Thanks, Martin. It is unfortunate to hear such news, but they are of course accurate. Hopefully this affects a small subset of subjects, and I will be able to add a covariate to it. Regards, Pedro Rosa.
On Wednesday, April 1, 2015 at 12:30 PM, Martin Reuter wrote: > Hi Pedro, > > there is really no way to fix it. Especially if all you subjects changed > acquisition. If it is only a small subset, you can then include a co-variable > to account for this in your stats. You should then also test whether one > group has more of these cases than the other, or if it is distributed evenly > (in case you run a group analysis). If you are interested in analyzing other > co-variates (drug dose) you need to test if there is a correlation with > acquisition, etc. > > Reslicing will not help at all. Adding another reslicing step to only some > images will clearly bias results. > > If this change in acquisition has happened for most or all your subjects, you > can scan a subset back-to-back (with removal from scanner), with the > different protocols to see how large the effect is. The problem here is that > you need to scan a decent number to trust those results. > > Best, Martin > > > On 04/01/2015 11:21 AM, Pedro Rosa wrote: > > Hi Martin, > > Thank you for your answer. > > Is there a way to fix it? Can reslicing help? > > Or to try compenate for it in the processing or statistics? > > Regards > > > > -- > > Pedro Rosa > > > > > > On Apr 1, 2015, at 12:13, Martin Reuter <mreu...@nmr.mgh.harvard.edu > > (mailto:mreu...@nmr.mgh.harvard.edu)> wrote: > > > > > Hi Pedro, > > > > > > yes, there was a bug (well, not really a bug but the check was > > > oversensitive). It was testing too many image parameters, some of them > > > could be problematic (e.g. different voxel sizes across time), and some > > > not. > > > > > > Looking at your attached files, you can see that the voxel sizes differ > > > significantly between the baseline and the follow-up > > > Baseline: > > > dimensions: 256 x 256 x 124 > > > voxel sizes: 0.8594, 0.8594, 1.5000 > > > Follow-up: > > > dimensions: 256 x 256 x 124 > > > voxel sizes: 1.0938, 1.0938, 1.5000 > > > > > > This can induce a bias. You need to keep imaging parameters fixed in a > > > longitudinal study, else you'll not know if changes are anatomical > > > changes or induced by the different imaging. > > > > > > Best, Martin > > > > > > On 04/01/2015 06:43 AM, Pedro Rosa - Gmail wrote: > > > > Dear FreeSurfers, I have read in the Mailing list > > > > (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32753.html > > > > and others) other users asking questioning in regard of a Warning from > > > > FreeSurfer 5.3 longitudinal pipeline (-base step): > > > > \n******************************************************************************* > > > > WARNING: Image geometries differ across time, maybe due to aquisition > > > > changes? This can potentially bias a longitudinal study! Will continue > > > > in 10s. > > > > *******************************************************************************\n > > > > I am working in a sample with a longotudinal design which receives > > > > this warn, although there was no change in hardware, and (supposedly) > > > > the acquisition protocol was the same. As requested by Martin in former > > > > posts in the Mailing List, I attached the output from mri_info > > > > */rawavg.mgz. I would like to know if these differences should be > > > > considered a bias in a longitudinal study and, if they should, if there > > > > is a way to fix it. Regards, Pedro Rosa. > > > > > > > > > > > > > > > > _______________________________________________ Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School > > > Assistant in Neuroscience Dept. of Radiology, Massachusetts General > > > Hospital Dept. of Neurology, Massachusetts General Hospital Research > > > Affiliate Computer Science and Artificial Intelligence Lab, Dept. of > > > Electrical Engineering and Computer Science, Massachusetts Institute of > > > Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth > > > Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: > > > mreu...@nmr.mgh.harvard.edu (mailto:mreu...@nmr.mgh.harvard.edu) > > > reu...@mit.edu (mailto:reu...@mit.edu) Web : http://reuter.mit.edu > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu (mailto: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. > > > > > > _______________________________________________ Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant > in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of > Neurology, Massachusetts General Hospital Research Affiliate Computer Science > and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer > Science, Massachusetts Institute of Technology A.A.Martinos Center for > Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 > Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu > (mailto:mreu...@nmr.mgh.harvard.edu) reu...@mit.edu (mailto:reu...@mit.edu) > Web : http://reuter.mit.edu > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu (mailto: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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