glad to hear it worked out
Bruce
On Sun, 8 Feb 2015, Liu Y wrote:

Hi Douglas and Bruce,

Thanks for your suggestions. I found the reason. The mistake begins from the
compressing dcm to nii by using dcm2nii. In the first 3 dcm images, two of
them have same index, then the dcm2nii could not keep the original
information of voxel size. I omitted the first 3 dcm images then it worked
during freesurfer analysis.

Cheers

Yawu



On Fri, Feb 6, 2015 at 6:26 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
      and what was the recon-all -i command line? Does the rawavg.mgz
      look correct? You can send us whatever file you gave to
      recon-all -i and we'll see why it is being converted
      incorrectly, or you can try the mri_convert command line I gave
      below (check out mri_convert --help) to override the voxel size
      info we read out of the header

      On Fri, 6 Feb 2015, Liu Y wrote:

            Hi Bruce,The full recon-all command line is
            "recon-all -cw256 -s T8_1 -all"
            and the input format is mgz. The mgz file is created
            by
            running recon-all -i. The 001.mgz under /mri/orig
            looks just normal, but
            when complete the  "recon-all -cw256 -s T8_1 -all",
             the orig.mgz was
            re-scaled (stretched) in left-right direction, and
            could not see the left
            and right boundaries of the brain. 
            Thanks,
            Yawu

            On Fri, Feb 6, 2015 at 3:18 PM, Bruce Fischl
            <fis...@nmr.mgh.harvard.edu>
            wrote:
                  Hi Yawu

                  what was the full recon-all command line? What
            is your input
                  format? If
                  all else fails you can mri_convert your input
            volume nifti or
                  mgz and
                  override what is in the header (e.g.
            mri_convert -iks 1 ...)

                  cheers
                  Bruce
                  On Fri, 6 Feb
                  2015, Liu Y wrote:

                  > Dear Experts,
                  > When I run recon-all -cw256 -s problemcase
            -all, the program
                  seems not able
                  > accurately to recognize the voxel size in
            this problematic
                  case, in other
                  > cases there is no problem. The program gave
            a warning like
                  this:
                  >
                 
>WARNING==================++++++++++++++++++++++++=========================
            =
                  =======
                  > ======
                  > The physical sizes are (240.00 mm, 240.00
            mm, 338.00 mm),
                  which cannot fit
                  > in 256^3 mm^3 volume.
                  > The resulting volume will have 338 slices.
                  > If you find problems, please let us know
                  (freesurfer@nmr.mgh.harvard.edu).
                 
>==================================================++++++++++++++++++++++++
            =

                  > ==============
                  >
                  > $Id: mri_convert.c,v 1.179.2.7 2012/09/05
            21:55:16 mreuter Exp
                  $
                  > reading from
                 
            /usr/local/src/freesurfer/subjects/T8_1/mri/rawavg.mgz...
                  > TR=8.08, TE=0.00, TI=0.00, flip angle=0.00
                  > i_ras = (0, -1, 0)
                  > j_ras = (0, 0, 1)
                  > k_ras = (1, 0, 0)
                  > Original Data has (1, 1, 2) mm size and
            (240, 240, 169)
                  voxels.
                  > Data is conformed to 1 mm size and 338
            voxels for all
                  directions
                  > changing data type from float to uchar
            (noscale = 0)...
                  > MRIchangeType: Building histogram
                  > Reslicing using trilinear interpolation
                  > writing to
                 
            /usr/local/src/freesurfer/subjects/Turku8_1/mri/orig.mgz...
                  >
                  > ****************************************
                  > ERROR! FOV=338.000 > 256
                  > Include the flag -cw256 with recon-all!
                  > Inspect orig.mgz to ensure the head is fully
            visible.
                  > ****************************************
                  >
                  > Then I checked the orig.mgz, the image was
            re-scaled
                  (stretched) in
                  > left-right direction, and could not see the
            left and right
                  boundaries of the
                  > brain. The program said that the Original
            Data has (1, 1, 2)
                  mm size, but
                  > actually the voxel size is 1*1*1 mm3.
                  >
                  > The freesurfer version 5.3, Ubuntu 12.04
                  >
                  > Thanks,
                  >
                  > Yawu
                  >
                  >
                  >
                  >
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