[Freesurfer] Interscanner variability

2021-07-04 Thread AJ 
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Hi,
I am running Freesurfer on longitudinal datasets all obtained on 3T
scanners. Unfortunately,  many of the MRIs were done on different
scanners,  Phillips and GE.
Would longitudinal pipeline help reduced scanner variability or should I
process crossectionally each time point separately and normalize these time
points with eTIV?

Many thanks
AJ
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[Freesurfer] Transformation Applied to T1.mgz during recon-all

2021-07-04 Thread Alexander Rockhill 
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Hash: SHA256

Hello,

   I am trying to replicate the processing steps that occur between when a T1 
is given as input to recon-all and the T1.mgz that is stored in the 
$SUBJECTS_DIR/$SUBJECT/mri directory for mne-bids and dealing with mne's 
internal dependency on the surface RAS coordinate frame.

   It is my impression that 1) the image is resampled to 256 x 256 x 256 and 
then 2) the image is reoriented to head-first supine aka LIA aka scanner space. 
But when I replicate these steps using nibabel, the affine is off by a rotation 
and translation:

T1.mgz
--

  [[ -1.,  -0.0015,  -0.0003, 132.77600098],
   [  0.0003,   0.0001,   1., -94.00223541],
   [ -0.0002,  -1.0012,  -0.0001, 149.55487061],
   [  0.,   0.,   0.,   1.]]

orig resampled and translated
-

  [[ -0.5208,  -0.00905184,   0.00373623, 164.44344257],
   [  0.00337327,   0.03978604,   0.99920255, -98.49012464],
   [  0.00919327,  -0.9991672 ,   0.03975359, 141.93864847],
   [  0.,   0.,   0.,   1.]]

orig to T1.mgz transform affine
---

  [[  0.5203,  -0.00337331,  -0.00919312, -30.68693093],
   [  0.0037362 ,   0.99920251,   0.03975359,  -1.8476189 ],
   [  0.00905186,  -0.03978605,   0.99916736,   2.32735433],
   [  0.,   0.,   0.,   1.]]

Since there are off-diagonal entries in the last affine, I assume there is some 
kind of rotation, and since there are non-zero entries in the last column, I 
assume there is some kind of translation as well. I am not sure what either of 
those would be from so any advice or help would be appreciated.

Alex Rockhill
PhD Candidate University of Oregon

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