Try something like this. Run mri_vol2vol with --help to get info about
each of the flags
mri_vol2vol --mov $invol --reg $reg \
--tal --talres $res --talxfm $talxfm --interp $interp \
--no-save-reg --o $outvol
On 4/15/15 10:03 AM, Xiaomin Yue wrote:
Because resampling from 1.5 to 0.25 will generate a huge data.
Xiaomin
------------------------------------------------------------------------
Date: Wed, 15 Apr 2015 09:11:10 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2vol
But why do you need to have the same resolution as the original
functional?
On 4/14/15 10:30 PM, Xiaomin Yue wrote:
yes, that's precisely what I want. the reason is the following.
A subject was scanned multiple times across days with slightly
different slice position for each time. What I need is to extract
a peak response when a stimuli was presented. In order to make
the voxels match from one scan to another, I thought that all
scans have to be in same space, so that the data extracted for a
voxel from different scans match. Could there be a better way to
do this?
Thanks,
Xiaomin
------------------------------------------------------------------------
Date: Tue, 14 Apr 2015 21:08:15 -0400
From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2vol
So you want it to be in a volume with field of view 256mm in all
three dimensions, but the voxel size to be that of the functional
data? It is possible to do, but not easy to set up. Can you say
why you would want to do that?
On 4/14/15 8:20 PM, Xiaomin Yue wrote:
Thanks for your response. The command you gave will generate
a new function data with the spatial resolution of the
anatomical data, which in my case is much higher than those of
functional data. What i want is to generate a new functional
data in the anatomical space, with spatial resolution of the
original function data. Is it possible? I thought that
--fstalres would give me a choice to keep the spatial
resolution of the original function data.
Xiaomin
------------------------------------------------------------------------
Date: Tue, 14 Apr 2015 18:22:00 -0400
From: gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_vol2vol
sorry, I don't understand. fstal would imply that you want
talairach space. If you want to map the functional into the
anatomical space, then
mri_vol2vol --mov res-001.nii --o res-001.t1.space.nii --reg
register.dof6.dat --fstarg
On 4/14/15 11:36 AM, Xiaomin Yue wrote:
Hi Doug,
I like to convert a native functional data into the
anatomical space using mri_vol2vol with --fstal, so that
the resample data has same spatial resolution as the
original function data. However, mri_vol2vol give a
error: --fstal unknown. I also tried using --fstalres as
suggested in the help document, with same error. I am
using fs5.3. the command is: mdi_vol2vol --mov
res-001.nii --fstarg --fstal 1.5 --o res-001.t1.space.nii
--reg register.dof6.dat
Thanks,
Xiaomin
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer
mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing
list Freesurfer@nmr.mgh.harvard.edu
<mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://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
_______________________________________________
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.
