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 greve@nmr.mgh.harvard.edu *To:* "Yue, Xiaomin" yuexm1@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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *To:* "Yue, Xiaomin" yuexm1@yahoo.com mailto:yuexm1@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 greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *To:* "Yue, Xiaomin" yuexm1@yahoo.com mailto:yuexm1@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 <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* "Yue, Xiaomin" <yuexm1@yahoo.com mailto:yuexm1@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 <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* "Yue, Xiaomin" <yuexm1@yahoo.com mailto:yuexm1@yahoo.com
<mailto:yuexm1@yahoo.com mailto:yuexm1@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 <greve@nmr.mgh.harvard.edu
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*To:* martinos-tech@yahoogroups.com
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*Cc:* "Yue, Xiaomin" <yuexm1@yahoo.com
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*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 <greve@nmr.mgh.harvard.edu
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> *To:* martinos-tech@yahoogroups.com
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> *Cc:* "Yue, Xiaomin" <yuexm1@yahoo.com
mailto:yuexm1@yahoo.com <mailto:yuexm1@yahoo.com mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com mailto:yuexm1@yahoo.com <mailto:yuexm1@yahoo.com mailto:yuexm1@yahoo.com>> <mailto:yuexm1@yahoo.com mailto:yuexm1@yahoo.com <mailto:yuexm1@yahoo.com mailto:yuexm1@yahoo.com> <mailto:yuexm1@yahoo.com mailto:yuexm1@yahoo.com <mailto:yuexm1@yahoo.com mailto:yuexm1@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
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