Hi Erik, better late then never: you should use mri_convert --conform input output
Best, Martin > On 16. May 2018, at 12:19, Erik O'Hanlon <erikohan...@rcsi.ie> wrote: > > External Email - Use Caution > Thank Martin, > > I've been looking into this and it appears that the slight changes in the > sequence may have occurred software updates to the scanner. So essentially > from what you say, this drastically impacts any longitudinal analyses as > there will be a systematic bias across the data. Is there any point in trying > to do longitudinal analyses with such data as it will be a factor in all > output? Is it worth resampling all three time points to 1mm and then rerun > the analysis as it will be difficult to say if any patterns of change arent > due to the acquistions as you said? > > If I want to resample the data to a "standard 1mm3" voxel size, is there a FS > command for that or should I use something in FSL or AFNI tools and then feed > the resampled data back to the recon-all inistial step in FS. > > Thanks for the help and guidance. Much appreciated > > Erik > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Martin Reuter > <mreu...@nmr.mgh.harvard.edu <mailto:mreu...@nmr.mgh.harvard.edu>> > Sent: 15 May 2018 23:39 > To: Freesurfer support list > Subject: Re: [Freesurfer] Longitudinal errors, Voxel size differs > > Hi Erik, > > you should investigate why this is the case. Any difference in acquisition > will cause effects and it will be impossible to distinguish these from real > effects. > > Also you should never just resample one time point, as that will introduce > processing bias. I would advise to > - find out why, and you need to report this in any analysis so that people > are aware of this potential bias > - resample both time points to some 3rd space. Probably here simply conform > them to 1mm isotropic. > > Best, Martin > >> >> Erik O'Hanlon >> Postdoctoral researcher >> <rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png> >> RCSI Psychiatry >> Royal College of Surgeons in Ireland >> Beaumont Road, Beaumont D9 Ireland >> T: 8093740 >> E: erikohan...@rcsi.ie <mailto:erikohan...@rcsi.ie> W: www.rcsi.com >> <http://www.rcsi.com/> >> >> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan >> 2018-2022 <http://www.rcsi.ie/strategy2018> >> >> RCSI DEVELOPING HEALTHCARE LEADERS >> WHO MAKE A DIFFERENCE WORLDWIDE >> >> >> <both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png> >> >> On 15. May 2018, at 07:20, Erik O'Hanlon <erikohan...@rcsi.ie >> <mailto:erikohan...@rcsi.ie>> wrote: >> >> Hi FS Experts, >> >> I'm trying to run a longitudinal analysis across three timepoints and have >> run the cross steps for the data. I then ran the base step but found that my >> voxel dimensions are slightly different across the timepoints and I got the >> following error >> >> ERROR: MultiRegistration::loadMovables: images have different voxel sizes. >> Currently not supported, maybe first make conform? >> Debug info: size(2) = 0.881117, 0.881117, 0.881117 size(0) = 0.884507, >> 0.884507, 0.884507 >> MultiRegistration::loadMovables: voxel size is different >> /projects/pi-vokeane/HPC_16_00925/MC_FS_testdata_EOH/freesurfer/subjects/abd025_tp3/mri/norm.mgz. >> >> >> I assume I need to resample the data to the voxel size of the first time >> point and then rerun. Can you advise on what command to use to resample the >> images from time 2 and time 3 to those of time 1 before rerunning from >> scratch. I assume I can't avoid rerunning the initial reconall step once I >> resample my data. >> >> Any guidance is much appreciated >> >> Best regards >> >> Erik >> >> Erik O'Hanlon >> Postdoctoral researcher >> <rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png> >> RCSI Psychiatry >> Royal College of Surgeons in Ireland >> Beaumont Road, Beaumont D9 Ireland >> T: 8093740 >> E: erikohan...@rcsi.ie <mailto:erikohan...@rcsi.ie> W: www.rcsi.com >> <http://www.rcsi.com/> >> >> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan >> 2018-2022 <http://www.rcsi.ie/strategy2018> >> >> RCSI DEVELOPING HEALTHCARE LEADERS >> WHO MAKE A DIFFERENCE WORLDWIDE >> >> >> <both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png> >> >> _______________________________________________ >> 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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