The -gcam command requires 7 arguments. What would the seventh be? Please let me know. I really appreciate all your help! ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, July 18, 2017 3:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] reducing a matrix
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 \
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