Hello Dr. Greve, I ran the program below and got the following errors. Can you help??? I really would appreciate it. -Linda
Loading source LTA boldregister003.dat INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Loading GCAM Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /pkg64/brainmap/freesurfer-v6.0.0_x86_64/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Chaning Source LTA type to vox2vox The initial command that was run: mri_vol2vol --gcam run_003regraijNIFTI.nii boldregister003.dat Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 0 subject003matrix.nii ________________________________________ From: [email protected] <[email protected]> on behalf of Douglas N Greve <[email protected]> Sent: Tuesday, July 25, 2017 2:27 PM To: [email protected] Subject: Re: [Freesurfer] reducing a matrix Add another 0 after the register.lta On 07/25/2017 02:46 PM, Linda Eva Heidinger wrote: > The -gcam command requires 7 arguments. What would the seventh be? Please let > me know. I really appreciate all your help! > ________________________________________ > From: [email protected] > <[email protected]> on behalf of Douglas N Greve > <[email protected]> > Sent: Tuesday, July 18, 2017 3:31 PM > To: [email protected] > 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 \ >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIGaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=F4vpLZROq5u7kq8YbZVopqrYx7Jslz07HbbISgZfszY&s=1lVk1OkzVqlOUNNoWqTFzLK4e9pW4aOdftXwolSPlss&e= > -- > Douglas N. 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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 > [email protected] > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICJg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=GKqetTp2xTIvLtRg3X4KoRv99hJX9SmTpU_XT1IjyuA&m=BwvuPcL_GwlXte75Q7JwV6TVJGsYDUBNP4DpXf1qvGM&s=FCQZVwn1U_UHZLqMAWOqVofw-VdFBWCc-jkyCxfqeRk&e= > > -- Douglas N. 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