Hi,
I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with “the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.”
So, first, I change the native RAS cooridinate to Tal coordinate with “mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz”
srcsubject = noise0.5_0 srcval = thickness srctype = trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg Loading source data Reading surface file /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data
Then, I obtain the thickness asc file with Tal coordinate using this command “mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”
But, this has an error:
MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm
What’s wrong? Would you tell me how to resolve?
Thank you in advance!
Feng-Xian
you need to tell it what format to write the output in. Try using - --tfmt curv
I would have thought you needed --sfmt curv also. I'm just guessing though. Doug is the expert on this.
cheers, Bruce
On Tue, 4 Aug 2009, Feng-Xian Yan wrote:
Hi,
I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with ?the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.?
So, first, I change the native RAS cooridinate to Tal coordinate with ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz?
srcsubject = noise0.5_0 srcval = thickness srctype = trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg Loading source data Reading surface file /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data
Then, I obtain the thickness asc file with Tal coordinate using this command ?mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc?
But, this has an error:
MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm
What?s wrong? Would you tell me how to resolve?
Thank you in advance!
Feng-Xian
Hi,
I try again with you said. First, I type this command“mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”.
But, the error is the same.” MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm”
What’s wrong? Would you help me to resolve this problem? Because I really want to obtain the thickness ascii file with Tal coordinate. Or, have you another method to obtain the thickness ascii file with Tal coordinate?
Thank you in advance!
Feng-Xian
2009/8/4 Bruce Fischl fischl@nmr.mgh.harvard.edu
you need to tell it what format to write the output in. Try using - --tfmt curv
I would have thought you needed --sfmt curv also. I'm just guessing though. Doug is the expert on this.
cheers, Bruce
On Tue, 4 Aug 2009, Feng-Xian Yan wrote:
Hi,
I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with ?the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.?
So, first, I change the native RAS cooridinate to Tal coordinate with ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz?
srcsubject = noise0.5_0 srcval = thickness srctype = trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg
/usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg Loading source data Reading surface file
/usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data
Then, I obtain the thickness asc file with Tal coordinate using this command ?mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc?
But, this has an error:
MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm
What?s wrong? Would you tell me how to resolve?
Thank you in advance!
Feng-Xian
The output is not a curvature file, it is a surface.
doug
Feng-Xian Yan wrote:
Hi,
I try again with you said. First, I type this command“mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”.
But, the error is the same.” MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm”
What’s wrong? Would you help me to resolve this problem? Because I really want to obtain the thickness ascii file with Tal coordinate. Or, have you another method to obtain the thickness ascii file with Tal coordinate?
Thank you in advance!
Feng-Xian
2009/8/4 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
you need to tell it what format to write the output in. Try using - --tfmt curv I would have thought you needed --sfmt curv also. I'm just guessing though. Doug is the expert on this. cheers, Bruce On Tue, 4 Aug 2009, Feng-Xian Yan wrote: Hi, I had asked two problems before; one is what is coordinates when I type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with ?the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.? So, first, I change the native RAS cooridinate to Tal coordinate with ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz? srcsubject = noise0.5_0 srcval = thickness srctype = trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg Loading source data Reading surface file /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Then, I obtain the thickness asc file with Tal coordinate using this command ?mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc? But, this has an error: MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm What?s wrong? Would you tell me how to resolve? Thank you in advance! Feng-Xian
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I change the input and output from curv to surface, but the error is the same. So, how do I do to resolve it?
Thank you in advance!
Feng-Xian
2009/8/5 Douglas N Greve greve@nmr.mgh.harvard.edu
The output is not a curvature file, it is a surface.
doug
Feng-Xian Yan wrote:
Hi,
I try again with you said. First, I type this command“mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”.
But, the error is the same.” MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm”
What’s wrong? Would you help me to resolve this problem? Because I really want to obtain the thickness ascii file with Tal coordinate. Or, have you another method to obtain the thickness ascii file with Tal coordinate?
Thank you in advance!
Feng-Xian
2009/8/4 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>
you need to tell it what format to write the output in. Try using - --tfmt curv I would have thought you needed --sfmt curv also. I'm just guessing though. Doug is the expert on this. cheers, Bruce On Tue, 4 Aug 2009, Feng-Xian Yan wrote: Hi, I had asked two problems before; one is what is coordinates whenI
type mris_convert -c lh.thickness lh.white lh.thickness.asc, and another is if the asc file doesn't use Tal coordinate, what commands do I type to obtain the thickness asc with Tal coordinate?, and then you responded me with ?the coordinates are native RAS. You can use mri_surf2surf to convert the surface to tal coords with the talairach.xfm.? So, first, I change the native RAS cooridinate to Tal coordinate with ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh --sval-tal-xyz orig --tval-xyz? srcsubject = noise0.5_0 srcval = thickness srctype = trgsubject = noise0.5_0 trgval = noise0.5_0_tal.xfm trgtype = surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 Reading source surface reg/usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg
Loading source data Reading surface file/usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig
Applying MNI305 talairach transform 0.966 0.002 -0.004 0.426; 0.018 0.989 0.041 -19.382; -0.006 0.032 0.962 17.438; 0.000 0.000 0.000 1.000; INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Then, I obtain the thickness asc file with Tal coordinate using this command ?mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc? But, this has an error: MRISreadBinaryCurvature: incompatible vertex number in file ./lh.noise0.5_0_tal.xfm What?s wrong? Would you tell me how to resolve? Thank you in advance! Feng-Xian
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
what is your new command line?
Feng-Xian Yan wrote:
Hi, I change the input and output from curv to surface, but the error is the same. So, how do I do to resolve it?
Thank you in advance!
Feng-Xian
2009/8/5 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
The output is not a curvature file, it is a surface. doug Feng-Xian Yan wrote: > > Hi, > > I try again with you said. First, I type this command“mri_surf2surf > --srcsubject noise0.5_0 --srcsurfval thickness --sfmt curv > --trgsubject noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --tfmt curv > --hemi lh --sval-tal-xyz orig --tval-xyz”, then I type “mris_convert > -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc”. > > But, the error is the same.” MRISreadBinaryCurvature: incompatible > vertex number in file ./lh.noise0.5_0_tal.xfm” > > > What’s wrong? Would you help me to resolve this problem? Because I > really want to obtain the thickness ascii file with Tal coordinate. > Or, have you another method to obtain the thickness ascii file with > Tal coordinate? > > Thank you in advance! > > Feng-Xian > > > > 2009/8/4 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > you need to tell it what format to write the output in. Try using - > --tfmt curv > > I would have thought you needed --sfmt curv also. I'm just > guessing though. Doug is the expert on this. > > cheers, > Bruce > > > > On Tue, 4 Aug 2009, Feng-Xian Yan wrote: > > Hi, > > I had asked two problems before; one is what is coordinates when I > type mris_convert > -c lh.thickness lh.white lh.thickness.asc, and another is if > the asc file > doesn't use Tal coordinate, what commands do I type to obtain > the thickness > asc with Tal coordinate?, and then you responded me with ?the > coordinates > are native RAS. You can use mri_surf2surf to convert the > surface to tal > coords with the talairach.xfm.? > > > > So, first, I change the native RAS cooridinate to Tal > coordinate with > ?mri_surf2surf --srcsubject noise0.5_0 --srcsurfval thickness > --trgsubject > noise0.5_0 --trgsurfval noise0.5_0_tal.xfm --hemi lh > --sval-tal-xyz orig > --tval-xyz? > > srcsubject = noise0.5_0 > srcval = thickness > srctype = > trgsubject = noise0.5_0 > trgval = noise0.5_0_tal.xfm > trgtype = > surfreg = sphere.reg > srchemi = lh > trghemi = lh > frame = 0 > fwhm-in = 0 > fwhm-out = 0 > Reading source surface reg > /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.sphere.reg > Loading source data > Reading surface file > /usr/local/freesurfer/subjects/analysis/noise_analysis//noise_0.5_1_5//noise0.5_0/surf/lh.orig > Applying MNI305 talairach transform > 0.966 0.002 -0.004 0.426; > 0.018 0.989 0.041 -19.382; > -0.006 0.032 0.962 17.438; > 0.000 0.000 0.000 1.000; > INFO: surfcluster: NOT fixing group surface area > INFO: trgsubject = srcsubject > Saving target data > > > > Then, I obtain the thickness asc file with Tal coordinate > using this command > ?mris_convert -c lh.noise0.5_0_tal.xfm lh.white lh.thickness.asc? > > > > But, this has an error: > > MRISreadBinaryCurvature: incompatible vertex number in file > ./lh.noise0.5_0_tal.xfm > > > What?s wrong? Would you tell me how to resolve? > > > > Thank you in advance! > > > > Feng-Xian > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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Bruce Fischl -
Douglas N Greve -
Feng-Xian Yan