Re: [Freesurfer] Longitudinal data from different sequences and scanners

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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 mreuter@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 matt@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

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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 -

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Right-WM-hypointensities -

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non-WM-hypointensities -

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6.8 Left-non-WM-hypointensities -

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Right-non-WM-hypointensities -

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Optic-Chiasm 322.9 238.7 300.8 318.2 293.4 CC_Posterior 1,296.8 1,302.2

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