[Freesurfer] mapping surface file??
Hi! I was able to use mri_convert to reslice aprc+aseg.mgz to the original dicom coordinates/space. However, I wonder if I need to do the same for all surface files, i.e. mapping vertex coordinate to different one. If I need to do that, which utility should I use? Gen This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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.
[Freesurfer] Normalization of wmparc.stats?
Hi all, Regarding the white matter parcellations in the wmparc.stats file, is it necessary to normalize these values by eTIV or by another factor? Or should this step be skipped as with the cortical thickness measures (?h.aparc, etc.)? Thanks! -Jason ___ 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.
Re: [Freesurfer] {Disarmed} {Disarmed} Re: hippocampus volume
are your subject elderly or do they have AD? The ADNI subjects will hae smaller than normal hippocampal volumes On Fri, 6 Aug 2010, Zhangyuanchao wrote: ok, however, why it is larger than I expected, the volume of one hippocampus from aseg.stats is larger than 4000mm^3, but I noticed that the hippocampus volume for each hemisphere from ADNI data is mostly between 2000mm^3-3000mm^3, I do not know why the difference is so great. Thanks! --- 10ÿÿ8ÿÿ6, Bruce Fischl ÿÿ ÿÿ: Bruce Fischl : Re: [Freesurfer] hippocampus volume ÿÿ: "Zhangyuanchao" : freesurfer@nmr.mgh.harvard.edu : 2010ÿÿ8ÿÿ6ÿÿ,,10:59 the volume of each is given separately. I think what PPJ was saying is that you can sum them to get the total if you want On Fri, 6 Aug 2010, Zhangyuanchao wrote: hi, thanks for your quick reply. I am a little puzzled, if volume of the line corresponding to Left hippocampus is the sum of the left and the right, why the volume corresponding to the right hippocampus is different from the left? How can I obtain the left and right volume of hippocampus respectively? Could you explain how to measure subcortical volume in detail? Do the volume corresponding to other subcortical structures have the same problem as the hippocampus? Is there any detailed description on aseg.stats? Thanks! --- 10ÿÿ8ÿÿ6, Pedro Paulo de Magalhães Oliveira Junior ÿÿ ÿÿ: Pedro Paulo de Magalhães Oliveira Junior : Re: [Freesurfer] hippocampus volume ÿÿ: "Zhangyuanchao" : freesurfer@nmr.mgh.harvard.edu : 2010ÿÿ8ÿÿ6ÿÿ,,10:22 look at the aseg.stats sum left with right - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Fri, Aug 6, 2010 at 11:17, Zhangyuanchao wrote: Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. Thanks a lot ! Yuanchao Zhang ___ 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. ___ 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.
{Disarmed} [Freesurfer] {Disarmed} Re: hippocampus volume
ok, however, why it is larger than I expected, the volume of one hippocampus from aseg.stats is larger than 4000mm^3, but I noticed that the hippocampus volume for each hemisphere from ADNI data is mostly between 2000mm^3-3000mm^3, I do not know why the difference is so great. Thanks! --- 10年8月6日，周五, Bruce Fischl 写道： 发件人: Bruce Fischl 主题: Re: [Freesurfer] hippocampus volume 收件人: "Zhangyuanchao" 抄送: freesurfer@nmr.mgh.harvard.edu 日期: 2010年8月6日,周五,下午10:59 the volume of each is given separately. I think what PPJ was saying is that you can sum them to get the total if you want On Fri, 6 Aug 2010, Zhangyuanchao wrote: > hi, thanks for your quick reply. > > I am a little puzzled, if volume of the line corresponding to Left > hippocampus is the sum of the left and the right, why the volume > corresponding to the right hippocampus is different from the left? How can I > obtain the left and right volume of hippocampus respectively? > > Could you explain how to measure subcortical volume in detail? > Do the volume corresponding to other subcortical structures have the same > problem as the hippocampus? > > Is there any detailed description on aseg.stats? > > Thanks! > > > --- 10ÿÿ8ÿÿ6, Pedro Paulo de Magalhães Oliveira Junior > ÿÿ > > > ÿÿ: Pedro Paulo de Magalhães Oliveira Junior > : Re: [Freesurfer] hippocampus volume > ÿÿ: "Zhangyuanchao" > : freesurfer@nmr.mgh.harvard.edu > : 2010ÿÿ8ÿÿ6ÿÿ,,10:22 > > > look at the aseg.stats > > > sum left with right > - > Pedro Paulo de Magalhães Oliveira Junior > Diretor de Operações > Netfilter & SpeedComm Telecom > -- www.netfilter.com.br > -- For mobile: http://www.netfilter.com.br/mobile > > > > > > On Fri, Aug 6, 2010 at 11:17, Zhangyuanchao wrote: > > > > > > > Hi, expert, > > I would like to measure the volume of hippocampus, is there any way i can > obtain the raw volume of hippocampus for each subject? How can I obtain it? > > In fact, in the folder stats, there is a file named aseg.stat, where I can > find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 > StructName normMean normStdDev normMin normMax normRange", I wonder > whether the corresponding volume of the Left-hippocampus is what I want. I > mean the volume of the left hippocampus. > > > Thanks a lot ! > > Yuanchao Zhang > > ___ > 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. > > > > > > ___ 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.
Re: [Freesurfer] hippocampus volume
the volume of each is given separately. I think what PPJ was saying is that you can sum them to get the total if you want On Fri, 6 Aug 2010, Zhangyuanchao wrote: hi, thanks for your quick reply. I am a little puzzled, if volume of the line corresponding to Left hippocampus is the sum of the left and the right, why the volume corresponding to the right hippocampus is different from the left? How can I obtain the left and right volume of hippocampus respectively? Could you explain how to measure subcortical volume in detail? Do the volume corresponding to other subcortical structures have the same problem as the hippocampus? Is there any detailed description on aseg.stats? Thanks! --- 10ÿÿ8ÿÿ6, Pedro Paulo de Magalhães Oliveira Junior ÿÿ ÿÿ: Pedro Paulo de Magalhães Oliveira Junior : Re: [Freesurfer] hippocampus volume ÿÿ: "Zhangyuanchao" : freesurfer@nmr.mgh.harvard.edu : 2010ÿÿ8ÿÿ6ÿÿ,,10:22 look at the aseg.stats sum left with right - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Fri, Aug 6, 2010 at 11:17, Zhangyuanchao wrote: Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. Thanks a lot ! Yuanchao Zhang ___ 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. ___ 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.
Re: [Freesurfer] hippocampus volume
hi, thanks for your quick reply. I am a little puzzled, if volume of the line corresponding to Left hippocampus is the sum of the left and the right, why the volume corresponding to the right hippocampus is different from the left? How can I obtain the left and right volume of hippocampus respectively? Could you explain how to measure subcortical volume in detail? Do the volume corresponding to other subcortical structures have the same problem as the hippocampus? Is there any detailed description on aseg.stats? Thanks! --- 10年8月6日，周五, Pedro Paulo de Magalhães Oliveira Junior 写道： 发件人: Pedro Paulo de Magalhães Oliveira Junior 主题: Re: [Freesurfer] hippocampus volume 收件人: "Zhangyuanchao" 抄送: freesurfer@nmr.mgh.harvard.edu 日期: 2010年8月6日,周五,下午10:22 look at the aseg.stats sum left with right - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Fri, Aug 6, 2010 at 11:17, Zhangyuanchao wrote: Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. Thanks a lot ! Yuanchao Zhang ___ 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. ___ 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.
Re: [Freesurfer] hippocampus volume
the Volume_mm3 entry is the raw volume in native space. cheers Bruce On Fri, 6 Aug 2010, Zhangyuanchao wrote: Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. > Thanks a lot ! Yuanchao Zhang ___ 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.
Re: [Freesurfer] hippocampus volume
look at the aseg.stats sum left with right - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Fri, Aug 6, 2010 at 11:17, Zhangyuanchao wrote: > Hi, expert, > > I would like to measure the volume of hippocampus, is there any way i can > obtain the raw volume of hippocampus for each subject? How can I obtain it? > > In fact, in the folder stats, there is a file named aseg.stat, where I can > find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 > StructName normMean normStdDev normMin normMax normRange", I wonder > whether the corresponding volume of the Left-hippocampus is what I want. I > mean the volume of the left hippocampus. > > > Thanks a lot ! > > Yuanchao Zhang > > > ___ > 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. > > ___ 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.
[Freesurfer] hippocampus volume
Hi, expert, I would like to measure the volume of hippocampus, is there any way i can obtain the raw volume of hippocampus for each subject? How can I obtain it? In fact, in the folder stats, there is a file named aseg.stat, where I can find a line which contains "ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange", I wonder whether the corresponding volume of the Left-hippocampus is what I want. I mean the volume of the left hippocampus. Thanks a lot ! Yuanchao Zhang ___ 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.
Re: [Freesurfer] eTIV and aseg.stats
no, all volumes are in native space. We also provide the eTIV so you can do whatever you want for correction. cheers Bruce On Fri, 6 Aug 2010, Yolanda Vives wrote: > Hi all, > > I have read about the eTIV and how to obtain it in the paper from Buckner > et al. but I have a question related to the implementation of it in > Freesurfer, just to be sure that I have correctly understood it. Regarding > the volumes of the subcortical structures presented in "aseg.stats", are > these volumes measured in atlas space and therefore, it is not necessary to > normalize them to the TIV or should we apply a normalization method (i.e. > covariance method) using the eTIV (ICV from aseg.stats)? > > Thank you for your time, > Yolanda > ___ 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.
Re: [Freesurfer] Command line to map volume data to surface data
Thank you very much, Doug!
On Fri, Aug 6, 2010 at 9:24 AM, Douglas Greve wrote:
> It's an empirical relationship based on the number of iterations needed to
> get a delta function to look like a gaussian of a certain FWHM. You can
> still specify the number of iterations with --nsmooth. See the --help.
>
> doug
>
> On 8/5/10 5:34 PM, Xinian Zuo wrote:
>>
>> Nice to know the gold standard, now going with the mri_vol2surf :)
>> One more question: As for the overlay surface smoothing option, in
>> tksurfer gui, I can set it by following ' tools -> surface -> smooth
>> overlay -> number of steps', or give an value to option ' --surf-fwhm
>> ' in the command. What is the relationship between the two?
>>
>> xinian
>>
>> On Thu, Aug 5, 2010 at 2:13 PM, Douglas N Greve
>> wrote:
>>>
>>> I'm not entirely sure how tksurfer is sampling from the volume to the
>>> surface. mri_vol2surf is the gold standard, so use that.
>>>
>>> doug
>>>
>>> Xinian Zuo wrote:
Hey Doug,
Following your suggestions, I ran the command below:
mri_vol2surf --mov data.nii.gz --reg
${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o
./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre
--projfrac 0 --interp nearest
but, seems the values in rh.test.vol2surf.mgh is different (little
higher) from what I got from tksurfer gui by saving overlay surface.
any thoughts?
Thanks!
On Thu, Aug 5, 2010 at 11:04 AM, Douglas N Greve
wrote:
> mri_vol2surf is the right command. Have you looked at the help for it?
> You
> can get it by running
>
> mri_vol2surf --help
>
> I think tksurfer uses a projfrac of 0 and nearest neighbor
> interpolation.
> You can load the result directly into tksurfer to see if it looks the
> same.
>
> doug
>
>
> Xinian Zuo wrote:
>
>> Dear surfers,
>>
>> Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
>> surface in the way:
>>
>> tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg
>>
>> , then save surface overlay as a mgh file. My question is, how can I
>> get the identical mgh data by using a command line without launching
>> the tksurfer gui? I found there is a command mri_vol2surf, but not
>> sure about these default settings in tksurfer gui. Really appreciate
>> it if some know and like to give your suggestions.
>>
>>
>>
> --
> 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
>
>
>
>>> --
>>> 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
>>>
>>>
>>
>>
>
>
--
Xinian Zuo, Ph.D
Associate Research Scientist
Institute for Pediatric Neuroscience
NYU Child Study Center
215 Lexington Ave., 14th Floor
New York, NY 10016
Phone: (212) 263 2485
___
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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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.
[Freesurfer] eTIV and aseg.stats
Hi all, I have read about the eTIV and how to obtain it in the paper from Buckner et al. but I have a question related to the implementation of it in Freesurfer, just to be sure that I have correctly understood it. Regarding the volumes of the subcortical structures presented in "aseg.stats", are these volumes measured in atlas space and therefore, it is not necessary to normalize them to the TIV or should we apply a normalization method (i.e. covariance method) using the eTIV (ICV from aseg.stats)? Thank you for your time, Yolanda ___ 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.
Re: [Freesurfer] Command line to map volume data to surface data
It's an empirical relationship based on the number of iterations
needed to get a delta function to look like a gaussian of a certain
FWHM. You can still specify the number of iterations with --nsmooth. See
the --help.
doug
On 8/5/10 5:34 PM, Xinian Zuo wrote:
> Nice to know the gold standard, now going with the mri_vol2surf :)
> One more question: As for the overlay surface smoothing option, in
> tksurfer gui, I can set it by following ' tools -> surface -> smooth
> overlay -> number of steps', or give an value to option ' --surf-fwhm
> ' in the command. What is the relationship between the two?
>
> xinian
>
> On Thu, Aug 5, 2010 at 2:13 PM, Douglas N Greve
> wrote:
>> I'm not entirely sure how tksurfer is sampling from the volume to the
>> surface. mri_vol2surf is the gold standard, so use that.
>>
>> doug
>>
>> Xinian Zuo wrote:
>>> Hey Doug,
>>>
>>> Following your suggestions, I ran the command below:
>>>
>>> mri_vol2surf --mov data.nii.gz --reg
>>> ${FREESURFER_HOME}/average/mni152.register.dat --hemi rh --o
>>> ./rh.test.vol2surf.mgh --trgsubject fsaverage --surf inflated_pre
>>> --projfrac 0 --interp nearest
>>>
>>> but, seems the values in rh.test.vol2surf.mgh is different (little
>>> higher) from what I got from tksurfer gui by saving overlay surface.
>>> any thoughts?
>>>
>>> Thanks!
>>>
>>> On Thu, Aug 5, 2010 at 11:04 AM, Douglas N Greve
>>> wrote:
>>>
mri_vol2surf is the right command. Have you looked at the help for it?
You
can get it by running
mri_vol2surf --help
I think tksurfer uses a projfrac of 0 and nearest neighbor interpolation.
You can load the result directly into tksurfer to see if it looks the
same.
doug
Xinian Zuo wrote:
> Dear surfers,
>
> Hi, I used freeesurfer to visualize my volume from FEAT outputs on the
> surface in the way:
>
> tksurfer fsaverage rh inflated_pre -overlay data.nii.gz -mni152reg
>
> , then save surface overlay as a mgh file. My question is, how can I
> get the identical mgh data by using a command line without launching
> the tksurfer gui? I found there is a command mri_vol2surf, but not
> sure about these default settings in tksurfer gui. Really appreciate
> it if some know and like to give your suggestions.
>
>
>
--
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
>>>
>>>
>>>
>> --
>> 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
>>
>>
>
>
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