Hi Chikku, the -qcache command is for cross sectional processing. It is not done in the base and does not need to be done there.
The base is like an additional time point so it does run from the start and even contains some extra steps. 12hrs are not unlikely. You will need to also run the recon all again on all time points with the -long flag. Then, once those are processed, you have several options for the analysis, see http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics we recommend linear mixed effects, described here: http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels but in your simple setup (2 time points for each subject), you can also use the direct analysis of atrophy. For that you'd do a) run some processing scripts that compute the rate of change in each subject (e.g. long_mris_slopes or long_stats_slopes) b) use mri_glmfit or qdec to analyze those rates (one for each subject) across groups etc. That is described here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial Best, Martin On 02/27/2013 11:19 AM, Varghese Chikku wrote: > Dear all, > I am bit confused with the Qdec process. > I finished recon all for 2 time points and want to create > longitudinal data.From FS tutorial I learned to create > within-subject templates for processing,which is running now with > recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all. > Now,in an other link of tutorial it says ,Qdec needs each subject to > have a pre-computed smoothed data for the target surface ,recon-all -s > <subjid> -qcache > So my first is question is, recon-all -base <templateID> -tp <tp1id> > -tp <tp2id> ... -all will do recon-all -s <subjid> -qcache along or I > have to run it separately. > Second,recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all > is almost 12 hrs now and wondering if this is processing images > from the very begining. > Many Thanks > chikku > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT 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 reu...@mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list 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.
