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,
> > >
> > > 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:
> > >
> > > # s
[Freesurfer] unpacking multiecho data
I was wondering if there was a center standard for how multiecho data should be 1) unpacked 2) the individual echo sequences parsed out Thanks! Eliz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] unpacking multiecho data
Hi Eliz,
you can convert them to .mgz with:
mri_convert -nth ${echo} mef_echo${echo}.mgz
where $echo runs from 0 to 7 for Andre's standard multi-echo sequence.
cheers,
Bruce
On Mon, 19 Dec 2005, Elizabeth Fenstermacher wrote:
I was wondering if there was a center standard for how multiecho data should
be
1) unpacked
2) the individual echo sequences parsed out
Thanks!
Eliz
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RE: [Freesurfer] Defining one's own atlas in FreeSurfer
Hi Bruce,
I;d like to take up your offer of sending a subject with the annot file, as I'm
quite stuck.
Where can I upload it to? I can't seem to find the link on the wiki.
Also, I only retained the mri, surf, and label subdirectories, although the tar
is still quite big (~125 MB). Are there specific files that you need?
Cheers,
Alex
Alex Fornito
M.Psych/PhD (clin. neuro.) candidate
Melbourne Neuropsychiatry Centre and Department of Psychology
The University of Melbourne
[EMAIL PROTECTED]
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 16/12/2005 12:25 PM
To: Fornito, Alexander
Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
yes, sulc represents large scale structure of the folding patterns and
preferences deep folds over shallow ones, while curv is a differential
measure (mean curvature) and is much noiser. The sulc alignment comes
first and aligns the major folds, then the curv alignment moves secondary
folds such as the hand area into alignment where they are consistent.
Don't know why you can't create a .annot file. I'm waiting for Kevin to
respond. You could try sending us the subject with the .annot file and we
can take a look, or maybe the .xdebug_tksurfer file has some clue?
cheers,
Bruce
On
Fri, 16 Dec 2005, Fornito, Alexander wrote:
> Hi Bruce,
> Is there a reason why use sulc and curv together would be better than one
> alone?
> Also, any ideas as to why I can't create my annotations?
> Thanks again for your help,
> Alex
>
> Alex Fornito
> M.Psych/PhD (clin. neuro.) candidate
> Melbourne Neuropsychiatry Centre and Department of Psychology
> The University of Melbourne
> [EMAIL PROTECTED]
>
>
>
> -Original Message-
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Fri 16/12/2005 11:34 AM
> To: Fornito, Alexander
> Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer
>
> -n 2 tells it to use 2 feature dimensions (sulc and curv)
> -t tells it to use the color LUT in
> On Fri, 16 Dec
> 2005, Fornito, Alexander wrote:
>
>> Hi,
>> I'm also trying to create my own custom atlas, but can't seem to create an
>> annotation file.
>> I load my files in tksurfer, than click the "Export annotation" option and
>> save the file.
>> When I then try to re-import the annotation, nothing appears, and I get the
>> message:
>>
>> % surfer: WARNING: no labels imported; annotation was empty
>>
>> Any help is much appreciated!
>>
>> PS - Greg, I noticed that you used -n and -t in your command line. What do
>> these flags refer to? I can't seem to get options in the usage.
>>
>> Alex Fornito
>> M.Psych/PhD (clin. neuro.) candidate
>> Melbourne Neuropsychiatry Centre and Department of Psychology
>> The University of Melbourne
>> [EMAIL PROTECTED]
>>
>>
>>
>> -Original Message-
>> From: [EMAIL PROTECTED] on behalf of Greg Harris
>> Sent: Thu 15/12/2005 4:21 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: [Freesurfer] Defining one's own atlas in FreeSurfer
>>
>> By snooping in the log files in scripts/ and considering the instruction
>> to train and then label with commands such as
>>
>> mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg
>> iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs
>>
>> which prepares the way for
>>
>> mris_ca_label ${SUBJECT} rh sphere.reg
>> /opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs
>>
>> it becomes evident that the -autorecon3 step applies the MGH standard
>> parcellation atlas from
>>
>> /opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs
>>
>> and thus, the "standard" atlas is known as
>> "curvature.buckner40.filled.desikan_killiany".
>>
>> When we evaluate our own atlas, we compare hand-traced labels
>> with the labels produced by mris_ca_label.
>>
>> Now my question: Is there a way we could access the training data
>> for "curvature.buckner40.filled.desikan_killiany",
>> so we can compare how mris_ca_label approximates the MGH atlas's
>> gold standard with how it approximates the Iowa atlas's gold standard?
>>
>> We are curious how many subjects went into the standard atlas at
>> mris_ca_train, too. Is there a paper (a pdf?) where this is reported?
>>
>> Greg Harris
>> University of Iowa
>> Psychiatry Brain Imaging Lab
>>
>> ___
>> Freesurfer mailing list
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>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>>
>>
>>
>
>
>
>
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