I think this may have been a problem with our nifti reader that I fixed a few months ago. I see from the log file that you are using a freesurfer version that is about a year old. So, can you try using the versions of reg-feat2anat, mri_convert, and tkregister2 that I put in tp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve? The last two are binaries compiled for Linux.
doug
uzay emir wrote:
Hi,
Actually I have the same problem. Here is my log file,
Regards
Uzay
Doug Greve greve@nmr.mgh.harvard.edu wrote:
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
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In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Thu May 17 10:05:02 EEST 2007 /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig /home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat --feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz reading from /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz... TR=11.00, TE=4.92, TI=4.92, flip angle=15.00 i_ras = (-1, 2.56273e-11, 6.83856e-10) j_ras = (-1.17877e-09, -2.94451e-16, -1) k_ras = (3.0538e-12, 1, -9.84868e-13) writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag
Initializing exf2anat from crude std2anat tkregister2 --targ /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz --mov /usr/local/fsl/etc/standard/avg152T1_brain.img --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit target volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brain.mgz movable volume /usr/local/fsl/etc/standard/avg152T1_brain.img reg file Akkaya_Zuhre_1_9++.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 /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/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 /usr/local/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 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000;
---- Input registration matrix -------- 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --------------------------- 1.000 0.000 0.000 1.414; -0.000 -0.000 1.000 -30.612; 0.000 -1.000 -0.000 -44.496; 0.000 0.000 0.000 1.000; register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat written FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1 mri_matrix_multiply -fsl -bin -iim Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -iim Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat -om Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.init.fsl.mat betfunc Akkaya_Zuhre_1_9++.feat//example_func Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet Thu May 17 10:05:15 EEST 2007 flirt -ref Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz -in Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet.nii.gz -init Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.init.fsl.mat -out Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90
tkregister2 --s akkaya --mov Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat --fslreg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat --noedit --mgz niiRead(): unsupported timing pattern in Akkaya_Zuhre_1_9++.feat//example_func.nii.gz ---- FSL registration matrix -------- 0.048 -0.934 -0.353 222.836; -0.334 0.318 -0.887 157.631; 0.941 0.161 -0.297 19.434; 0.000 0.000 0.000 1.000;
INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz reg file Akkaya_Zuhre_1_9++.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 Akkaya_Zuhre_1_9++.feat//example_func.nii.gz as 24 ERROR: tkregister2
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