Hi Sarah.
I cannot comment on 5.1 vs waiting for 5.3.

About the single time point. The reason is not that we need the base. We just want to make sure that that image undergoes the same processing steps as all other images to avoid a processing bias.
Mixed effects models allow inclusion of subjects with single time points so it makes sense to include them to gain power.
Best Martin

Sarah Whittle <swhittle@unimelb.edu.au> wrote:
Hi,

Given the issues discovered with 5.2, we're now wondering whether we should just go back to 5.1 or wait until 5.3 (under a bit of time pressure).

Can I just clarify the how the capability of 5.2 (and 5.3) to run subjects with single time points in longitudinal analysis (by creating an artificial, upright and straight base image) is better than just using the cross-sectional output from single subject data in longitudinal analysis?

Is it because for linear mixed effects models analysis you need a base template for each time point?

Thanks,

Sarah

From: Sarah Whittle
Sent: Friday, 22 March 2013 6:50 AM
To: Martin Reuter
Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Longitudinal analysis of one timepoint

Ok, thank you.

From: Martin Reuter
[mreuter@nmr.mgh.harvard.edu]
Sent: Friday, 22 March 2013 12:36 AM
To: Sarah Whittle
Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you should be able to find out how to split strings and loop over
entries somewhere online. there is lots of documentations and forums
concerned with shell scripting out there.

something like:
read each string
split it at the ','
take the first as base and loop over the rest

I probably would use python for it.

Best, Martin

On 03/21/2013 06:26 AM, Sarah Whittle wrote:
Hi Martin,

Just following up on the below, we're having trouble deciding the best way to run all of the images through the longitudinal stream.

We have a text
file (subjects.txt), specifying the base, and time point ID's for each participant. Base comes first, and follow-up images are the base ID_timepoint (e,g., _1, _2, _3). An example for just a few subjects:

110,110_1,110_2,110_3
2403,2403_1,2403_3
2928,2928_1,2928_2,2928_3
2932,2932_1,2932_2
3026,3026_1
3335,3335_1,3335_2,3335_3
352,352_1,352_2,352_3
5115,5115_2,5115_3

Then we run a script to allocate these files to base, time point 1, time point 2, etc.:

SUBJLIST=`cat subjecs..txt`
for SUBJ in $SUBJLIST

do

TEMPID=`echo $SUBJ|awk '{print $1}' FS=","`
TP1=`echo $SUBJ|awk '{print $2}' FS=","`
TP2=`echo $SUBJ|awk '{print $3}' FS=","`
TP3=`echo $SUBJ|awk '{print $4}' FS=","`

-v SUBJ_TEMPID=$TEMPID,SUBJ_TP1=$TP1,SUBJ_TP2=$TP2,SUBJ_TP3=$TP3

done

recon-all -base $SUBJ_TEMPID -tp $SUBJ_TP1 -tp $SUBJ_TP2 -tp $SUBJ_TP3 -all -nuintensitycor-3T

recon-all -long $SUBJ_TP1 $SUBJ_TEMPID -all -nuintensitycor-3T

recon-all -long $SUBJ_TP2 $SUBJ_TEMPID -all -nuintensitycor-3T"

recon-all -long $SUBJ_TP3 $SUBJ_TEMPID -all -nuintensitycor-3T"

This falls over because there's not base + three images in each row of the subject list. I assume we'll have to make some kind of IF THEN statements to run these commands separately or individuals that have had 1, 2 or 3 scans?

Is there a simpler way of doing this though?? I feel like we're making things more complicated than they need to be!

Thanks,

Sarah


From: Martin Reuter [mreuter@nmr.mgh.harvard.edu]
Sent: Thursday, 7 March 2013 10:22 AM
To: Sarah Whittle
Cc: Nick Schmansky; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sarah,

you deal with the time during post-processing (statistical analysis).

Yes, you have differently many rows for each subject.
Years could be time from baseline, or time from start of study (e.g.
start of drug treatment). It may be the same, but if some subjects are
missing the baseline scan in a drug study it may be better to use the
start of the drug instead of the first scan.

Mixed effects model is the way to go.

Best, Martin

On 03/06/2013 05:17 PM, Sarah Whittle wrote:
Thanks Martin and Nick,

We have a number of subjects with single time points too, so I think 5.2 is the best way to go.

Is there a way to specify which subjects have data at what time points. For example, if one subject has data at Time 1 and Time 3, and another has data at Time 2 and Time 3, can this info be fed into freesurfer somehow? Or, do you just deal with this during post
processing by specifying the years between scans (which would be different for these two cases)?

Also, when creating the longitudinal .dat file, I assume you would have a different number of rows for each subject depending on how many time points they have, and the value you would enter for 'years' would just be years since baseline?

Finally, can you use QDEC with three time points? Or would linear mixed effects models be the way to go?

Thanks,

Sarah

From: Martin Reuter [mreuter@nmr.mgh.harvard.edu]
Sent: Thursday, 7 March 2013 5:41 AM
To: Nick Schmansky
Cc: Sarah Whittle; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal analysis of one timepoint

Hi Sara,

yes, should work, just make sure that all cross are 5.1  (and not mixed)
to remain consistent.
By the way 5.1 can process differently many time points for each
subject. Just not subjects with a
single time point only. To include
those you'd need 5.2


Best, Martin

On 03/06/2013 01:32 PM, Nick Schmansky wrote:
Sarah,

I'm cc'ing martin reuter on this, but yes, you should be able to use
your cross-sectionally processed scans from v5.1 in a longitudinal
analysis using v5.2.

Nick


On Wed, 2013-03-06 at 05:46 +0000, Sarah Whittle wrote:
Hi,

RE the below post, we have longitudinal data from three time points,
but a number of participants have scans for only one or two time
points. We've done all of the cross-sectional analysis (including a
lot of manual editing) and are ready to run everything through the
longitudinal stream. Our
plan was to run sets of analyses for all of
the possible combinations of longitudinal scans.

e.g., Time 1, Time 2, Time 3;
Time 1, Time 2;
Time 1, Time 3;
Time 2, Time 3

Obviously the new feature in version 5.2 (i.e., being able to run all
images together, regardless of whether some time points are missing
for some people) would be MUCH better. Is this possible to do using
our 5.1 cross-sectionally processed images? Given the time we've put
into manual editing, we really wouldn't want to have to run everything
again through 5.2.

Thanks,

Sarah

....
Hi Henk-Jan,

to avoid bias between subjects with single time points and others, we
run them through the same steps. This way it is possible to include them
into the statistical analysis. (For this an artificial base is created
with the head in an upright and straight position).

This feature will be
available in 5.2. Nothing with respect to
processing commands changes, you will simply pass only a single time
point to the -base and then run it with -long.
Nice and transparent :-).

Anyway, you probably should wait till 5.2. There is several programs
that changed for this to work. Also the current recon-all contains many
changes not related to this. If you absolutely cannot wait, let me know
and I'll take a look at how difficult it is to go back and adjust 5.1.

Best, Martin



On Tue, 2012-12-04 at 17:06 +0000, Westeneng, H.J. wrote:
Hi Freesurfer experts,



This week a read the article of Bernal-Rusiel et al. titled
“Statistical analysis of longitudinal neuroimage data with Linear
Mixed Effects models”. In this article you described the submission of
single time-point scans to the longitudinal pipeline of Freesurfer.
I’m very interested in how to do this. Your help will be appreciated.



Thanks in advance,



Henk-Jan





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Dr. Martin Reuter
Assistant in Neuroscience - Massachusetts
General Hospital
Instructor in Neurology   - Harvard Medical School
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A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
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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:
mreuter@nmr.mgh.harvard.edu
reuter@mit.edu
Web  : http://reuter.mit.edu






--
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:
mreuter@nmr.mgh.harvard.edu
reuter@mit.edu
Web  : http://reuter.mit.edu






--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.