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/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?





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            --
            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 



--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2115@columbia.edu