Great, thanks! On Mon, Apr 11, 2011 at 6:59 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote:
> 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 >> <gr...@nmr.mgh.harvard.edu<mailto: >> gr...@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 <mwas...@mit.edu >>> <mailto:mwas...@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 >>> <tseib...@ucsd.edu <mailto:tseib...@ucsd.edu>> wrote: >>> >>> Screenshot2 attached >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Tyler Seibert* <tseib...@ucsd.edu >>> <mailto:tseib...@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 >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > > gr...@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 > > -- Tyler Seibert Dept. of Bioengineering Medical Scientist Training Program University of California, San Diego
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