Dear Martin,
the differences between the structural sequences are rather small and I would expect - if any - only a very subtle influence on preprocessing. The bias would be only important if you would like to analyze the structural data only.
However, to minimize any potential bias you could try to create a customized Dartel template using all structural data and apply Dartel registration to your (co-registered) fMRI data.
If the reviewers still have doubts about a potential bias, you could try to use one of the patient's data set with 1mm slice thickness and resample this data set to the slice thickness of the control data of 1.33mm and compare the estimated connectivity estimates between both approaches.
Best,
Christian
On Tue, 4 Sep 2018 17:50:29 -0700, Martin Juneja <[log in to unmask]> wrote:
>Hello experts,
>
>I have two data sets (patients and controls). I am interested in comparing
>resting-state directional connectivity within specific nodes (using MNI
>coordinates from literature) using DCM.
>
>Scanning protocol for resting-state data is identical between two groups
>but the protocol for structural data is different between two groups as
>following, although both data sets are collected using the same scanner and
>I used the same MNI template for normalization/interpolation with standard
>space (traditional SPM pipeline for preprocessing).
>
>I was wondering if this difference in scanning parameters will/may bias my
>connectivity results in some way or the other. If so, is there any solution
>to this problem, and if no, how can I justify this in my manuscript.
>
>I would really appreciate any help.
>
>Thanks!
>-----------------------------------------------------------------------------------------------------------
>*For controls:*
>
>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
>
>
>
>
>*For patients:*
>
>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 =
>1.1441
>
> : x_a = -1.0000, y_a = -0.0000, z_a = 0.0000, c_a =
>20.7797
>
> : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
>17.5932
>
>Orientation : PIL
>
>Primary Slice Direction: sagittal
>
>
>voxel to ras transform:
>
> -0.0000 -0.0000 -1.0000 89.1441
>
> -1.0000 -0.0000 0.0000 148.7797
>
> 0.0000 -1.0000 0.0000 145.5932
>
> 0.0000 0.0000 0.0000 1.0000
>
>
>voxel-to-ras determinant -1
>
>
>ras to voxel transform:
>
> -0.0000 -1.0000 -0.0000 148.7797
>
> -0.0000 -0.0000 -1.0000 145.5932
>
> -1.0000 -0.0000 -0.0000 89.1441
>
> -0.0000 -0.0000 -0.0000 1.0000
>
|