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