Hi Dr. Greve,

After I compare the two protocols (after using mri_info in FSL on raw dicom file), I get following parameters used in both the protocols. After looking at both the protocols parameters below, could you please share your thoughts on whether parameters are in match enough to go ahead and do the analysis i.e. patients data collected using protocol 1 and controls data using protocol 2 or is it still a bad idea to compare.

Protocol 1:

INFO: loading series header info.

INFO: sorting.

RunNo = 1

sdfiSameSlicePos() eps = 0.000001

INFO: (256 256 176), nframes = 1, ismosaic=0

sdfi->UseSliceScaleFactor 0

datatype = 4, short=4, float=3

PE Dir ROW ROW

AutoAlign matrix detected 

AutoAlign Matrix --------------------- 

 1.00000   0.00000   0.00000   0.00000;

 0.00000   1.00000   0.00000   0.00000;

 0.00000   0.00000   1.00000   0.00000;

 0.00000   0.00000   0.00000   1.00000;

Volume information for IM-0001-0001-0001.dcm

          type: siemens_dicom

    dimensions: 256 x 256 x 176

   voxel sizes: 1.000000, 1.000000, 1.000000

          type: SHORT (4)

           fov: 256.000

           dof: 0

        xstart: -128.0, xend: 128.0

        ystart: -128.0, yend: 128.0

        zstart: -88.0, zend: 88.0

            TR: 2100.00 msec, TE: 2.30 msec, TI: 1100.00 msec, flip angle: 12.00 degrees

       nframes: 1

       PhEncDir: ROW

       FieldStrength: 3.000000

ras xform present

    xform info: x_r =  -0.0000, y_r =  -0.0000, z_r =  -1.0000, c_r =     2.5000

              : x_a =  -1.0000, y_a =  -0.0000, z_a =  -0.0000, c_a =    14.0000

              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =     2.0000

Orientation   : PIL

Primary Slice Direction: sagittal

voxel to ras transform:

               -0.0000  -0.0000  -1.0000    90.5000

               -1.0000  -0.0000  -0.0000   142.0000

                0.0000  -1.0000   0.0000   130.0000

                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1

ras to voxel transform:

               -0.0000  -1.0000  -0.0000   142.0000

               -0.0000  -0.0000  -1.0000   130.0000

               -1.0000  -0.0000  -0.0000    90.5000

               -0.0000  -0.0000  -0.0000     1.0000


Protocol 2:

INFO: (256 256 128), nframes = 1, ismosaic=0

sdfi->UseSliceScaleFactor 0

datatype = 4, short=4, float=3

PE Dir ROW ROW

Volume information for IM-0001-0001-0001.dcm

          type: siemens_dicom

    dimensions: 256 x 256 x 128

   voxel sizes: 1.000000, 1.000000, 1.330000

          type: SHORT (4)

           fov: 256.000

           dof: 0

        xstart: -128.0, xend: 128.0

        ystart: -128.0, yend: 128.0

        zstart: -64.0, zend: 64.0

            TR: 2100.00 msec, TE: 2.25 msec, TI: 1100.00 msec, flip angle: 12.00 degrees

       nframes: 1

       PhEncDir: ROW

       FieldStrength: 3.000000

ras xform present

    xform info: x_r =  -0.0202, y_r =   0.0424, z_r =  -0.9989, c_r =   -23.2439

              : x_a =  -0.9989, y_a =  -0.0441, z_a =   0.0184, c_a =    53.2183

              : x_s =   0.0433, y_s =  -0.9981, z_s =  -0.0432, c_s =   -12.5170

Orientation   : PIL

Primary Slice Direction: sagittal

voxel to ras transform:

               -0.0202   0.0424  -1.3285    58.9497

               -0.9989  -0.0441   0.0244   185.1541

                0.0433  -0.9981  -0.0575   113.3820

                0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -1.33

ras to voxel transform:

               -0.0202  -0.9989   0.0433   181.2290

                0.0424  -0.0441  -0.9981   118.8377

               -0.7511   0.0138  -0.0325    45.4015

               -0.0000  -0.0000  -0.0000     1.0000

Thanks a lot.

On Mon, Oct 3, 2016 at 11:42 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
I would still say no -- the differences could still be due to
differences in acquisition parameters


On 10/03/2016 02:30 PM, Martin Juneja wrote:
> Thanks Dr. Harms and Dr. Greve.
> So can I do the cortical thickness comparison if we have healthy
> controls data from the same scanner but acquired using different
> protocol e.g. if we get access of age-matched healthy controls data
> from another lab who used the same scanner?
>
> Thanks.
>
> On Fri, Sep 30, 2016 at 12:02 PM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
>     You can do the comparison, but the interpretation is difficult. If you
>     see a difference, how do you know it is not due to the scanner?
>     There's
>     not much you can do ...
>
>
>     On 09/29/2016 02:54 PM, Martin Juneja wrote:
>     > Hello FS experts,
>     >
>     > I have a data set of 20 subjects (patients) collected at location-1
>     > with 3T Siemens scanner. Also, I have a set of age-matched 20
>     subjects
>     > (controls) collected at location-2 with 3T Siemens scanner.
>     >
>     > I am interested in comparing cortical thickness between controls and
>     > patients using FreeSurfer but I am not sure if I can do that since I
>     > have both the data sets collected at two different locations.
>     >
>     > I would really appreciate any inputs on this.
>     >
>     > I tried to find some papers on scanner differences but all I could
>     > find was between 1.5 T vs 3T or 3T vs 7T. Is there any special
>     > covariates I need to define for this purpose (if so then at
>     which step
>     > during analysis?) or is it not possible at all?
>     >
>     > Thanks.
>     >
>     >
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>     --
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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