External Email - Use Caution The space i created from all subjects using make_average_subject.
Douglas N. Greve <dgr...@mgh.harvard.edu> schrieb am Fr. 27. März 2020 um 15:32: > What do you mean by "the average space of the subjects"? > > > On 3/24/2020 2:01 PM, Benjamin Ineichen wrote: > > 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 > > _______________________________________________ > 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
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