External Email - Use Caution Thanks, but I want to transform my ROI to the average space from my subjects (as created by make_average_subject). How do i get the xfm file to convert my ROI to this average space?
/Ben Am Fr., 27. März 2020 um 16:27 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > oK, this will not be that pretty, but you can > mri_vol2vol --mov yourRoi.mgz --targ orig.mgz --interp nearest --regheader > --o yourRoiOrig.mgz > mri_convert yourRoiOrig.mgz yourRoiOrigAverageSpace.mgz --apply_transform > subject/mri/transforms/talairach.xfm -rt nearest > > > On 3/27/2020 11:03 AM, Benjamin Ineichen wrote: > > 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 > > _______________________________________________ > 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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