Hi,
As a related question, we have been using FSL 5.3. I would like to use LME methods. I noticed that FSL 5.3 "Allows processing of subjects with single time point through the longitudinal stream to include them without bias into statistical analysis (LME)." but the Matlabs LME tools are only mentioned for FSL 6.0.
Does FSL 5.3 allow for LME, but not through matlab tools? Is it possible to use the matlab LME with data processed on 5.3?
Thanks, Michelle
On Fri, Aug 25, 2017 at 5:25 PM, Michelle VanTieghem < michelle.vantieghem@gmail.com> 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/fsd ata/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