Hi chikku. Yes all steps are necessary (see the description on the wiki). First all time points need to be processed cross sectionally. Best Martin
Varghese Chikku chikkuv@tcd.ie wrote:
Martin, Forgive my ignorance and sorry to pester you. From what you said in the mail, *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´´ * In this case Do I need to run recon-all -s autorecon-all at all.If i have a patient can i omit the initial recon-all process and straight away go ahead and do recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ...? Much appreciate your feedback, In Thanks chikku
On 27 February 2013 21:30, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
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
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