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 <swhit...@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 [mreu...@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 [mreu...@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 [mreu...@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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>______________________________________________________________________
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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:
>>> mreu...@nmr.mgh.harvard.edu
>>> reu...@mit.edu
>>> Web : http://reuter.mit.edu
>>>
>>>
>>>
>>> The information in this e-mail is intended only for the person to
>whom it is
>>> addressed. If you believe this e-mail was sent to you in error and
>the e-mail
>>> contains patient information, please contact the Partners Compliance
>HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to
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>>> but does not contain patient information, please contact the sender
>and properly
>>> dispose of the e-mail.
>>>
>>>
>>>
>> --
>> 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
>>
>>
>>
>>
>>
>
>--
>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
--
Sent from my Android phone with K-9 Mail. Please excuse my brevity._______________________________________________
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