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 <chik...@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 <mreu...@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
>>
>> Phone: +1-617-724-5652
>> Email:
>> mreu...@nmr.mgh.harvard.edu
>> reu...@mit.edu
>> Web : http://reuter.mit.edu
>>
>>
>>
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--
Sent from my phone, please excuse brevity.
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