-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/talairach.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?
>>
>>
>>
>>
>>
>> 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
>> mrv2...@columbia.edu
>>
>>


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