External Email - Use Caution Martin,
Thanks for the feedback. Given our data set (1mm^3 timepoint1 and 0.8mm^3 timepoint 2), what would be the best way to salvage this data and look for longitudinal changes? Would it be possible to upsample/downsample the images so that they are the same resolution (i.e. using mriconvert)? Also, would a normalized measure like ventricle-brain-ratio theoretically be resistant to these scanner/acquisition induced biases? Thanks, James On Mon, Apr 16, 2018 at 5:15 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi, > > never switch hardware or protocols in a longitudinal study. This is a good > example for what happens: you will find effects that are caused by > different acquisition rather than anatomical differences. It will be > impossible to disentangle true change from scanner/acquisition induced > changes, especially with only a few time points and no or little subjects > scanned on both scanners or with both protocols. > > Also 5mm resolution is too low for freesurfer and anything can come out of > that. It won’t be reliable. > > Best, Martin > > > On 6. Apr 2018, at 21:21, Matthew Grecsek <m...@grecsek.com> wrote: > > Here are some statistics I generated for one of my subjects processed > through the longitudinal stream with T0 as the initial scan and T1 18 mos > later. (not sure if the inline tables will be properly formatted so I > attached text files of them). > > Unfortunately the only initial scan I had was a 5mm resolution for T0 > versus 1mm for T1. I understand FS recommends a resolution not exceeding > 1.5mm, but we gave it a try anyway to see if there was anything useful. My > expectation was that the stats would be off by a consistent ratio due to > the different resolutions, however I was surprised by the variability. > > In particular, as James found, for some ROIs there are net increases in > cortical thickness and brain volume over time. > > Is this simply a factor that the algorithms are confused by the different > image resolutions and therefore no possible longitudinal study can reliably > be presumed in this circumstance? > > Should we expect similar anomalies in cross-sectional studies, such as if > my subjects have 1mm resolutions and a collaborating institution has 0.8mm > subjects? > > Cheers, > > -Matt > > Aseg Stats > Measure:volume T0 T1 Base T0.long.base T1.long.base > Left-Lateral-Ventricle 9,455.2 13,085.8 > 12,344.2 10,928.1 13,268.0 > Left-Inf-Lat-Vent 61.8 174.1 > 171.7 90.3 303.3 > Left-Cerebellum-White-Matter 26,892.5 18,563.1 > 17,066.4 23,905.6 17,597.8 > Left-Cerebellum-Cortex 57,390.8 66,458.7 > 64,631.3 60,374.1 65,898.6 > Left-Thalamus-Proper 10,757.3 9,094.2 > 9,918.5 10,350.8 9,588.3 > Left-Caudate 3,619.4 3,673.8 > 3,608.8 3,588.7 3,872.7 > Left-Putamen 5,463.7 5,439.2 > 5,171.0 5,602.0 5,721.7 > Left-Pallidum 2,380.9 2,208.6 > 1,897.1 2,270.8 2,147.9 > 3rd-Ventricle 1,181.8 1,174.6 > 1,328.7 1,432.2 1,416.9 > 4th-Ventricle 1,209.1 1,602.0 > 1,547.7 1,322.4 1,981.1 > Brain-Stem 25,154.2 26,141.3 > 25,890.7 > 25,988.7 25,954.6 > Left-Hippocampus 4,205.3 4,335.6 > 4,378.0 4,478.2 4,407.2 > Left-Amygdala 1,488.1 1,725.9 > 1,588.6 1,531.3 1,638.0 > CSF 1,440.9 1,321.0 1,551.0 > 1,910.1 1,394.7 > Left-Accumbens-area 295.0 273.2 > 327.7 274.9 380.0 > Left-VentralDC 5,086.1 4,935.5 > 5,429.6 5,106.9 5,041.7 > Left-vessel - 16.6 > 7.7 - 48.5 > Left-choroid-plexus 221.6 419.4 > 271.7 429.5 734.2 > Right-Lateral-Ventricle 6,465.1 9,581.5 > 8,695.5 6,893.5 9,713.9 > Right-Inf-Lat-Vent 360.0 333.7 > 408.5 400.5 518.0 > Right-Cerebellum-White-Matter 21,673.2 16,458.6 > 14,923.8 21,877.6 15,850.3 > Right-Cerebellum-Cortex 57,831.7 68,348.9 > 65,845.5 60,300.5 68,194.1 > Right-Thalamus-Proper 9,219.0 9,128.7 > 9,229.9 9,560.8 9,177.7 > Right-Caudate 3,727.7 3,729.9 > 3,221.4 3,590.4 3,915.1 > Right-Putamen 5,401.9 5,515.4 > 5,088.3 5,410.8 5,894.9 > Right-Pallidum 2,470.8 2,259.8 > 1,965.1 2,211.6 1,999.4 > Right-Hippocampus 4,071.4 4,189.8 > 4,256.0 4,259.8 4,026.3 > Right-Amygdala 1,591.1 1,982.6 > 1,836.8 1,733.3 1,950.0 > Right-Accumbens-area 522.2 605.3 > 594.3 545.3 599.0 > Right-VentralDC 4,692.4 4,600.8 > 4,948.9 4,844.5 4,824.4 > Right-vessel - 15.0 > - - 59.3 > Right-choroid-plexus 353.5 590.1 > 506.4 956.9 1,234.4 > 5th-Ventricle - - > - 6.4 > 2.5 > WM-hypointensities 99,547.8 930.7 > 59,648.6 25,495.7 35,013.7 > Left-WM-hypointensities - > - - - > - > Right-WM-hypointensities - > - - - > - > non-WM-hypointensities - > - - 1.0 > 6.8 > Left-non-WM-hypointensities - > - - - > - > Right-non-WM-hypointensities - > - - - > - > Optic-Chiasm 322.9 238.7 > 300.8 318.2 293.4 > CC_Posterior 1,296.8 1,302.2 > > ... > > [Message clipped] > _______________________________________________ > 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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