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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> 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 = 0.000001 > > > > 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> > <mailto: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>> > > <mailto: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>> > > > <mailto: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>> > > > > <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>> > > <mailto: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>> > > <tel: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>> <tel: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>> > > > <http://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>> > > > <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>> > > > > <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 > <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/>> > > > > <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>> > > <mailto: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>> > > > > > > <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>> > > > <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> > > <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>> > > > > > > > > > > _______________________________________________ > > 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 > Fax: 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
