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:greve@nmr.mgh.harvard.edu] 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:greve@nmr.mgh.harvard.edu] 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 greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu 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 greve@nmr.mgh.harvard.edu 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