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
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
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 437CD31F.4040700@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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 437CD31F.4040700@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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 437E113F.9070202@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 437CD31F.4040700@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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
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
-- Dr Jane Aspell Department of Experimental Psychology, University of Oxford, South Parks Road, Oxford, OX1 3UD
In message 437CD31F.4040700@nmr.mgh.harvard.edu Doug Greve greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu 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
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
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 Pine.LNX.4.62.0511280225500.19611@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
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@minerva.nmr.mgh.harvard.edu Nick Schmansky nicks@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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@icebox.nmr.mgh.harvard.edu Doug
Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
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@minerva.nmr.mgh.harvard.edu Nick Schmansky nicks@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@icebox.nmr.mgh.harvard.edu Doug Greve greve@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@icebox.nmr.mgh.harvard.edu Doug
Greve greve@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@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
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 1134599450.17318.34.camel@minerva.nmr.mgh.harvard.edu Nick Schmansky nicks@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@minerva.nmr.mgh.harvard.edu Nick Schmansky nicks@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@icebox.nmr.mgh.harvard.edu
Doug
Greve greve@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@icebox.nmr.mgh.harvard.edu Doug
Greve greve@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@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
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 1134599450.17318.34.camel@minerva.nmr.mgh.harvard.edu Nick Schmansky nicks@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@minerva.nmr.mgh.harvard.edu Nick Schmansky nicks@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@icebox.nmr.mgh.harvard.edu
Doug
Greve greve@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@icebox.nmr.mgh.harvard.edu Doug
Greve greve@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@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 >
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu 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
I've created a new mailing list for discussions among fMRI researchers that are not directly related to any particular software analysis package. There are a variety of software packages available, and each of them has their own discussion list, but there is no list available for more general discussions, for example, questions about hardware, experimental designs, job advertisements, etc. Currently many of these discussions take place on software- specific lists, where they are not strictly appropriate and people often post the same topics to multiple such lists to reach the widest audience, since until not a more appropriate forum did not exist.
To subscribe to this new "fMRIList", visit the web site: https:// rcbi.rochester.edu/mailman/listinfo/fmrilist
keith
----- Keith Schneider Assistant Professor Rochester Center for Brain Imaging University of Rochester Rochester, NY
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Jane Aspell -
Keith Schneider -
Nick Schmansky -
Stephanie McMains