25 Aug
2017
25 Aug
'17
8:37 p.m.
Hi Michelle
the wm segmentation is kind of irrelevant - it's the ?h.white surfaces that matter (and maybe not even those if you only care about subcortical things)
cheers Bruce On Fri, 25 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce, I got this to work, but we are still having the same problem wth over-inclusion of pial matter in the white matter segmentations even when using skullstrip from other packages (AFNI , FSL, ANTs).
I am mainly interested in the subcortical volumes, and I want to do a longitudinal analysis of the subcortical volumes. Does the longitudinal freesurfer pipeline depend on good quality segmentation across whole brain? or can I use it to obtain longitudinal subcortical volumes and ignore the fact that the white matter segmentation is less than perfect for many subjects? Is it a problem that the whole-brain volume measures will be off due to the over-inclusion of skull in WM?
I would appreciate any advice or insights you may have!
Thanks, Michelle
On Wed, Aug 9, 2017 at 6:39 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: are you sure you created the brainmask with -rl orig.mgz? It should have the same dimensions afterwards.
On Wed, 9 Aug 2017, Michelle VanTieghem wrote: -bash-4.1$ mri_info orig.mgz Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 3.0505 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -0.9364 talairach xfm :/vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri/transforms/talaira ch.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 122.7709 0.0000 0.0000 1.0000 -124.9495 0.0000 -1.0000 0.0000 127.0636 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 122.7709 -0.0000 -0.0000 -1.0000 127.0636 -0.0000 1.0000 -0.0000 124.9495 0.0000 0.0000 0.0000 1.0000 --------------------------------------------------------------------------- ------------- -bash-4.1$ mri_info brainmask.mgz Volume information for brainmask.mgz type: MGH dimensions: 221 x 274 x 261 voxel sizes: 1.0000, 1.0000, 1.0000 type: SHORT (4) fov: 274.000 dof: 0 xstart: -110.5, xend: 110.5 ystart: -137.0, yend: 137.0 zstart: -130.5, zend: 130.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -5.2291 : x_a = 0.0000, y_a = -1.0000, z_a = 0.0000, c_a = 3.0505 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = -0.9364 talairach xfm : Orientation : LPS Primary Slice Direction: axial voxel to ras transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 0.0000 0.0000 1.0000 -131.4364 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: -1.0000 0.0000 0.0000 105.2709 0.0000 -1.0000 0.0000 140.0505 -0.0000 -0.0000 1.0000 131.4364 0.0000 0.0000 0.0000 1.0000 --------------------------------------------------------------------------- ------------------------------ Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 84 (84), valley at 0 (-1) csf peak at 42, setting threshold to 70 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 83 (83), valley at 0 (-1) csf peak at 41, setting threshold to 69 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 4 minutes and 23 seconds. #-------------------------------------------- #@# Mask BFS Wed Aug 9 02:03:44 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB020_fu1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask Linux reno.cc.columbia.edu 2.6.32-696.el6.x86_64 #1 SMP Tue Feb 21 00:53:17 EST 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SB020_fu1 exited with ERRORS at Wed Aug 9 02:03:46 EDT 2017 On Wed, Aug 9, 2017 at 4:11 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: can you send us the output of mri_info on orig.mgz and brainmask.mgz created with the -rl flag? And also send us the full screen output of the command that fails? thanks Bruce On Wed, 9 Aug 2017, Michelle VanTieghem wrote: Hi, I originally used mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz and I re-did it using the -rl flag as you recommended. it did not influence anything, same problem. I'd appreciate any trouble shooting tips. Thanks, M On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: what was your mri_convert command line? It should be something like mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz cheers Bruce On Mon, 7 Aug 2017, Michelle VanTieghem wrote: Hi Bruce, Here is what I did. For each subject: a) used the original (non-skull stripped) brain for the 001.mgz file as input - located in the Subnum/mri directory b) used mri_convert to get the afni skull-stripped brains and renamed them "brainmask.mgz" , located in the Subnum/mri directory. c) Then I ran the following command: recon-all -all -3T -mprage -s processed/Subnum I get the following error: -------------------------------------------------- #@# Mask BFS Sat Aug 5 01:31:09 EDT 2017 /vega/psych/users/mrv2115/fsdata/processed/SB002/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 ERROR: dimension mismatch between source and mask ------------------------------------------------- Can you please advise? The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu-- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115@columbia.edu