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 = 0.000001 > > 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 <mailto: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> > <mailto: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. > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > <https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2>> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > _______________________________________________ > 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
