I would like to take 3 different scan volumes of the same subject and compare their parcellation values. I want to make sure that motion between the scans will not change the parcellation values. Is mri_motion_correct the proper tool to use for aligning the scans before proceeding with the processing stream?
-Keyma
Hi Keyma,
I use fsl_rigid_register for this kind of thing, which is a wrapper Doug wrote to use FLIRT. It works quite well, and writes out a transform (and transforms the volume if you want).
Bruce
On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote:
I would like to take 3 different scan volumes of the same subject and compare their parcellation values. I want to make sure that motion between the scans will not change the parcellation values. Is mri_motion_correct the proper tool to use for aligning the scans before proceeding with the processing stream?
-Keyma _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Would you recommend using this command on the orig volume before I start the rest of the processing stream? Or can it be used further down the line?
-Keyma
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
YOU> Hi Keyma, YOU> YOU> I use fsl_rigid_register for this kind of thing, which is a wrapper Doug YOU> wrote to use FLIRT. It works quite well, and writes out a transform (and YOU> transforms the volume if you want). YOU> YOU> Bruce YOU> YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> YOU> > I would like to take 3 different scan volumes of the same subject and YOU> compare YOU> > their parcellation values. I want to make sure that motion between the YOU> scans YOU> > will not change the parcellation values. Is mri_motion_correct the YOU> proper tool YOU> > to use for aligning the scans before proceeding with the processing YOU> stream? YOU> > YOU> > -Keyma YOU> > _______________________________________________ YOU> > Freesurfer mailing list YOU> > Freesurfer@nmr.mgh.harvard.edu YOU> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer YOU> > YOU>
Hi Keyma,
I think all you care about is the transform, correct? In which case you can do it anytime.
Bruce
On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote:
Would you recommend using this command on the orig volume before I start the rest of the processing stream? Or can it be used further down the line?
-Keyma
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
YOU> Hi Keyma, YOU> YOU> I use fsl_rigid_register for this kind of thing, which is a wrapper Doug YOU> wrote to use FLIRT. It works quite well, and writes out a transform (and YOU> transforms the volume if you want). YOU> YOU> Bruce YOU> YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> YOU> > I would like to take 3 different scan volumes of the same subject and YOU> compare YOU> > their parcellation values. I want to make sure that motion between the YOU> scans YOU> > will not change the parcellation values. Is mri_motion_correct the YOU> proper tool YOU> > to use for aligning the scans before proceeding with the processing YOU> stream? YOU> > YOU> > -Keyma YOU> > _______________________________________________ YOU> > Freesurfer mailing list YOU> > Freesurfer@nmr.mgh.harvard.edu YOU> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer YOU> > YOU>
I ran the fsl_rigid_register command and I received the following error. I am not sure what flirt it is looking for.
Here is the command I used also: fsl_rigid_register -r TFL_2107_2test/mri/T1/ -i TFL_2107_8test/mri/T1/ -o TFL_2107_8test/mri/resample/
/home/freesurfer/freesurfer-20040218/freesurfer/subjects flirt -in /tmp/fsl_rigid_register.3734/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.3734/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.3734/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.3734/initxfm.fslmat -omat /tmp/fsl_rigid_register.3734/outvol.fsl_rigid_register.fslmat flirt: Command not found. ERROR: running flirt
-Keyma
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
YOU> Hi Keyma, YOU> YOU> I think all you care about is the transform, correct? In which case you YOU> can do it anytime. YOU> YOU> Bruce YOU> YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> YOU> > Would you recommend using this command on the orig volume before I start YOU> the YOU> > rest of the processing stream? Or can it be used further down the line? YOU> > YOU> > -Keyma YOU> > YOU> > Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: YOU> > YOU> > YOU> Hi Keyma, YOU> > YOU> YOU> > YOU> I use fsl_rigid_register for this kind of thing, which is a wrapper YOU> Doug YOU> > YOU> wrote to use FLIRT. It works quite well, and writes out a transform YOU> (and YOU> > YOU> transforms the volume if you want). YOU> > YOU> YOU> > YOU> Bruce YOU> > YOU> YOU> > YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> > YOU> YOU> > YOU> > I would like to take 3 different scan volumes of the same subject YOU> and YOU> > YOU> compare YOU> > YOU> > their parcellation values. I want to make sure that motion YOU> between the YOU> > YOU> scans YOU> > YOU> > will not change the parcellation values. Is mri_motion_correct YOU> the YOU> > YOU> proper tool YOU> > YOU> > to use for aligning the scans before proceeding with the YOU> processing YOU> > YOU> stream? YOU> > YOU> > YOU> > YOU> > -Keyma YOU> > YOU> > _______________________________________________ YOU> > YOU> > Freesurfer mailing list YOU> > YOU> > Freesurfer@nmr.mgh.harvard.edu YOU> > YOU> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer YOU> > YOU> > YOU> > YOU> YOU> > YOU> > YOU> > YOU>
you have to install the fsl stuff from Oxford.
Bruce
On Thu, 12 Aug 2004, Chekema Nayasha Prince wrote:
I ran the fsl_rigid_register command and I received the following error. I am not sure what flirt it is looking for.
Here is the command I used also: fsl_rigid_register -r TFL_2107_2test/mri/T1/ -i TFL_2107_8test/mri/T1/ -o TFL_2107_8test/mri/resample/
/home/freesurfer/freesurfer-20040218/freesurfer/subjects flirt -in /tmp/fsl_rigid_register.3734/invol.fsl_rigid_register.hdr -out /tmp/fsl_rigid_register.3734/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /tmp/fsl_rigid_register.3734/refvol.fsl_rigid_register.hdr -init /tmp/fsl_rigid_register.3734/initxfm.fslmat -omat /tmp/fsl_rigid_register.3734/outvol.fsl_rigid_register.fslmat flirt: Command not found. ERROR: running flirt
-Keyma
Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:
YOU> Hi Keyma, YOU> YOU> I think all you care about is the transform, correct? In which case you YOU> can do it anytime. YOU> YOU> Bruce YOU> YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> YOU> > Would you recommend using this command on the orig volume before I start YOU> the YOU> > rest of the processing stream? Or can it be used further down the line? YOU> > YOU> > -Keyma YOU> > YOU> > Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu: YOU> > YOU> > YOU> Hi Keyma, YOU> > YOU> YOU> > YOU> I use fsl_rigid_register for this kind of thing, which is a wrapper YOU> Doug YOU> > YOU> wrote to use FLIRT. It works quite well, and writes out a transform YOU> (and YOU> > YOU> transforms the volume if you want). YOU> > YOU> YOU> > YOU> Bruce YOU> > YOU> YOU> > YOU> On Wed, 11 Aug 2004, Chekema Nayasha Prince wrote: YOU> > YOU> YOU> > YOU> > I would like to take 3 different scan volumes of the same subject YOU> and YOU> > YOU> compare YOU> > YOU> > their parcellation values. I want to make sure that motion YOU> between the YOU> > YOU> scans YOU> > YOU> > will not change the parcellation values. Is mri_motion_correct YOU> the YOU> > YOU> proper tool YOU> > YOU> > to use for aligning the scans before proceeding with the YOU> processing YOU> > YOU> stream? YOU> > YOU> > YOU> > YOU> > -Keyma YOU> > YOU> > _______________________________________________ YOU> > YOU> > Freesurfer mailing list YOU> > YOU> > Freesurfer@nmr.mgh.harvard.edu YOU> > YOU> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer YOU> > YOU> > YOU> > YOU> YOU> > YOU> > YOU> > YOU>
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chekema Nayasha Prince