Hi,
I just noticed that when I open my volume file in tksurfer using --overlay
it gives a better volume to surface mapping than when I do mri_vol2surf.
Do you know what .dat file is used implicitly when tksurfer is called with
a volume overlay? It also seems to work well when the subject is fsaverage
and when it is 32k_fs_LR. Thank you.
On Wed, Apr 5, 2017 at 9:54 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> If you have a 3mm MNI152 space, then you should run bbregister to
> fsaverage to create a new register.dat file. Alternatively, you can
> register it directly to 32k_fs_LR and cut out the middle man (make sure to
> use --9 to account for scaling). Please ignore my comment about fsaverage.
> In that case it was actually fine.
>
>
>
> On 4/4/17 9:40 PM, Rita Elena Loiotile wrote:
>
> Hi Doug,
>
> Thanks for the email. It is in 3mm space, so I guess I should reslice.
> Can you please clarify the comment about fsaverage? Does the --mni152reg
> flag not apply to that subject? I'm not sure what you mean about the
> inclusion indicating ambiguity.
>
> Thanks again,
> Rita
>
> On Tue, Apr 4, 2017 at 9:21 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
> wrote:
>
>> The --mni152reg flag is only appropriate if the mov file is in the 2mm
>> mni152 space. The inclusion of fsaverage as the source subject indicates
>> some ambiguity about this
>>
>> On 4/3/17 1:56 PM, Rita Elena Loiotile wrote:
>>
>> Hi,
>>
>> I'm trying to compare analyses that I've done entirely on the surface to
>> analyses I've done in the volume. I'm comparing the analyses by projecting
>> the volume analyses to the surface (HCP's 32k_fs_LR).
>>
>> The commands I'm using are:
>> mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0
>> 1 0.2 --o ${giftiFile}.$hemi.gii;
>> mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii
>> --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi};
>> It seems that the FSL volumes look identical to the surface analysis, when
>> mapped. (Our surface analysis is mainly FSL-based, so this makes sense.)
>> The SPM mapping, however, looks very odd. It isn't just that the
>> intensity differs, but the localization of high intensity areas also
>> varies. It seems that everything is shifted a bit superior and, possibly,
>> posterior to the true location (as seen on the surface analysis).
>> I'm wondering if I'm doing anything obviously wrong in my command usage.
>> The brains were normalized to the MNI ICBM 152 template in SPM. I *think*
>> it's suitable to use the -mni152reg flag in the command.
>>
>> I can attach pictures of the comparison if you'd like.
>>
>> Thanks in advance,
>> Rita
>>
>>
>> _______________________________________________
>> Freesurfer mailing
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> _______________________________________________ Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e
>> du/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
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> 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.
