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 <fis...@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
            <fis...@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 
            mrv2...@columbia.edu




--
Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University 
mrv2...@columbia.edu

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