Almost true.
The stacking (smoothing and mapping to eg fsaverage) is done outside of matlab, using mris_preproc and that uses the .long.base names.

Matlab only opens that single file (stack) and reads additional info from the qdec table. Matlab does not need access to the .long.base directories directly.

Best martin


Sent via my smartphone, please excuse brevity.

-------- Original message --------
From: Anna Jonsson
Date:06/25/2014 10:00 AM (GMT+01:00)
To: Freesurfer support list
Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table

Ok, so even though in the qdec table you only specify the cross names as your fsid's, when you actually do the analysis the longs need to be in the same directory as the cross and bases (ie everything in the same directory) and matlab automatically uses the .long files, even though only the cross and fsid's are specified in the qdec table? Is this correct? Kind regards, Anna


On Tue, Jun 24, 2014 at 7:11 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Anna, 

the matlab tools don't know. They only look at the other co-variates that you might want to include into your study (the fsid-base for grouping, the time variable and others from the table). The stack of thickness maps needs to be in the same order as the rows in the qdec table. That is why it is a good idea to use the same table to assemble the stack (and for that you'd use the -long-qdec flag and it uses the .long.base file names).

Best, Martin


On Jun 24, 2014, at 5:23 PM, Anna Jonsson <ajonsson09@gmail.com> wrote:

Thank you. I just another question about the fsid groupings for the qdec table for lme. If in the qdec I specify only the fisid (eg nt the longitudinally processed subject with XX.long), and the XX.longs are in a different folder, than how when I do the matlab lme tools does freesurfer know to use the XXX.long scans? This is confusing me.

Thanks for help,.

Regards Anna


On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Anna
I am not a statistician, but I would not control for duration separately, but rather use the time variable for that. 
It does not need to be in years (can be days out months).
Measures closer in time are more correlated than measures further apart. Lme makes use of that information through the time variable.
Best Martin
Best Martin

Sent via my smartphone, please excuse brevity.

-------- Original message --------
From: Anna Jonsson
Date:06/24/2014 11:52 AM (GMT+01:00)
To: Martin Reuter
Cc: Freesurfer support list
Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table

thank you. and one other question; rather than putting years as the time variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut control for time between scans instead?


On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Anna, whenever it says qdec-long the table is in qdec format (with a fsid-base as second column. It would then use the longitudinally processed results, which is what you want , both for lme and 2 stage model.
Best Martin


Sent via my smartphone, please excuse brevity.

-------- Original message --------
From: Anna Jonsson
Date:06/09/2014 3:47 PM (GMT+01:00)
To: Freesurfer support list
Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table

Hi, sorry for more questions, but i have a few. When running the first step of the lme implemented tools, doing the command mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh (assembles your thickness data into a single lh.thickness.mgh file), am I correct that this just needs to be a "normal" cross-sectional qdec table that free surfer subsequently makes into long format by --qdec-long option? so the lnogitudinal qdec table is only used in the two stage modell? This too just uses the cross-sectionally derived scans?  Im confused where the .long runs become used?

thank you and kind wishes


On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Anna,
Fsid is the cross sectionall name without the .long.
Best martin


Sent via my smartphone, please excuse brevity.


-------- Original message --------
From: Anna Jonsson
Date:06/04/2014 7:22 AM (GMT-05:00)
To: Freesurfer support list
Subject: [Freesurfer] free-surfer longitudinal Qdec table

Hi,

I would like to make my freesurfer longitudinal qdec table for the to use in the lme matlab tools. However, does the fsid need to refer to the longitidunally derived subject; eg XXX.long, or the cross-sectionally derived subject, eg XXX. Im not sure based on the specification online.
 Kind Regards

Anna

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---------------------------------
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: 


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