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 <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 >>>>>>> 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>______________________________________________________________________ >>>>>>> >>>>>>> De informatie opgenomen in dit bericht kan vertrouwelijk zijn en >>is >>>>>>> uitsluitend bestemd voor de geadresseerde. Indien u dit bericht >>>>>>> onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken >>en de >>>>>>> afzender direct te informeren door het bericht te retourneren. >>Het >>>>>>> Universitair Medisch Centrum Utrecht is een publiekrechtelijke >>>>>>> rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en >>>>>>> Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer >>van >>>>>>> Koophandel voor Midden-Nederland onder nr. 30244197. >>>>>>> >>>>>>> Denk s.v.p aan het milieu voor u deze e-mail afdrukt. >>>>>>> >>>>>>> >>>>>>> >>______________________________________________________________________ >>>>>>> >>>>>>> This message may contain confidential information and is intended >>>>>>> exclusively for the addressee. If you receive this message >>>>>>> unintentionally, please do not use the contents but notify the >>sender >>>>>>> immediately by return e-mail. University Medical Center Utrecht >>is a >>>>>>> legal person by public law and is registered at the Chamber of >>>>>>> Commerce for Midden-Nederland under no. 30244197. >>>>>>> >>>>>>> Please consider the environment before printing this e-mail. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer at nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>>> >>>> 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 >>you in error >>>> 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
