In version 5 there is actually already a flag for this in bbregister. Try running it with --spm-nii.
doug
Tyler Seibert wrote:
Thanks, Doug and Michael--that did the trick! What is the status of this issue for newer versions of FreeSurfer (e.g., 5.0)?
Tyler
On Tue, Mar 29, 2011 at 8:17 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
As Michael says, with spm8 you have to use nifti. When 4.5 was
written, spm8 was not around (or not used much), so this was never
a problem. One way you can get around it is to modify your copy of
spmregister (in $FREESURFER_HOME/bin). There is a line in there
that indicates the format to use
set fmt = img # Format for temporary volumes
Try changing this to:
set fmt = nii # Format for temporary volumes
doug
On 3/29/11 2:15 AM, Tyler Seibert wrote:
Hi Michael,
Thank you for your help! I tried the --spm-nii option you
suggested, but it causes an error:
ERROR: Flag --spm-nii unrecognized.
Also, that option is not listed in the output of bbregister
--help on my system (I am using version 4.5, build-stamp.txt:
freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0). Is the
--spm-nii option only available on some other version?
Tyler
On Mon, Mar 28, 2011 at 8:07 PM, Michael Waskom <mwaskom@mit.edu<mailto:mwaskom@mit.edu>> wrote:
Hi Tyler,
Doug can correct me if I'm wrong, but I believe if you use
the --spm-nii option it will fix this.
Cheers,
Michael
On Mon, Mar 28, 2011 at 1:47 PM, Tyler Seibert<tseibert@ucsd.edu <mailto:tseibert@ucsd.edu>> wrote:
Screenshot2 attached
---------- Forwarded message ----------
From: *Tyler Seibert* <tseibert@ucsd.edu<mailto:tseibert@ucsd.edu>>
Date: Thu, Mar 17, 2011 at 4:02 PM
Subject: bbregister bug? with init-spm option--flips left
and right
To: freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Hello,
I hope this is the correct email list--this is my first
time posting (just subscribed).
I have been using bbregister to calculate a tranformation
matrix between a T2 image (T2brain.nii.gz) and the
subject's T1.mgz for subsequent use with mri_vol2surf. I
have found that the init-fsl option frequently gives very
poor registrations (e.g., registered T2 is rotated 30+
degrees from T1). The init-spm option seemed to be
working great. However, upon close inspection, I became
suspicious this option was actually flipping the T2 so
that the left hemisphere became right and vice versa. I
am using FreeSurfer version 4.5 and have spm8 referenced
in my matlab path.
I used a directory ~/bbreg_test in my home directory for
the test (linux), which consisted simply of running
bbregister with init-fsl and init-spm options. The
attached log file (log.txt) contains the commands I used.
The terminal output from each test was saved in text
files as well, also attached.
I have also attached two screenshots of the tkregister2
output for these tests. In each screenshot the far left
image is the registered T2 using init-spm, and the far
right image is the registered T2 using init-fsl. As the
init-fsl version is clearly wrong, the middle image in
each screenshot is the init-fsl output again, but
manually rotated several degrees to the left to better
emphasize the mirror-image relationship between the
init-spm (far left) and init-fsl (middle and far right)
output images.
Please let me know if there is anything further you need
from me to investigate this or if there is any insight
you can give me as far as how to avoid this error. I
noticed at line 209 of the spm_test.txt log file there is
a message stating that RAS coordinate system is assumed
(see below, where I have copied lines 208-213 for
convenience). This may very well be the problem, as the
T2brain.nii.gz volume is in LAS, according to mri_info
output. However, I do not see where I can override this
RAS assumption.
>> >> >> >> >> >> >> >> >>
/home/tylers/apps/spm8/spm_coreg.m
>> >> >> >> >> INFO: Assuming RAS coordinate system
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> using
/home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/refvol.spmregister.img
as the target image
>> using
/home/tylers/bbreg_test/init-spm/tmp.bbregister.15515/spmregister/movvol.spmregister.img
as the source image
>> >> >> >> >> >> >> >> >> >> >> >> >> >>
Thank you,
-- Tyler Seibert
Dept. of Bioengineering
Medical Scientist Training Program
University of California, San Diego
-- Tyler Seibert
Dept. of Bioengineering
Medical Scientist Training Program
University of California, San Diego
_______________________________________________
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Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the
person to whom it is
addressed. If you believe this e-mail was sent to you in
error and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail
was sent to you in error
but does not contain patient information, please contact
the sender and properly
dispose of the e-mail.
-- Tyler Seibert
Dept. of Bioengineering
Medical Scientist Training Program
University of California, San Diego
_______________________________________________
Freesurfer mailing list
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.
--
Tyler
--
Douglas N. Greve, Ph.D.
MGH-NMR Center Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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