Hello Lilla, thank you the clarifications. I managed to get mri_vol2vol running, but I have one remaining obstacle - when I use the CVS template as target volume, the EPIs get resampled to 1mm isotropic voxels. I need to get a 3x3x3mm resolution. I tried to use mri_convert -vs 3 3 3 norm.mgz norm333.mgz on the template and then use norm333.mgz in the mri_vol2vol commandline (mri_vol2vol --targ /home/marcel/freesurfer/subjects/cvs_avg35_inMNI152/mri/norm333.mgz --m3z final_CVSmorph_tocvs_avg35_inMNI152.m3z --noDefM3zPath --reg register.dof6.dat --mov onevol.nii.gz --o fmri_cvs333.nii.gz), but the fmri_cvs333.nii.gz volume produced by this command is empty. One option is to resample the normalized EPI in CVS template space, but interpolating the image twice is not a very good idea... Can you think of any solutions to this issue?
Best regards, Marcel 2013/8/8 Lilla Zollei <lzol...@nmr.mgh.harvard.edu> > > Hi Marcel, > > First, you will find a lot of details about the usage of mri_cvs_register > if you use the --help flag in the terminal. > > See detailed responses to your questions below: > > > I'm trying to use mri_cvs_register (whose registration accuracy is, by >> the way, jaw-dropping) for EPI images. However, the descriptions which I've >> found on the web do not make the task easier. >> My goal is to get functional images in cvs_avg35_inMNI152 space, >> resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm >> taking following steps: >> >> 1. recon-all on anatomical data (obvious) >> >> 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov >> subject) >> >> I do not understand what the files stored in cvs folder are needed for. >> As far as I understand the normalization process, I need a file which >> stores the subject -> template warp. Which file is >> it? Do I need to use the --nocleanup option in mri_cvs_register to get >> the aforementioned file? >> > > The file ddescritions are detailed if you run mri_cvs_register --help. For > your purposes you do not need to use the --nocleanup option. The final > ransformation that you will need is called final*norm.m3z > > In the wiki page a following command line is recommended to reconstruct >> this warp when the --nocleanup options was not used: >> >> createMorph --out fullCVSmorph.tm3d --template template.mgz \ >> * --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph >> el_reg_toTEMPLATE.tm3d >> >> However, there is no single *.tm3d file in my cvs directory... Here are >> the files that are present: >> >> el_reg_tocvs_avg35_inMNI152.**affine.mgz >> el_reg_tocvs_avg35_inMNI152_**aseg.mgz >> el_reg_tocvs_avg35_inMNI152.**mgz >> final_CVSmorphed_tocvs_avg35_**inMNI152_aseg.mgz >> final_CVSmorphed_tocvs_avg35_**inMNI152_norm.mgz >> final_CVSmorph_tocvs_avg35_**inMNI152.m3z >> lh.dbg_surf.pial >> lh.dbg_surf.white >> lh.resample.aparc.annot >> lh.resample.pial >> lh.resample.white >> nlalign-afteraseg-norm.mgz >> nlalign-aseg.mgz >> rh.dbg_surf.pial >> rh.dbg_surf.white >> rh.resample.aparc.annot >> rh.resample.pial >> rh.resample.white >> step1_CVSmorphed_tocvs_avg35_**inMNI152_aseg.mgz >> step1_CVSmorphed_tocvs_avg35_**inMNI152_norm.mgz >> summary.AC1004_to_cvs_avg35_**inMNI152.mri_cvs_register.**1308031447.log >> transform.txt >> > > These comments are wrt to an older version of the code. We do not use the > tm3d format any more. I will update the wiki. > > > In my particular case, which images should be entered as arguments to >> --template and --subject ? >> > > "template" is always your target (atlas space where you are registering > TO) and subject is the moving image that you are registering. > > > 3. standard EPI pre-processing, which results in motion-correction >> parameters and realigned images >> >> 4. coregistration of EPI to anatomical data with BBR. The transformation >> is stored as register.dof6.dat, which contain the mapping EPI -> anatomical >> >> I understand that the next step is combining the registrations from step >> (2) and (4) in order to get EPI images in cvs_MNI space. This can be >> accomplished with mri_vol2vol. However, I do not >> understand which files should be used for this registration. >> > > > You will need the m3z file from cvs and the rigid registration that you > get from BBR. > > Lilla > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > 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. >
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