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
