Freesurfer RedHat 9 version
on SUSE Linux 9.3
Cheers
Carolyn
-----Original Message-----
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Mon 04/06/2007 16:36
To: Furlong, Carolyn
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] reg -feat2anat error reg -feat2anat error
what platform are you running on?
Furlong, Carolyn wrote:
> Hi Doug
>
> This is what happened when I ran it with --debug
>
> Kate/Flatmap1> reg-feat2anat --feat
> /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat --subject AMoore --debug
> 'nknown option: `-
> Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
>
> After I replaced the binaries that you suggested in previous emails,
> the other processes would now no longer run...
>
> Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz
> -subjid Colton -autorecon1
> mri_convert: error while loading shared libraries: libstdc++.so.6:
> cannot open shared object file: No such file or directory
>
> Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
> tkregister2: error while loading shared libraries: libtix8.1.8.4.so:
> cannot open shared object file: No such file or directory
>
> I changed mri_convert and tkregister2 back to their original version
> and they worked fine again. When I run the old version of
> reg-feat2anat I still get the original error:
>
> ERROR: could not read
> /disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/example_func.nii.gz as 24
>
> Not sure what is going on?
>
> Best wishes
> Carolyn
>
>
>
>
>
>
> -----Original Message-----
> From: Doug Greve [mailto:[EMAIL PROTECTED]
> Sent: Mon 04/06/2007 15:07
> To: Furlong, Carolyn
> Cc: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] reg -feat2anat error reg -feat2anat error
>
> wow, not sure what's going on there. Can you add --debug to the cmd
> line, caputre the terminal output, and send it to me?
>
> Furlong, Carolyn wrote:
>
> > Hi Doug
> >
> > we tried adding the binaries Doug sent us (MRI_convert, reg2anat and
> > tkregister2, make average subject, make average surface anfd make
> > avergae volume), but now we get a different error:reg-feat2anat --feat
> > ./disc2/Kate/Data_FSL/Pre_AM/AM_preAM_BET.feat/reg/ --subject AMoore
> >
> > 'nknown option: `-
> > Usage: tcsh [ -bcdefilmnqstvVxX ] [ argument ... ].
> >
> > What should I do?
> >
> > Best wishes
> > Carolyn
> >
> > -----Original Message-----
> > From: Doug Greve [mailto:[EMAIL PROTECTED]
> > Sent: Mon 21/05/2007 17:16
> > To: Furlong, Carolyn
> > Cc: Freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] reg -feat2anat error
> >
> > Did you see my email from last week? It looks like the problem was
fixed
> > with new versions of a few programs.
> >
> > doug
> >
> > Furlong, Carolyn wrote:
> >
> > >
> > > Hi Doug
> > >
> > > Please find attached the logfile that you requested, sorry for the
> > > delay, I am only able to work on this one day a week.
> > >
> > > Best wishes
> > > Carolyn
> > >
> > >
> > >
> > >
> > >
> > > Actually, I wanted the log file found in
> > > featdir/reg/freesurfer/reg-feat2anat.log.
> > >
> > > doug
> > >
> > > Furlong, Carolyn wrote:
> > >
> > > > Hi
> > > >
> > > >
> > > > niiRead(): unsupported timing pattern in
> > > Pre_DB/DB_Prelip_BET.feat/example_func.nii.gz
> > > >
> > > > sorry for the delay,
> > > >
> > > > Best wishes
> > > >
> > > > Carolyn
> > > >
> > > > can you send the log file?
> > > >
> > > > Furlong, Carolyn wrote:
> > > >
> > > >> Hi,
> > > >>
> > > >> When I try to register my functional data to anatomical data
using
> > > >>
> > > >> reg-feat2anat --feat feat_directory --subject subject_name
> > > >>
> > > >> I get the following error message
> > > >>
> > > >> ERROR: could not read ///example_func.nii.gz as 24
> > > >>
> > > >> What does this mean? And how can I fix this?
> > > >>
> > > >> Best wishes
> > > >> Carolyn
> > > >>
> > > >>
> > > >>_______________________________________________
> > > >>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
> > > >
> > > >In order to help us help you, please follow the steps in:
> > > >surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > > >
> > > >
> > > >
> > > >_______________________________________________
> > > >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
> > >
> > > In order to help us help you, please follow the steps in:
> > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > >
> > >
> >
>
>------------------------------------------------------------------------
> > >
> > >Mon May 21 10:38:18 BST 2007
> > >/disc2/Kate/Flatmap1
> > >/home/progs/freesurfer/bin//reg-feat2anat
> > >--feat /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat --subject
AMoore
> > >Linux dh108101 2.6.11.4-20a-smp #1 SMP Wed Mar 23 21:52:37 UTC 2005
> > i686 i686 i386 GNU/Linux
> > >mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
> > >mri_convert /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
> > >reading from /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz...
> > >TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> > >i_ras = (-1, 0, 0)
> > >j_ras = (0, 0, -1)
> > >k_ras = (0, 1, 0)
> > >writing to
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz...
> > >example_func ras_good_flag
> > >-------------------------------------------------------
> > >Initializing exf2anat from crude std2anat
> > >tkregister2 --targ /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz --mov
> > /home/progs/fsl/etc/standard/avg152T1_brain.img --reg
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
> > --fslregout
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat
> > --regheader --noedit
> > >target volume /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
> > >movable volume /home/progs/fsl/etc/standard/avg152T1_brain.img
> > >reg file
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
> > >LoadVol 0
> > >$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
> > >Diagnostic Level -1
> > >INFO: loading target /disc2/Kate/Flatmap1/AMoore/mri/brain.mgz
> > >Ttarg: --------------------
> > >-1.000 0.000 0.000 128.000;
> > > 0.000 0.000 1.000 -128.000;
> > > 0.000 -1.000 0.000 128.000;
> > > 0.000 0.000 0.000 1.000;
> > >INFO: loading movable /home/progs/fsl/etc/standard/avg152T1_brain.img
> > >Tmov: --------------------
> > >-2.000 0.000 0.000 91.000;
> > > 0.000 0.000 2.000 -91.000;
> > > 0.000 -2.000 0.000 109.000;
> > > 0.000 0.000 0.000 1.000;
> > >mkheaderreg = 1, float2int = 0
> > >---- Input registration matrix (computed) --------
> > > 1.000 0.000 0.000 0.000;
> > > 0.000 0.000 1.000 30.861;
> > > 0.000 -1.000 0.000 -52.627;
> > > 0.000 0.000 0.000 1.000;
> > >---------------------------------------
> > >---- Input registration matrix --------
> > > 1.000 0.000 0.000 0.000;
> > > 0.000 0.000 1.000 30.861;
> > > 0.000 -1.000 0.000 -52.627;
> > > 0.000 0.000 0.000 1.000;
> > >subject = subject-unknown
> > >RegMat ---------------------------
> > > 1.000 0.000 0.000 0.000;
> > > 0.000 0.000 1.000 30.861;
> > > 0.000 -1.000 0.000 -52.627;
> > > 0.000 0.000 0.000 1.000;
> > >register: file
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2std.register.dat
> > written
> > >FSLOUTPUTTYPE NIFTI_GZ
> > >tkreg2FSL: mov det = -8, ref det = -1
> > >mri_matrix_multiply -fsl -bin -iim
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/example_func2standard.mat
> > -iim
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/std2anat.fsl.mat
> > -om
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
> > >betfunc /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func
> >
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet
> > >Mon May 21 10:38:32 BST 2007
> > >flirt -ref
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/anat.nii.gz
> > -in
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exfbet.nii.gz
> > -init
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.init.fsl.mat
> > -out
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/tmp/exf-in-anat
> > -interp trilinear -omat
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat
> > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz
-90 90
> > >-------------------------------------------------------
> > >tkregister2 --s AMoore --mov
> > /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz
> > --reg
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat
> > --fslreg
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/exf2anat.fsl.mat
> > --noedit --mgz
> > >niiRead(): unsupported timing pattern in
> > /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz
> > >---- FSL registration matrix --------
> > > 0.974 0.200 0.103 12.477;
> > >-0.093 -0.059 0.994 75.631;
> > > 0.205 -0.978 -0.039 180.824;
> > > 0.000 0.000 0.000 1.000;
> > >---------------------------------------
> > >INFO: no target volume specified, assuming FreeSurfer orig volume.
> > >target volume orig
> > >movable volume
> > /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz
> > >reg file
> >
>
/disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/reg/freesurfer/anat2exf.register.dat
> > >LoadVol 0
> > >$Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $
> > >Diagnostic Level -1
> > >ERROR: could not read
> > /disc2/Kate/Data_FSL/Pre_AM/AM_prelip_BET.feat/example_func.nii.gz
as 24
> > >ERROR: tkregister2
> > >
> > >
> >
>
>------------------------------------------------------------------------
> > >
> > >_______________________________________________
> > >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
> >
> > In order to help us help you, please follow the steps in:
> > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> >
>
>------------------------------------------------------------------------
> >
> >_______________________________________________
> >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
> After changing the fi
> After changing the files as you suggested these processes now no
> longer run...
>
> Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz
> -subjid Colton -autorecon1
> mri_convert: error while loading shared libraries: libstdc++.so.6:
> cannot open shared object file: No such file or directory
>
> Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
> tkregister2: error while loading shared libraries: libtix8.1.8.4.so:
> cannot open shared object file: No such file or directory
>
> with the versions that I was already using, I didn't have any problem
> with the reconstruction steps until reg feat2anat les as you suggested
> these processes now no longer run...
>
> Healthy_Volunteers/Colton_Structural> mri_convert -i Colton.nii.gz
> -subjid Colton -autorecon1
> mri_convert: error while loading shared libraries: libstdc++.so.6:
> cannot open shared object file: No such file or directory
>
> Flatmap1/Healthy_Volunteers> tkregister2 --mgz --s Colton -fstal
> tkregister2: error while loading shared libraries: libtix8.1.8.4.so:
> cannot open shared object file: No such file or directory
>
> with the versions that I was already using, I didn't have any problem
> with the reconstruction steps until reg feat2anat
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
