I dont think you did anytyhing wrong. You can use mri_vol2vol with the lta from the base/mri/transforms to map the seg into the base (same as long) space. But this resample will probably change the volume by 5%
On 9/12/2022 2:11 PM, Bernardoni, Fabio wrote: > External Email - Use Caution > > dear douglas, > > you are right a visual comparison is the thing to do. I hope I can ask you an > advice on that. > > I used freeview to open the mri data + segmentation for both participants: > > freeview -v $subj/mri/brainmask.mgz > $subj/mri/aseg.mgz:colormap=lut:opacity=0.2 $subjlongi/mri/brainmask.mgz > $subjlongi/mri/aseg.mgz:colormap=lut:opacity=0.9 & > > once they are open I can play with the opacity and visualize the differences. > > my problem is that the brainmasks are shifted wrt each other. when I try to > fix this setting the MNI305 coordinates to be the same, it does not work, it > is set in such a way that the TkregRAS/RAS coordinates are the same. how can > I change that? > > until I fix this, I can't tell because I see differences in the snapshots I > see but they are due to the fact I am looking at different slices of the > brain... > > or is this already indicative I did something wrong in the longi preproc > because the brainmasks should be the same? > > thanks a lot > > fabio > > > Dr. Fabio Bernardoni > wiss. Mitarbeiter > > Division of Psychological & Social Medicine and Developmental Neurosciences > http://secure-web.cisco.com/1kxESuMC8skdvctmEgROrtKwaJL655wWIo_gJPtdDtG7MZKUWGPBXwAOW9wVYj65KrkAt6AWDMPBykCVYpF4SiusK6DdviP4y94PoS1MBXfrHjauRSTBVkOFejSGQap3zkd5At3s-YHYI21EPwtIFV-ed2lN4QU8QRtdegkVrU-zYJYNk76vlDQcrE7qBBTzHjDusMPUXQIEJtdvknVW1ZvWkAzgRt_r-Czdl1wV4cbAn42Xdl_7OnaLp_Uf5WAyQeby_8l_JziMO6lWFC-3ciFa0HfORGIHBXvzAIxZfMCeJZDpO_o55bdpVySgHe2pG/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/1tdk375N1bvnxaho69MlzdIF7hK5pp1_6mJIaJnfKuaEBEPH4Pc2i2Uyg3vuRiEOee-CCv01jyHwUuZQLJAqTXYq1_3_trVKrhE6QwVbEkjsmJHovu3fBOEFQaR4YAJ1N-dPwRtSuTPfnYyESba8G02PUs8pdUIxT7bwgCepORO4UQ4yHILnLZhTFeFokC39wTAbgwtQEEz5yeR8_LaZFamy6MzT0fFaQ8EPhLAoKiTM8JHb1raj7loboFa3uH8dDsBuPCBAbus2DfeFzjwmuJfmhN5nGiryayNLe-LxV6ffQ_x0PgU430-kf76rhzg0l/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +49 (0351) 458-5245 > Universitätsklinikum Carl Gustav Carus > an der Technischen Universität Dresden > Anstalt des öffentlichen Rechts des Freistaates Sachsen > Fetscherstraße 74, 01307 Dresden > http://secure-web.cisco.com/1qFmNP2I6ZW2c6fyju_um89S6jNiAseV1vZiFSxV7kCVZJq6RJkhAjs7Ae-lIPABLRvK3uT3OLZvJlbuEQMC8_NehUzQqzTQIZOw7g4pjIo9YTvQ-_qB0qOHYySWwKT-xmbe3OQhQ3cQefzCvkVVfHUUGq4dgWpEKsjzzw-PuhKqAZK2Cp3CFpSQhxPlB5aqCdf_5Np0Csq2K0GzYkgzJ5jgH-lUDBv0Y21TP-5CHLiDqJmhS4qZp1OrSPBTTktfHF0Aey55IcDtb75cXtGeTbIsRON5Nuk2Tbpe8d3QXQbf3tkdN_-f2u5PgnI7bXfTa/http%3A%2F%2Fwww.uniklinikum-dresden.de > > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk > Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > http://secure-web.cisco.com/1qFmNP2I6ZW2c6fyju_um89S6jNiAseV1vZiFSxV7kCVZJq6RJkhAjs7Ae-lIPABLRvK3uT3OLZvJlbuEQMC8_NehUzQqzTQIZOw7g4pjIo9YTvQ-_qB0qOHYySWwKT-xmbe3OQhQ3cQefzCvkVVfHUUGq4dgWpEKsjzzw-PuhKqAZK2Cp3CFpSQhxPlB5aqCdf_5Np0Csq2K0GzYkgzJ5jgH-lUDBv0Y21TP-5CHLiDqJmhS4qZp1OrSPBTTktfHF0Aey55IcDtb75cXtGeTbIsRON5Nuk2Tbpe8d3QXQbf3tkdN_-f2u5PgnI7bXfTa/http%3A%2F%2Fwww.uniklinikum-dresden.de > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > ________________________________________ > Von: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve > <dgr...@mgh.harvard.edu> > Gesendet: Montag, 12. September 2022 16:14 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] volume differences between longitudinal and > crosssectional preprocessing > > What you show for the lateral ventricle is not really concerning to me. > Oftentimes there are differences on border voxels, and border voxels can > easily make 5% or more of a structure. If you compare them visually, do you > see big differences? > > On 9/12/2022 7:41 AM, Bernardoni, Fabio wrote: > > External Email - Use Caution > > dear freesurfer experts > > comparing the results of longitudinal vs. crosssectional preprocessing for > single time point participants I have noticed that there are some quite > substantial differences (>5% for some sub cortical regions). I wonder whether > this is normal, or whether I should suspect that I am using some wrong > setting. the differences are there both when using freesurfer 5.3 and > freesurfer 7.1. > > > I have always used the flag: -nuintensitycor-3T (our scanner is a 3 Tesla one) > > > I would say that I more often have smaller volumes in the longi preprocessing > (80% of the cases), but I haven't checked this systematically. > > This are the first 5 regions from the aseg.stats file: > > FS5 CROSS > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev > normMin normMax normRange > 1 4 4772 4772.4 Left-Lateral-Ventricle 45.4073 > 12.8146 24.0000 92.0000 68.0000 > 2 5 133 132.6 Left-Inf-Lat-Vent 51.9800 > 10.2799 28.0000 77.0000 49.0000 > 3 7 13488 13488.1 Left-Cerebellum-White-Matter 91.1006 > 5.2419 37.0000 106.0000 69.0000 > 4 8 57562 57561.8 Left-Cerebellum-Cortex 72.0094 > 8.7033 24.0000 96.0000 72.0000 > 5 10 8428 8428.3 Left-Thalamus-Proper 94.7674 > 7.1110 52.0000 111.0000 59.0000 > > FS5 LONGI > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev > normMin normMax normRange > 1 4 4542 4541.9 Left-Lateral-Ventricle 42.8623 > 13.5582 22.0000 94.0000 72.0000 > 2 5 131 130.5 Left-Inf-Lat-Vent 50.6667 > 11.1812 23.0000 81.0000 58.0000 > 3 7 13576 13576.1 Left-Cerebellum-White-Matter 86.1990 > 4.5161 40.0000 100.0000 60.0000 > 4 8 57615 57614.7 Left-Cerebellum-Cortex 68.7623 > 8.6206 17.0000 92.0000 75.0000 > 5 10 8658 8658.2 Left-Thalamus-Proper 91.2531 > 6.7374 52.0000 107.0000 55.0000 > > FS7 CROSS > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev > normMin normMax normRange > 1 4 4871 5297.0 Left-Lateral-Ventricle 43.9799 > 11.8868 24.0000 91.0000 67.0000 > 2 5 145 202.9 Left-Inf-Lat-Vent 53.7310 > 10.0009 28.0000 79.0000 51.0000 > 3 7 14703 15351.7 Left-Cerebellum-White-Matter 86.7391 > 5.5097 35.0000 100.0000 65.0000 > 4 8 57694 57174.0 Left-Cerebellum-Cortex 68.6875 > 9.0320 29.0000 95.0000 66.0000 > 5 10 8674 8354.1 Left-Thalamus 89.9416 > 8.1369 40.0000 107.0000 67.0000 > > > FS7 longi > > > # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev > normMin normMax normRange > 1 4 4898 5154.3 Left-Lateral-Ventricle 41.0488 > 12.0309 22.0000 79.0000 57.0000 > 2 5 165 214.4 Left-Inf-Lat-Vent 52.3939 > 11.2687 27.0000 84.0000 57.0000 > 3 7 14655 15364.2 Left-Cerebellum-White-Matter 83.1088 > 4.9509 39.0000 98.0000 59.0000 > 4 8 58759 58163.3 Left-Cerebellum-Cortex 65.8093 > 8.7269 25.0000 90.0000 65.0000 > 5 10 8757 8542.9 Left-Thalamus 85.7984 > 6.8821 47.0000 102.0000 55.0000 > > > > > thanks for any hint, and of course please let me know in case I should > provide more informations! > > > fabio bernardoni > > > Dr. Fabio Bernardoni > wiss. Mitarbeiter > > Division of Psychological & Social Medicine and Developmental Neurosciences > http://secure-web.cisco.com/1kxESuMC8skdvctmEgROrtKwaJL655wWIo_gJPtdDtG7MZKUWGPBXwAOW9wVYj65KrkAt6AWDMPBykCVYpF4SiusK6DdviP4y94PoS1MBXfrHjauRSTBVkOFejSGQap3zkd5At3s-YHYI21EPwtIFV-ed2lN4QU8QRtdegkVrU-zYJYNk76vlDQcrE7qBBTzHjDusMPUXQIEJtdvknVW1ZvWkAzgRt_r-Czdl1wV4cbAn42Xdl_7OnaLp_Uf5WAyQeby_8l_JziMO6lWFC-3ciFa0HfORGIHBXvzAIxZfMCeJZDpO_o55bdpVySgHe2pG/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/1tdk375N1bvnxaho69MlzdIF7hK5pp1_6mJIaJnfKuaEBEPH4Pc2i2Uyg3vuRiEOee-CCv01jyHwUuZQLJAqTXYq1_3_trVKrhE6QwVbEkjsmJHovu3fBOEFQaR4YAJ1N-dPwRtSuTPfnYyESba8G02PUs8pdUIxT7bwgCepORO4UQ4yHILnLZhTFeFokC39wTAbgwtQEEz5yeR8_LaZFamy6MzT0fFaQ8EPhLAoKiTM8JHb1raj7loboFa3uH8dDsBuPCBAbus2DfeFzjwmuJfmhN5nGiryayNLe-LxV6ffQ_x0PgU430-kf76rhzg0l/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +49 (0351) 458-5245 > Universitätsklinikum Carl Gustav Carus > an der Technischen Universität Dresden > Anstalt des öffentlichen Rechts des Freistaates Sachsen > Fetscherstraße 74, 01307 Dresden > http://secure-web.cisco.com/1qFmNP2I6ZW2c6fyju_um89S6jNiAseV1vZiFSxV7kCVZJq6RJkhAjs7Ae-lIPABLRvK3uT3OLZvJlbuEQMC8_NehUzQqzTQIZOw7g4pjIo9YTvQ-_qB0qOHYySWwKT-xmbe3OQhQ3cQefzCvkVVfHUUGq4dgWpEKsjzzw-PuhKqAZK2Cp3CFpSQhxPlB5aqCdf_5Np0Csq2K0GzYkgzJ5jgH-lUDBv0Y21TP-5CHLiDqJmhS4qZp1OrSPBTTktfHF0Aey55IcDtb75cXtGeTbIsRON5Nuk2Tbpe8d3QXQbf3tkdN_-f2u5PgnI7bXfTa/http%3A%2F%2Fwww.uniklinikum-dresden.de > > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk > Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > http://secure-web.cisco.com/1qFmNP2I6ZW2c6fyju_um89S6jNiAseV1vZiFSxV7kCVZJq6RJkhAjs7Ae-lIPABLRvK3uT3OLZvJlbuEQMC8_NehUzQqzTQIZOw7g4pjIo9YTvQ-_qB0qOHYySWwKT-xmbe3OQhQ3cQefzCvkVVfHUUGq4dgWpEKsjzzw-PuhKqAZK2Cp3CFpSQhxPlB5aqCdf_5Np0Csq2K0GzYkgzJ5jgH-lUDBv0Y21TP-5CHLiDqJmhS4qZp1OrSPBTTktfHF0Aey55IcDtb75cXtGeTbIsRON5Nuk2Tbpe8d3QXQbf3tkdN_-f2u5PgnI7bXfTa/http%3A%2F%2Fwww.uniklinikum-dresden.de > Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer > Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner > USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1Ng65FC4DxBw2EPLG-ctRVJGDummLpC46FnbYMnECBbesX6e31kketPk0KSpBafDnu1g3IRV1MRQ_EfEjlkKbOc1baMnRMmY_6g9DtDiidX0tmykVB93o54hn36SkWznySpXv1m5CpFtfsiWujglN64mmUXbaEZZwP_9DGXh8ugpiInl0yvAEDGwTarkX0sxDTIunDes6UCa3K6USu9JhLiufHbipqDt4po2mJ3tgyK7U5vIK47ZNp-Nv_vYvI6Z_Ynlrk-4ud7aV_SNG9bMAcwO-K9bhTEkwuS3X72UCZEiNtfQNRC7ZKZvUvTDmRqeY/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > _______________________________________________ > 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 The information in this e-mail is intended only for the person to whom it is addressed. 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