How many volumes does this file have?  /myfolder/freesurfer/subject02_C/dmri/data.nii.gz

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Mazzetti, C. (Cecilia) <C.Mazzetti@donders.ru.nl>
Sent: Sunday, October 6, 2019 5:56 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors running TRACULA (data attached) - valid frame numbers

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Hi Anastasia,
Thank you for answering!
I think you are right and the problem is there, when checking the number of slices in the dwindling file I get:
dimensions: 104 x 104 x 72


Although the original dwindling data has: 104 x 104 x 72 x 111




  voxel sizes: 2.019231, 2.019231, 2.000000
         type: SHORT (4)
          fov: 210.000
          dof: 0
       xstart: -105.0, xend: 105.0
       ystart: -105.0, yend: 105.0
       zstart: -72.0, zend: 72.0
           TR: 3670.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
      nframes: 1
      PhEncDir: UNKNOWN
      FieldStrength: 0.000000
ras xform present
   xform info: x_r =  -0.9897, y_r =   0.1290, z_r =  -0.0618, c_r = -1.2731
             : x_a =  -0.1108, y_a =  -0.9647, z_a =  -0.2389, c_a =   -22.2682
             : x_s =  -0.0904, y_s =  -0.2296, z_s =   0.9691, c_s =    12.8890
Orientation   : LPS
Primary Slice Direction: axial

voxel to ras transform:
              -1.9985   0.2605  -0.1236    93.5531
              -0.2238  -1.9480  -0.4778   107.8607
              -0.1826  -0.4636   1.9382   -23.2834
               0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant 8.15459

ras to voxel transform:
              -0.4901  -0.0549  -0.0448    50.7312
               0.0639  -0.4778  -0.1137    42.9079
              -0.0309  -0.1194   0.4845    27.0558
               0.0000   0.0000   0.0000     1.0000

I don’t understand why, given those are outputs of recon-all ..

Do you think you know what’s happening?


Thank you very much!​