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I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo
T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions
and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume
in that orig.mgz is in coronal and in the .mgz format.
I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space
for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz
then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex.
when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use
mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume.
so can someone tell me what is the proper way to cook this goose
Greg
Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1.
On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
External Email - Use Caution
I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo
T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions
and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume
in that orig.mgz is in coronal and in the .mgz format.
I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space
for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz
then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex.
when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use
mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume.
so can someone tell me what is the proper way to cook this goose
Greg
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
thanks Doug, one more thing to make sure I get it correct.
If I have a volume of quantitative MR volumes in the native space of the T1 and I want them to be in registration with the freesurfer space
of this subject I woiuld
mri_convert -it nii -ot mgz vin.nii vout.mgz and then
mri_convert vout.mgz vc.mgz --conform --no_scale --nochange
so that it is in the freesurfer space but not scaled and not changed from float to uchar, correct ?
thanks
greg
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, October 22, 2018 11:58:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] resampling data onto cortical surface
Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1.
On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
External Email - Use CautionI have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo
T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions
and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume
in that orig.mgz is in coronal and in the .mgz format.
I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space
for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz
then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex.
when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use
mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume.
so can someone tell me what is the proper way to cook this goose
Greg
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
I would just do mri_vol2vol --i vin.nii --regheader --targ orig.mgz --o vout.mgz
On 10/22/2018 05:52 PM, GREGORY R KIRK wrote:
External Email - Use Caution
thanks Doug, one more thing to make sure I get it correct.
If I have a volume of quantitative MR volumes in the native space of the T1 and I want them to be in registration with the freesurfer space
of this subject I woiuld
mri_convert -it nii -ot mgz vin.nii vout.mgz and then
mri_convert vout.mgz vc.mgz --conform --no_scale --nochange
so that it is in the freesurfer space but not scaled and not changed from float to uchar, correct ?
thanks
greg
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu *Sent:* Monday, October 22, 2018 11:58:51 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] resampling data onto cortical surface Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1.
On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
External Email - Use Caution
I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo
T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions
and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume
in that orig.mgz is in coronal and in the .mgz format.
I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space
for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz
then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex.
when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use
mri_vol2surf --mov sig.nii \to resample the data onto the cortical
surface
--reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
to resample the epi data onto the cortical surface. however in this
case the R1 data
is already in perfect registration to the T1 other than the
reorientation and reslicing
done to prepare the orig.mgz volume.
so can someone tell me what is the proper way to cook this goose
Greg
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
there is some misunderstanding ? I said to resample onto the cortical surface not
into a volume
you say Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). but this is not mri_vol2surf mri_vol2surf does not have --s as an option.
the volume is already in registration with orig.mgz for the subject so i can't use --reg register.dat
I need to use an identity transformation somehow.
i tried mri_vol2surf --mov vout.mgz --regheader 311140 --hemi lh --o R1.mgz
and that seemed to work, is this correct ?
greg
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, October 22, 2018 11:58:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] resampling data onto cortical surface
Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1.
On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
External Email - Use CautionI have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo
T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions
and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume
in that orig.mgz is in coronal and in the .mgz format.
I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space
for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz
then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex.
when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use
mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume.
so can someone tell me what is the proper way to cook this goose
Greg
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
Hi Greg,
yes, that sounds correct cheers Bruce On Mon, 29 Oct 2018, GREGORY R KIRK wrote:
External Email - Use Caution
there is some misunderstanding ? I said to resample onto the cortical surface not
into a volume
you say Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). but this is not mri_vol2surf mri_vol2surf does not have --s as an option.
the volume is already in registration with orig.mgz for the subject so i can't use --reg register.dat
I need to use an identity transformation somehow.
i tried mri_vol2surf --mov vout.mgz --regheader 311140 --hemi lh --o R1.mgz
and that seemed to work, is this correct ?
greg
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Monday, October 22, 2018 11:58:51 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] resampling data onto cortical surface Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1.
On 10/22/2018 12:55 PM, GREGORY R KIRK wrote:
External Email - Use Caution
I have R1 values that I want to resample onto the cortical surface. The R1 values were computed from a multi echo
T1 sequence that was also used to create the T1 weighted image that was used in recon-all to produce the cortical surface reconstructions
and thus is inherently in registration to the 001.mgz that was used to start recon. There will be a difference in orientation in the volume
in that orig.mgz is in coronal and in the .mgz format.
I was thinking that if I run the first step of recon-all it should give me an volume named orig.mgz that is in registration to the freesurfer space
for the subject ... or else some call to mri_convert reslice_as or whatever is used in the recon-all script to convert 001.mgz to orig.mgz
then my problem is to get a file with the resampling of the R1 onto the cortical surface withR1 values at each vertex.
when i work with fmri data I run bbregister and get the transformation from the epi volume to the freesurfer space and then use
mri_vol2surf --mov sig.nii \to resample the data onto the cortical surface --reg bb.register.dat \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh
to resample the epi data onto the cortical surface. however in this case the R1 data is already in perfect registration to the T1 other than the reorientation and reslicing done to prepare the orig.mgz volume.
so can someone tell me what is the proper way to cook this goose
Greg
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
GREGORY R KIRK -
Greve, Douglas N.,Ph.D.