Not sure. In principle no, but it might cause the brain to be non-centered or out of the field of view. I would just run tkregister2 --fstal --s subject and get it more-or-less right (or at least check that it is not out of the field of view). doug
On 06/12/2012 09:32 AM, Yue, Xiaomin wrote: > Hi Doug, > > Sorry for the slow response. The isxconcat went through without > errors. I apology for confusion my question caused. My original > question should this. After reconstructing a monkey brain with a lot > of manual intervention, I generated a talairach.xfm manually from an > identity matrix. my question was whether this 'arbitrary' > talairach.xfm would cause any fundamental problem in > the functional data analysis. > > Thanks, > Xiaomin > > ------------------------------------------------------------------------ > *From:* Douglas Greve <gr...@nmr.mgh.harvard.edu> > *To:* "Yue, Xiaomin" <yue...@yahoo.com> > *Sent:* Friday, June 8, 2012 10:29 PM > *Subject:* Re: [martinos-tech] isxconcat-sess problem > > so, there was not an error in that output. I'm confused. Can you try > running isxconcat again? > > On 6/8/12 7:03 PM, Yue, Xiaomin wrote: >> It can write to the location. I just gave a wrong directory. >> Attached is the output. >> >> Xiaomin >> >> ------------------------------------------------------------------------ >> *From:* Douglas Greve <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu> >> *To:* "Yue, Xiaomin" <yue...@yahoo.com> <mailto:yue...@yahoo.com> >> *Sent:* Friday, June 8, 2012 6:51 PM >> *Subject:* Re: [martinos-tech] isxconcat-sess problem >> >> ok, that's a different error. Why can't it write to that location? >> >> On 6/8/12 6:28 PM, Yue, Xiaomin wrote: >>> Here is the terminal output: >>> >>> dromos/misc/data41/yuex/monkeyfMRI/mky_curvature/subjs% (stable450) >>> >mri_vol2vol --mov >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature/mask.nii >>> >>> --reg >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> >>> --o >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvat >>> >>> re-mask-tal.mgh --no-save-reg --interp nearest --tal --talres 2 >>> movvol >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature/mask.nii >>> outvol >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature-mask-tal.mgh >>> regfile >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> invert 0 >>> tal 1 >>> talres 2 >>> regheader 0 >>> noresample 0 >>> interp nearest (0) >>> precision float (3) >>> Gdiag_no -1 >>> Compute R for talairach space >>> >>> Final tkRAS-to-tkRAS Matrix is: >>> 0.499 -0.027 0.001 -3.313; >>> 0.018 0.335 0.371 2.944; >>> -0.021 -0.370 0.336 16.638; >>> 0.000 0.000 0.000 1.000; >>> >>> >>> Vox2Vox Matrix is: >>> 0.666 0.001 0.036 7.194; >>> -0.027 0.448 0.493 -32.996; >>> -0.024 -0.494 0.447 14.848; >>> 0.000 0.000 0.000 1.000; >>> >>> Resampling >>> mghWrite(butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature-mask-tal.mgh, >>> >>> -1): could not open file >>> INFO: writing registration matrix to >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature-mask-tal.mgh.reg >>> >>> mri_vol2vol done >>> >>> >>> Xiaomin >>> ------------------------------------------------------------------------ >>> *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu> >>> *To:* "Yue, Xiaomin" <yue...@yahoo.com> <mailto:yue...@yahoo.com> >>> *Sent:* Friday, June 8, 2012 6:15 PM >>> *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> >>> I can't replicate. Can you run this command and send me the terminal >>> output? >>> >>> mri_vol2vol --mov >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> >>> --reg >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> >>> --o >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature--mask-tal.mgh >>> >>> --no-save-reg --interp nearest --tal --talres 2 >>> >>> On 06/08/2012 06:05 PM, Yue, Xiaomin wrote: >>> > The anatomical data is here: >>> /cluster/tootell/xiaomin/3/NIH_projects/butters >>> > The functional data is here: >>> /cluster/tootell/xiaomin//3/NIH_projectos/mky_curvature/butters022712 >>> > >>> > Thanks, >>> > Xiaomin >>> > >>> > >>> ------------------------------------------------------------------------ >>> > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> > *To:* "Yue, Xiaomin" <yue...@yahoo.com <mailto:yue...@yahoo.com>> >>> > *Sent:* Friday, June 8, 2012 5:59 PM >>> > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > >>> > Can you tar up the anatomical analysis? Not the functional >>> analysis, just the anatomical. You can put it on the mgh network or >>> upload it to our file drop. >>> > doug >>> > >>> > On 06/08/2012 05:49 PM, Yue, Xiaomin wrote: >>> > > attached. If more convenient, I can upload the whole analysis >>> directory to space under my MGH account. >>> > > >>> > > Xiaomin >>> > > >>> > > >>> ------------------------------------------------------------------------ >>> > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>>> >>> > > *To:* "Yue, Xiaomin" <yue...@yahoo.com <mailto:yue...@yahoo.com> >>> <mailto:yue...@yahoo.com <mailto:yue...@yahoo.com>>> >>> > > *Sent:* Friday, June 8, 2012 5:44 PM >>> > > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > > >>> > > Can you send me the result of >>> > > mri_info >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> >>> >>> > > >>> > > On 06/08/2012 05:37 PM, Yue, Xiaomin wrote: >>> > > > attached are the files. >>> > > > >>> > > > Thanks, >>> > > > Xiaomin >>> > > > >>> > > > >>> ------------------------------------------------------------------------ >>> > > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>> >>> > > > *To:* martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com>> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com>>> >>> > > > *Cc:* "Yue, Xiaomin" <yue...@yahoo.com >>> <mailto:yue...@yahoo.com> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com>> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com>>>> >>> > > > *Sent:* Friday, June 8, 2012 5:32 PM >>> > > > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > > > >>> > > > Can you send the talairach.xfm and the >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> >>> ? >>> > > > >>> > > > On 06/08/2012 05:18 PM, Yue, Xiaomin wrote: >>> > > > > I am sorry for the long delay to your response. What I did >>> try was to use a identity matrix for the talairach.xfm. >>> > > > > >>> > > > > Transform_Type = Linearl >>> > > > > Linear_Transform = >>> > > > > 1.0 0.0 0.0 0.0 >>> > > > > 0.0 1.0 0.0 0.0 >>> > > > > 0.0 0.0 1.0 0.0 >>> > > > > >>> > > > > Is it right? >>> > > > > >>> > > > > Thanks >>> > > > > Xiaomin >>> > > > > >>> > > > > >>> ------------------------------------------------------------------------ >>> > > > > *From:* Douglas Greve <gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>>> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>>> >>> > > > > *To:* martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com>> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com>>> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com>> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com> >>> <mailto:martinos-t...@yahoogroups.com >>> <mailto:martinos-t...@yahoogroups.com>>>> >>> > > > > *Cc:* "Yue, Xiaomin" <yue...@yahoo.com >>> <mailto:yue...@yahoo.com> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com>> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com>>> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com>> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com> <mailto:yue...@yahoo.com >>> <mailto:yue...@yahoo.com>>>>> >>> > > > > *Sent:* Friday, March 16, 2012 1:53 PM >>> > > > > *Subject:* Re: [martinos-tech] isxconcat-sess problem >>> > > > > >>> > > > > >>> > > > > >>> > > > > Check the talairach.xfm for those subjects. Even if it is >>> monkey, it needs to be something that will bring the brains into >>> alignment. >>> > > > > doug >>> > > > > >>> > > > > On 3/16/12 12:43 PM, Yue, Xiaomin wrote: >>> > > > >> Hi All, >>> > > > >> >>> > > > >> I am runing a isxconcat-sess on two session of an animal >>> scans. I got the following error. I checked mask.nii and >>> register.dat, both are there and looks like right. Any ideas? >>> > > > >> >>> > > > >> Thanks >>> > > > >> Xiaomin >>> > > > >> >>> > > > >> >>> ########################################################################################################################################## >>> > > > >> isxconcat-sess log file >>> > > > >> $Id: isxconcat-sess,v 1.25.2.7 2009/04/17 21:12:18 greve Exp $ >>> > > > >> Fri Mar 16 12:38:00 EDT 2012 >>> > > > >> Linux dromos 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:45:44 >>> EST 2012 x86_64 x86_64 x86_64 GNU/Linux >>> > > > >> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs >>> > > > >> /opt/freesurfer-450/fsfast/bin/isxconcat-sess >>> > > > >> -sf subjgrp -d . -a mkycurvature -all-contrasts -o >>> butteravg022712_031212 >>> > > > >> uid=34912(yuex) gid=11(braincop) groups=11(braincop) >>> > > > >> cd /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs >>> > > > >> isxconcat0-sess -reg register.dat -a mkycurvature -m mask >>> -o butteravg022712_031212/mkycurvature/tal.masks.nii -interp nearest >>> -fsd bold -talres 2 -sf subjgrp -d . >>> > > > >> ------------------------------------ >>> > > > >> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs >>> > > > >> mri_vol2vol --mov >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> >>> --reg >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> >>> --o >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature--mask-tal.mgh >>> >>> --no-save-reg --interp nearest --tal --talres 2 >>> > > > >> MatrixMultiply: m2 is null! >>> > > > >> >>> > > > >> movvol >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/mkycurvature//mask.nii >>> > > > >> outvol >>> butteravg022712_031212/mkycurvature/tmp-isxconcat0.21717-sess/butters022712-mkycurvature--mask-tal.mgh >>> > > > >> regfile >>> /misc/data41/yuex/monkeyfMRI/mky_curvature/subjs/butters022712/bold/register.dat >>> > > > >> invert 0 >>> > > > >> tal 1 >>> > > > >> talres 2 >>> > > > >> regheader 0 >>> > > > >> noresample 0 >>> > > > >> interp nearest (0) >>> > > > >> precision float (3) >>> > > > >> Gdiag_no -1 >>> > > > >> Compute R for talairach space >>> > > > >> No such file or directory >>> > > > >> >>> > > > > >>> > > > > >>> > > > > The information in this e-mail is intended only for the >>> person to whom it is >>> > > > > addressed. 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Greve, Ph.D. >>> > > MGH-NMR Center >>> > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu >>> <mailto:gr...@nmr.mgh.harvard.edu>> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > > >>> > > >>> > > >>> > >>> > -- Douglas N. Greve, Ph.D. >>> > MGH-NMR Center >>> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>> <mailto:gr...@nmr.mgh.harvard.edu <mailto: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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> > >>> > >>> >>> -- Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu <mailto: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 >>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> >>> >>> >> >> > > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
