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 <[EMAIL PROTECTED]> 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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--
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
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--
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
_______________________________________________
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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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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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--
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
