of paint-sess is: $Id: paint-sess,v 1.2 2003/08/06 00:53:50 greve Exp $ FAST Version 20031218 are only 3 colours (red=upper field/fovea, blue=horizontal meridian/parafovea, green=lower visual field/periphery) used to specify the polar angle and eccentricity? what should the overlay threshold settings be in tksurfer to correctly display them? thanks! Jane In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] retinotopy and FsFast
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 <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> 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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: error loading shared libraries
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 <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> Doug > > Greve <[EMAIL PROTECTED]> 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 > >> [EMAIL PROTECTED] > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: error loading shared libraries & retinotopy
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 (0x4021)
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 (0x4200)
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 (0x404f)
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 (0x4000)
In message <[EMAIL PROTECTED]> Nick
Schmansky <[EMAIL PROTECTED]> 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 +, 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* libti
Re: [Freesurfer] Re: error loading shared libraries & retinotopy
hi again
after installing:
itcl-3.2-88.i386.rpm
tix-8.1.4-88.i386.rpm
tkmedit and tksurfer are now working, thanks.
if anyone knows about interpreting the colour codes produced by retinotopy
analysis in FsFast please let me know!
thanks
Jane
In message <[EMAIL PROTECTED]> Nick
Schmansky <[EMAIL PROTECTED]> 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 +, 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 (0x4021)
> > 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 (0x4200)
> > 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 (0x404f)
> > 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 (0x4000)
> >
> >
> >
> > In message <[EMAIL PROTECTED]> Nick
> > Schmansky <[EMAIL PROTECTED]> 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 betwe
Re: [Freesurfer] Re: mk-fieldsign
Hi
I am still having problems 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 for your help!
Jane
In message <[EMAIL PROTECTED]> Nick
Schmansky <[EMAIL PROTECTED]> 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 +, 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 (0x4021)
> > 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 (0x4200)
> > 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 (0x404f)
> > 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 (0x4000)
> >
> >
> >
> > In message <[EMAIL PROTECTED]> Nick
> > Schmansky <[EMAIL PROTECTED]> writes:
> > > Jane,
> &g
Re: [Freesurfer] Re: mk-fieldsign problems
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 <[EMAIL PROTECTED]> Nick
Schmansky <[EMAIL PROTECTED]> 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 +, 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 (0x4021)
> > 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 (0x4200)
> > 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 (0x404f)
> > 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 (0x4000)
> >
> >
> >
> > In message <[EMAIL PROTECTED]> Nick
> > Schmansky <[EMA
Re: [Freesurfer] Re: mk-fieldsign problems
yes i already had the file. the one you sent me seemed to be a newer version
though, so i ran paint-sess using that, but it gives the same error message.
jane
In message <[EMAIL PROTECTED]> Bruce
Fischl <[EMAIL PROTECTED]> writes:
> hmmm, do you have it? If not, I've attached a copy.
>
> cheers,
> Bruc
> e
> On Tue, 3 Jan 2006, Jane Aspell wrote:
>
> > 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 <[EMAIL PROTECTED]> Nick
> > Schmansky <[EMAIL PROTECTED]> 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 +, 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 (0x4021)
> >>> libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x40226000)
> >>> libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x4022e000)
>
Re: [Freesurfer] Re: mk-fieldsign problems
hi again
we've been trying various things to get mk-fieldsign to work: installing the
development version of freesurfer and trying it on a different computer, but we
get the same error message. We thought that perhaps mk-fieldsign doesn't have
the same access permissions as the other tcl scripts or that it's not actually
looking in the same directory as for, e.g. tksurfer.tcl for which it gives the
full path:
surfer: using interface /home/jaspell/freesurfer/lib/tcl/tksurfer.tcl
Read /home/jaspell/freesurfer/surface_labels.txt, found 95 structures
tksurfer: run tcl script: mk-fieldsign.tcl
we are still stuck so would be really grateful for any tips!
thanks very much,
Jane
In message <[EMAIL PROTECTED]> Bruce
Fischl <[EMAIL PROTECTED]> writes:
> hmmm, do you have it? If not, I've attached a copy.
>
> cheers,
> Bruc
> e
> On Tue, 3 Jan 2006, Jane Aspell wrote:
>
> > 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 <[EMAIL PROTECTED]> Nick
> > Schmansky <[EMAIL PROTECTED]> 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 +, 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/freesu
[Freesurfer] FS-FAST registration across sessions
Hi My question was asked last year by Tommi Raij (see email pasted below) but I couldn't find a reply to it in the archives. I am analysing retinotopy data that was collected over several sessions but I cannot see how to register scans from multiple sessions together, and to the subject's anatomical scan. Although Fs-Fast appears to combine the data from multiple sessions during the retinotopy analysis it only seems to be possible to use one registration file (register.dat) when overlaying the results onto the anatomical. I would have thought that registering scans from multiple sessions together would be a feature that many people would require. Is there anyway to do it? Tommi gives some possible methods in his email below. When I do try and overlay my data onto a surface I see 'gaps' in the blue/yellow colouring of the fieldsign map overlaid onto the cortical surface. I wonder if this could be due to the inaccuracy of the registration given that I only used the register.dat from the registration of the first session. hope that makes sense! i'd be grateful for any help with this! Jane -- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD --- [Freesurfer] FS-FAST Registration Question: registration across sessions within subjects Tommi Raij Thu, 20 Oct 2005 15:43:46 -0700 Hi Doug/All, This is a question about registering several functional scans from the same subject in the same space. The functional scans are from different sessions, so even if the slice recording parameters are identical, the head will inavoidably be in different locations and with different rotation. The data have already been collected, so we cannot use any on-line corrections. Four different techniques come to mind that could be used to achieve this, but I would expect that the accuracy of the methods varies a lot. Optimally IMHO one should register the different functional runs with respect to each other directly, simply because the EPI images are very similar with respect to each other (or at least their T1 contrast is). The high-resolution structural image is very different compared to the EPI images so functional-to-structural registration is expected to be much more inaccurate. Here are the four different techniques (please tell me if you can think of more): 1. One possibility would be to use mc-sess for all runs from the same subject (place all the runs from the different sessions in a single "bold" directory and just run mc-sess). Possible problem: If I have understood correctly, mc- sess only corrects for motion within slices. Therefore the different head rotations would make this technique very inaccurate. Or does there exist an updated version of mc-sess that could handle even large displacements and rotations? 2. A second possibility would be to use one of the automatic functional-to- structural registration programs and register each functional run to the same hires structural image. However, based on the discussion above, there are expected to be inaccuracies in the functional-to- structural registration that could be large enough to make comparisons across the functional sessions meaningless (i.e., the differences would mainly be driven by inaccuracies in the registration). 3. A third possibility would be to use the same technique as for registration across subjects, i.e., resampling the different runs from the same subject into a spherical space calculated from this specific subject. Again this is just as variety of registration from functional to structural, and would be expected to provide suboptimal results. 4. A fourth possibility would be to find a method for registering all the functional images in a single space with respect to each other, e.g. by picking one of the functional sessions as the target space and resampling all other functional sessions from this subject into this space (without using the hires structurals at all). I guess this would be kind of motion correction but capable of handling rotations. If such a tool exists, it might be more accurate than any of the methods above, simply because the functional images are more similar compared to each other than compared to the subject's hires structural image. Any ideas/suggestions which method would give the most accurate result? And what kind of tools currently exist? Thanks, Tommi --- Tommi Raij MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS-FAST registration across sessions
hi doug i think i have actually already done what you suggest as my bold directory consists of all the retinotopy runs (in subdirs 001-010). this is the 'ls' of the bold directory: 001/ 003/ 005/ 007/ 009/ register.dat same-sess-reg.dat seq.info 002/ 004/ 006/ 008/ 010/ rtopy/scripts/ i ran the motion correction from the study directory as: >mc-sess -sf sessid -df sesspar and it completed successfully. -so will that have aligned all the runs together? if so, what can explain the fact that the field sign map is not continuous when overlaid on the cortex and shows gaps in the blue/yellow colouring? thanks! jane In message <[EMAIL PROTECTED]> Doug Greve <[EMAIL PROTECTED]> writes: > > You can try putting all the runs into a single bold directory. The > motion correction will (do it's best to) align them. > > doug > > > > > > > Jane Aspell wrote: > > >Hi > > > >My question was asked last year by Tommi Raij (see email pasted below) but I > >couldn't find a reply to it in the archives. I am analysing retinotopy data > >that was collected over several sessions but I cannot see how to register > >scans from multiple sessions together, and to the subject's anatomical scan. > >Although Fs-Fast appears to combine the data from multiple sessions during > >the > >retinotopy analysis it only seems to be possible to use one registration > >file > >(register.dat) when overlaying the results onto the anatomical. I would have > >thought that registering scans from multiple sessions together would be a > >feature that many people would require. Is there anyway to do it? Tommi > >gives > >some possible methods in his email below. > >When I do try and overlay my data onto a surface I see 'gaps' in the > >blue/yellow colouring of the fieldsign map overlaid onto the cortical > >surface. > >I wonder if this could be due to the inaccuracy of the registration given > >that > >I only used the register.dat from the registration of the first session. > >hope that makes sense! > >i'd be grateful for any help with this! > > > >Jane > > > > > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
