Sarah,
Hi, to help you decide, since I dont know what your study entails or the timeline, this is some info:
- bug in 5.2 affects just white and pial surface placement, so thickness and area data will be off. surface registration, and its off-shoot data, like aparc labels and inter-subject surface registration, are unaffected by the bug.
- we're doing everything we can to get the new release out in less than two weeks. but by monday, there should be a beta of each platform (centos6_x86_64 already there) posted here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-BETA/
if the extensive testing passes, then the beta becomes the release (although in between we will be updating freeview with new features and a speed increase in scrolling).
Hope this helps, sorry for the interruption!
Nick
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 > âStatistical analysis of longitudinal neuroimage data with Linear > Mixed Effects modelsâ. In this article you described the
submission of
> single time-point scans to the longitudinal pipeline of
Freesurfer.
> Iâm 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 MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
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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.