External Email - Use Caution Dear Freesurfer experts,
I am aware that these are busy times. Please still allow me to repost my FreeSurfer problem: I created manual masks on the Freesurfer input 001.mgz for several subjects. I would like to to transform all these individual masks to the average space of the subjects. For this, I first ran mri_vol2vol: mri_vol2vol --talres 1 --interp nearest --mov SW1-2039/BGmaskbin.nii.gz --s SW1-2039/001.nii --targ multiplems_average/mri/T1.mgz --regheader --o BG2039mask_avesp.mgz The output from that was then used to run mri_robust register mri_robust_register --mov BGmask2039_avesp.mgz --dst multiplems_average/mri/T1.mgz --lta BG_2039_reg.lta --mapmov BG_2039_reg.mgz --iscale --satit But this does not seem to do the job. How can I transform and register a mask to the average space? Many thanks for your help! Best regards, Ben Am Fr., 6. März 2020 um 18:33 Uhr schrieb Benjamin Ineichen < bv.ineic...@gmail.com>: > the space in which the image was aqcuired. > > Am Fr., 6. März 2020 um 18:31 Uhr schrieb Douglas N. Greve < > dgr...@mgh.harvard.edu>: > >> what is "native space"? >> >> On 3/6/2020 12:09 PM, Benjamin Ineichen wrote: >> >> External Email - Use Caution >> example.mgz is just some example mask created on a template in native >> space. And I would need to transform it to MNI space. Thus, I ran: >> mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz >> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o >> example.mni305.mgz >> >> The transformed mask (example.mni305) is located in a completely >> different brain region in the MNI template compared to the native mask in >> the native template (see screenshots). How I can I correct this? Do I need >> to register the native and MNI template first? >> >> Thanks! >> >> /Ben >> >> Am Fr., 6. März 2020 um 17:59 Uhr schrieb Douglas N. Greve < >> dgr...@mgh.harvard.edu>: >> >>> What is example.mgz? >>> >>> If you want to transfer the orig.mgz, you can do it with >>> mri_vol2vol --tal --talres 1 --interp nearest --mov orig.mgz --s subject >>> --o example.mni305.mgz >>> >>> >>> >>> On 2/20/2020 3:53 PM, Benjamin Ineichen wrote: >>> >>> External Email - Use Caution >>> Dear Freesurfer experts, >>> >>> In order to transform a segmentation mask (example.mgz) from native so >>> standard MNI space I ran: >>> mri_vol2vol --talres 1 --interp nearest --mov example.mgz --s 001.mgz >>> --targ $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --regheader --o >>> example.mni305.mgz >>> >>> the output example.mni305.mgz did somehow transform to a different space >>> as you can see in Screenshot orig where the native mask is white and the >>> transformed mask is red. However, the masks seems to be in a >>> completely different brain region in the native MNI space (Screenshot MNI). >>> But the point of transforming my segmentation mask is that the segmented >>> mask should be in the same brain region but just transformed to the >>> standard space. How can I correct this? >>> >>> Many thanks for the support! >>> >>> /Ben >>> >>> -- >>> ____________________________________ >>> Benjamin Victor Ineichen, MD PhD >>> Karolinska Institutet >>> Center for Molecular Medicine >>> Stockholm, Sweden >>> ineic...@protonmail.ch >>> +41 76 391 04 01 >>> >>> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen >>> Karolinska Institutet >>> Center for Molecular Medicine >>> Stockholm, Sweden >>> ineic...@protonmail.ch >>> +41 76 391 04 01 >>> >>> _______________________________________________ >>> 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 >> >> >> >> -- >> ____________________________________ >> Benjamin Victor Ineichen, MD PhD >> Karolinska Institutet >> Center for Molecular Medicine >> Stockholm, Sweden >> ineic...@protonmail.ch >> +41 76 391 04 01 >> >> Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen >> Karolinska Institutet >> Center for Molecular Medicine >> Stockholm, Sweden >> ineic...@protonmail.ch >> +41 76 391 04 01 >> >> _______________________________________________ >> 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 > > > > -- > ____________________________________ > Benjamin Victor Ineichen, MD PhD > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > > Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen > Karolinska Institutet > Center for Molecular Medicine > Stockholm, Sweden > ineic...@protonmail.ch > +41 76 391 04 01 > -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineic...@protonmail.ch +41 76 391 04 01
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