try
mri_vol2vol --gcam 005.mc.nii boldregister.dat
$SUBJECTS_DIR/$subject/cvs/final_CVSmorph_tocvs_avg35_inMNI152.m3z
$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0
output.nii.gz
This will sample it down to a 2mm space within the CVS atlas (should
overlap pretty well with the MNI152 2mm space)
On 07/18/2017 03:48 PM, Linda Eva Heidinger wrote:
>
> Dear experts in freesurfer,
>
> I myself am a very beginner in freesurfer but I come with a difficult
> question to answer. As you can see from the script below, I am trying
> to obtain the Bold in CVS35MNI152 template space which hopefully has
> better properties for accuracy and determination of location of a
> voxel for targeting in use with TMS. One can see that bbregister and
> mri_cvs_register were used followed by mri_vol2vol to register the
> Bold and transform it from subject space to the above template.
> Unfortunately, the template space is in freesurfer space (1mm^3,256^3)
> . When we try to run the result that we obtain after transformation in
> our AFNI programs, they couldn't run on our computers because of the
> size of the Bold matrix being too large. I am wondering if it is
> possible for mri_cvs_register to use a template that is of the same
> size as the T1? or really we should just somehow reformulate the
> transformation matrix resulting from mri_cvs_register which I believe
> is: final_CVSmorph_tocvs_avg35_MNI152.m3z to allow for a reduced final
> Bold matrix from mri_vol2vol which will have the same dimensions as
> the subject space which the original Bold had?
>
> I appreciate the time and attention you give this question.
>
> Thanks,
>
> -Linda
>
>
>
> # FreeSurfer commands
>
> nmr-std-env
>
> setenv SUBJECTS_DIR <path to the directory where all MRI data for this
> study reside>
>
> setenv SUBJECT <my subject code>
>
> cd $SUBJECTS_DIR
>
> # First, run FS recon-all on the T1 (MEMPRAGE) anatomical as usual.
>
> recon-all -subjid $SUBJECT -i temp_${SUBJECT}/001.mgz -all -openmp 4
>
> # Second, do co-registration at the individual level between the hires
> anatomical and the bold (functional) image.
> # In the below example the already motion corrected (and otherwise
> preprocessed) bold data for run 005 are in
> # $SUBJECTS_DIR/$SUBJECT/bold/005/005.mc.nii
> # Use boundary-based registration (bbregister) - this by far the most
> accurate tool.
> # Note: This is rigid 6 DOF. It is almost always best to use rigid DOF
> 6 for within-subject registration.
>
> bbregister
> --mov $SUBJECT/bold/005/005.mc.nii
> --frame 0
> --bold
> --s $SUBJECT
> --init-fsl
> --reg boldregister.dat
> --fslmat ${SUBJECT}_anat2bold.mat
>
> # Just in case, let us make FSL type coregistration matrices as well.
>
> convert_xfm
> -omat ${SUBJECT}_bold2anat.mat
> -inverse ${SUBJECT}_anat2bold.mat
>
>
> # Now, we will compute a group-level coregistration from the
> individual brain to a template brain for both volumetric non-linear
> morphing.
> # We will use the standard brain cvs_avg35_inMNI152 as the
> target/template.
>
> mri_cvs_register --mov $SUBJECT --mni --outdir
> $SUBJECT/cvs_CVS35MNI152 --openmp 8
>
> # Finally, we can move the bold image from the individual spac into
> the standard space:
>
> mri_vol2vol \
> --mov $SUBJECT/bold/005/005.mc.nii \
> --targ $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \
> --o Grand_Average/${SUBJECT}_CVS35MNI152_005.mc.nii \
> --m3z $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \
> --noDefM3zPath \
> --interp nearest \
> --reg $SUBJECT/bold/boldregister.dat \
> --no-save-reg \
>
>
>
> _______________________________________________
> Freesurfer mailing list
> [email protected]
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[email protected]
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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