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: [email protected]
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: [email protected]
> 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
> > >>[email protected]
> > >>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
> > >[email protected]
> > >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
> >[email protected]
> >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
>[email protected]
>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
