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 <gr...@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
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
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> >
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> > <https://gate.nmr.mgh.harvard.edu/filedrop2>
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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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> >
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> >
> >
> > 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
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
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