Screenshot2 attached
---------- Forwarded message ---------- From: Tyler Seibert 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
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,
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 wrote:
Screenshot2 attached
---------- Forwarded message ---------- From: Tyler Seibert 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
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
Freesurfer mailing list 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.
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 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 wrote:
Screenshot2 attached
---------- Forwarded message ---------- From: Tyler Seibert 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
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
Freesurfer mailing list 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.
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> 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 _______________________________________________ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 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.eduwrote:
Screenshot2 attached
---------- Forwarded message ---------- From: *Tyler Seibert* 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
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
Freesurfer mailing list 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list 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.
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> 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 _______________________________________________ Freesurfer mailing list Freesurfer@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@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@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
Great, thanks!
On Mon, Apr 11, 2011 at 6:59 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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.edumailto: 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> 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 _______________________________________________ Freesurfer mailing list Freesurfer@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
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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
greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Michael Waskom -
Tyler Seibert