[Freesurfer] question for preprocessing
External Email - Use Caution Dear expert， Thank you for reading! I want to do these four pre-processing steps: 1. Re-sampling each MR image to 256*256*256; 2. Using the N3 algorithm for intensity inhomogeneity correction; 3. Skull stripping; 4. Removing the cerebellum. Does " *recon-all"* do all the above 4 steps automatically? If so, which file is just finished with these four steps? If not, how can I do these steps? Your help is greatly appreciated. Best, ping ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] question for preprocessing
External Email - Use Caution Thank you for your reply. I also want to know which file has just finished with 1-3 steps? Is it nu.mgz? Or nu.mgz? *T1.mgz* aseg.presurf.mgz > aparc+aseg.mgz brain.finalsurfs.mgz* > norm.mgz > * aparc.DKTatlas+aseg.mgz *brain.mgz * > *nu.mgz*aparc.a2009s+aseg.mgz > brainmask.auto.mgz aseg.auto.mgzbrainmask.mgz > *orig.mgz * ctrl_pts.mgz >*orig_nu.mgz * wm.asegedit.mgzaseg.auto_noCCseg.mgz filled.mgz > rawavg.mgz wm.mgz aseg.mgzlh.ribbon.mgz >rh.ribbon.mgz wm.seg.mgz > aseg.presurf.hypos.mgz ribbon.mgz wmparc.mgz Best, ping Greve, Douglas N.,Ph.D. 于2019年6月23日周日 下午9:35写道： > It does 1-3. It also labels cerebellum which you could then use to perform > #4 > > On 6/23/2019 7:03 AM, ping cao wrote: > > External Email - Use Caution > Dear expert， > > Thank you for reading! > > I want to do these four pre-processing steps: > > 1. Re-sampling each MR image to 256*256*256; > 2. Using the N3 algorithm for intensity inhomogeneity correction; > > 3. Skull stripping; > > 4. Removing the cerebellum. > > Does " *recon-all"* do all the above 4 steps automatically? If so, which > file is just finished with these four steps? If not, how can I do these > steps? > > Your help is greatly appreciated. > > > Best, > ping > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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
[Freesurfer] question for files recon-all generated
External Email - Use Caution Dear expert, I want to know if the *norm.mgz* is already linearly registered？ And is the *T1.mgz *not linearly registered? They are all generated from *recon-all. * Is there any file non-linearly registered? Best wishes, ping ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] how to get the displacement from template to the linearly registered image
External Email - Use Caution Dear expert， I saw a paper mentioned this ： By using the *deformation field* from nonlinear registration, we can > build the correspondence between voxels in the template and each > linearly-aligned image. For instance, for each voxel (x, y, z) in the > template image, we can find its corresponding voxel (x + dx, y + dy, z + > dz) in each linearly-aligned image, where (dx, dy, dz) is the > *displacement* from the template image to the linearly-aligned image > defined by the deformation field. So, I want to get the deformation field from the template to the linearly registered image(flirt_T1). Can Freesurfer do this? Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field? Your help is greatly appreciated. Best, ping ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] how to get the displacement from template to the linearly registered image
External Email - Use Caution Dear Tim, Thank you for your reply! 1) I want the the deformation field is the displacement from the template image to the linearly-aligned image defined. 2) I just use the recon-all to generate the file. 3) What I want is to first linearly register to template to obtain a linearly registered image, and then perform nonlinear registration to obtain the deformation field from the origin image to the template. I don't know which image is linearly registered in freesurfer, which one is after nonlinear registration, and the deformation field file is 128*128*128*3, I can't think of it as displacement I want . Best, ping Tim Schäfer 于2019年8月28日周三 下午4:30写道： > External Email - Use Caution > > Could you explain what you are trying to achieve and which transformation > you are referring to? I don't get: > 1) what are the input and output files of the registration for which you > want the deformation field? > 2) What command did you use to perform the registration? > 3) Is it linear or nonlinear? > > (The file /mri/transforms/talairach.m3z stores a transformation > field of a nonlinear registration, but I'm not sure whether it is what you > want.) > > I find the quoted part a bit confusing (but that may just be me). The > first sentence talks about nonlinear registration, and the others talk > about linear registration -- but still mention a deformation field. Maybe > some more context would help. > > For a linear registration, an affine matrix should be all you need. > > > Tim > > > On August 28, 2019 at 9:55 AM ping cao wrote: > > > > > > External Email - Use Caution > > > > Dear expert， > > > > I saw a paper mentioned this ： > > > > By using the *deformation field* from nonlinear registration, we can > > > build the correspondence between voxels in the template and each > > > linearly-aligned image. For instance, for each voxel (x, y, z) in the > > > template image, we can find its corresponding voxel (x + dx, y + dy, z > + > > > dz) in each linearly-aligned image, where (dx, dy, dz) is the > > > *displacement* from the template image to the linearly-aligned image > > > defined by the deformation field. > > > > > > > > So, I want to get the deformation field from the template to the linearly > > registered image(flirt_T1). > > > > Can Freesurfer do this? Which file is a linearly registered image that > > does not contain an affine transformation? How can I get this deformation > > field? > > > > > > Your help is greatly appreciated. > > > > > > Best, > > ping > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Forschung - Klinische Bildgebung > Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und > Jugendalters > Universitätsklinikum Frankfurt / Haus 93, Raum A 305 > Deutschordenstr. 50, 60528 Frankfurt am Main > Tel.: +49 (0)69 6301 85832 > > ___ > 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
