subject:"\[Freesurfer\] Cortical thickness using qdec \(between scanners\)"

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-10-12 Thread Douglas N Greve

That is surface-based smoothing. the voxel size differences create 
differences in volume-based smoothing (a partial volume effect). I don't 
know of a good way to simulate volume-based PVC. This cannot be done in qdec


On 10/06/2016 06:36 PM, Martin Juneja wrote:
> Dear Dr. Greve,
>
> Thanks a lot for your inputs on this.
> In the manual- 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview,
>  
> in qdec it shows there is an option to select 'Smoothing (FWHM)' under 
> the step 'Design'. Could you please share your thoughts if there is 
> any optimal value here I can choose which does a close comparison for 
> the two different voxel size (1.3 vs 1) or may be if I can compare 
> without smoothing?
>
> Thanks.
>
> On Wed, Oct 5, 2016 at 3:21 PM, Douglas N Greve 
> > wrote:
>
> I think the difference in voxel size (1mm vs 1.3mm) is
> problematic. You
> will get more smoothing with the 1.3mm (ie, partial volume
> effects), and
> that could easily show up in the thickness measurements
>
>
> On 10/05/2016 12:19 PM, Martin Juneja wrote:
> > 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 = 0.01
> >
> > 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 -
> >
> >  1.0 0.0   0.0   0.0;
> >
> >  0.0 1.0   0.0   0.0;
> >
> >  0.0 0.0   1.0   0.0;
> >
> >  0.0 0.0   0.0   1.0;
> >
> > Volume information for IM-0001-0001-0001.dcm
> >
> > type: siemens_dicom
> >
> > dimensions: 256 x 256 x 176
> >
> >voxel sizes: 1.00, 1.00, 1.00
> >
> > 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: 3.00
> >
> > ras xform present
> >
> > xform info: x_r =  -0., y_r =  -0., z_r =  -1.,
> c_r =
> > 2.5000
> >
> >   : x_a =  -1., y_a =  -0., z_a =  -0., c_a =14.
> >
> >   : x_s =   0., y_s =  -1., z_s =   0., c_s = 2.
> >
> > Orientation   : PIL
> >
> > Primary Slice Direction: sagittal
> >
> > voxel to ras transform:
> >
> >   -0.  -0.  -1.90.5000
> >
> >   -1.  -0.  -0.   142.
> >
> > 0.  -1.   0.   130.
> >
> > 0.   0.   0. 1.
> >
> > voxel-to-ras determinant -1
> >
> > ras to voxel transform:
> >
> >   -0.  -1.  -0.   142.
> >
> >   -0.  -0.  -1.   130.
> >
> >   -1.  -0.  -0.90.5000
> >
> >   -0.  -0.  -0. 1.
> >
> >
> > *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: 1.00, 1.00, 1.33
> >
> > 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: 3.00
> >
> > 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 =

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-10-06 Thread Martin Juneja

Dear Dr. Greve,

Thanks a lot for your inputs on this.
In the manual-
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview,
in qdec it shows there is an option to select 'Smoothing (FWHM)' under the
step 'Design'. Could you please share your thoughts if there is any optimal
value here I can choose which does a close comparison for the two different
voxel size (1.3 vs 1) or may be if I can compare without smoothing?

Thanks.

On Wed, Oct 5, 2016 at 3:21 PM, Douglas N Greve 
wrote:

> I think the difference in voxel size (1mm vs 1.3mm) is problematic. You
> will get more smoothing with the 1.3mm (ie, partial volume effects), and
> that could easily show up in the thickness measurements
>
>
> On 10/05/2016 12:19 PM, Martin Juneja wrote:
> > 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 = 0.01
> >
> > 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 -
> >
> >  1.0 0.0   0.0   0.0;
> >
> >  0.0 1.0   0.0   0.0;
> >
> >  0.0 0.0   1.0   0.0;
> >
> >  0.0 0.0   0.0   1.0;
> >
> > Volume information for IM-0001-0001-0001.dcm
> >
> > type: siemens_dicom
> >
> > dimensions: 256 x 256 x 176
> >
> >voxel sizes: 1.00, 1.00, 1.00
> >
> > 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: 3.00
> >
> > ras xform present
> >
> > xform info: x_r =  -0., y_r =  -0., z_r =  -1., c_r =
> > 2.5000
> >
> >   : x_a =  -1., y_a =  -0., z_a =  -0., c_a =14.
> >
> >   : x_s =   0., y_s =  -1., z_s =   0., c_s = 2.
> >
> > Orientation   : PIL
> >
> > Primary Slice Direction: sagittal
> >
> > voxel to ras transform:
> >
> >   -0.  -0.  -1.90.5000
> >
> >   -1.  -0.  -0.   142.
> >
> > 0.  -1.   0.   130.
> >
> > 0.   0.   0. 1.
> >
> > voxel-to-ras determinant -1
> >
> > ras to voxel transform:
> >
> >   -0.  -1.  -0.   142.
> >
> >   -0.  -0.  -1.   130.
> >
> >   -1.  -0.  -0.90.5000
> >
> >   -0.  -0.  -0. 1.
> >
> >
> > *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: 1.00, 1.00, 1.33
> >
> > 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: 3.00
> >
> > 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  -1.328558.9497
> >
> >   -0.9989  -0.0441   0.0244   185.1541
> >
> > 0.0433  -0.9981  -0.0575   113.3820
> >
> > 0.   0.   0. 1.
> >
> > 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  -0.032545.4015
> >
> >   -0.  -0.  -0. 1.
> >
> > Thanks a lot.
> >
> > On Mon, Oct 3, 2016 at 11:42 AM, Douglas N Greve
> > > 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:
> > >

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-10-05 Thread Douglas N Greve

I think the difference in voxel size (1mm vs 1.3mm) is problematic. You 
will get more smoothing with the 1.3mm (ie, partial volume effects), and 
that could easily show up in the thickness measurements


On 10/05/2016 12:19 PM, Martin Juneja wrote:
> 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 = 0.01
>
> 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 -
>
>  1.0 0.0   0.0   0.0;
>
>  0.0 1.0   0.0   0.0;
>
>  0.0 0.0   1.0   0.0;
>
>  0.0 0.0   0.0   1.0;
>
> Volume information for IM-0001-0001-0001.dcm
>
> type: siemens_dicom
>
> dimensions: 256 x 256 x 176
>
>voxel sizes: 1.00, 1.00, 1.00
>
> 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: 3.00
>
> ras xform present
>
> xform info: x_r =  -0., y_r =  -0., z_r =  -1., c_r = 
> 2.5000
>
>   : x_a =  -1., y_a =  -0., z_a =  -0., c_a =14.
>
>   : x_s =   0., y_s =  -1., z_s =   0., c_s = 2.
>
> Orientation   : PIL
>
> Primary Slice Direction: sagittal
>
> voxel to ras transform:
>
>   -0.  -0.  -1.90.5000
>
>   -1.  -0.  -0.   142.
>
> 0.  -1.   0.   130.
>
> 0.   0.   0. 1.
>
> voxel-to-ras determinant -1
>
> ras to voxel transform:
>
>   -0.  -1.  -0.   142.
>
>   -0.  -0.  -1.   130.
>
>   -1.  -0.  -0.90.5000
>
>   -0.  -0.  -0. 1.
>
>
> *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: 1.00, 1.00, 1.33
>
> 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: 3.00
>
> 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  -1.328558.9497
>
>   -0.9989  -0.0441   0.0244   185.1541
>
> 0.0433  -0.9981  -0.0575   113.3820
>
> 0.   0.   0. 1.
>
> 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  -0.032545.4015
>
>   -0.  -0.  -0. 1.
>
> Thanks a lot.
>
> On Mon, Oct 3, 2016 at 11:42 AM, Douglas N Greve 
> > 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
> > 
>  >> 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

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-10-05 Thread Martin Juneja

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 = 0.01

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 -

 1.0   0.0   0.0   0.0;

 0.0   1.0   0.0   0.0;

 0.0   0.0   1.0   0.0;

 0.0   0.0   0.0   1.0;

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

  type: siemens_dicom

dimensions: 256 x 256 x 176

   voxel sizes: 1.00, 1.00, 1.00

  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: 3.00

ras xform present

xform info: x_r =  -0., y_r =  -0., z_r =  -1., c_r =
2.5000

  : x_a =  -1., y_a =  -0., z_a =  -0., c_a =
14.

  : x_s =   0., y_s =  -1., z_s =   0., c_s =
2.

Orientation   : PIL

Primary Slice Direction: sagittal

voxel to ras transform:

   -0.  -0.  -1.90.5000

   -1.  -0.  -0.   142.

0.  -1.   0.   130.

0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:

   -0.  -1.  -0.   142.

   -0.  -0.  -1.   130.

   -1.  -0.  -0.90.5000

   -0.  -0.  -0. 1.

*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: 1.00, 1.00, 1.33

  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: 3.00

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  -1.328558.9497

   -0.9989  -0.0441   0.0244   185.1541

0.0433  -0.9981  -0.0575   113.3820

0.   0.   0. 1.

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  -0.032545.4015

   -0.  -0.  -0. 1.
Thanks a lot.

On Mon, Oct 3, 2016 at 11:42 AM, Douglas N Greve 
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
> > > 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
>

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-10-03 Thread Douglas N Greve

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 
> > 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.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> 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
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
>
> 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
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>  . If the e-mail was sent
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> but does not contain patient information, please contact the
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> dispose of the e-mail.
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>
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-10-03 Thread Martin Juneja

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  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.
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> 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
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
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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
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Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-09-30 Thread Douglas N Greve

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.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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 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.

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

2016-09-29 Thread Harms, Michael







Hi,
Even if the two sites are the same Siemens model, you are going to have difficultly convincing people that any differences you find might not just be a site effect.  In my opinion, this falls into the “not possible at all” category.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Juneja <mj70...@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, September 29, 2016 at 1:54 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Cortical thickness using qdec (between scanners)





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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[Freesurfer] Cortical thickness using qdec (between scanners)

2016-09-29 Thread Martin Juneja

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.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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.

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

Re: [Freesurfer] Cortical thickness using qdec (between scanners)

[Freesurfer] Cortical thickness using qdec (between scanners)

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