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. 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