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
