Hi Freesurfer team,
I am sorry for writing again. Would you please be able to answer my last
question?
Best Regards,
Katarina Trojacanec, M.Sc.
Teaching and research assistant
Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Katarina Trojacanec
<katarina.trojaca...@finki.ukim.mk>
Sent: Friday, February 3, 2017 9:02 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fw: Analysis of rates or percent changes
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Hi Martin,
Apologies for multiple e-mails, but I got a message that something might be
wrong with the previous e-mail, so I forward it again.
Please find below my previous question.
Regards, Katarina
Katarina Trojacanec, M.Sc.
Teaching and research assistant
Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
________________________________
From: Katarina Trojacanec
Sent: Thursday, February 2, 2017 2:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Analysis of rates or percent changes
Hi Martin,
I dropped --generic-time flag as you suggested in the previous e-mail and run
the long_stats_slopes command again like this:
long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1
--do-spc --time years --stack-rate
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt
However, I got exactly the same results for stacked rate pc1/fit, spc (the
files long_AD_NL_TP1_2_3_4_m.aseg-*.stack.txt) as in the case with the
--generic-time flag. Is this reasonable?
As I read and understood, the --generic-time flag assumes that time difference
between the time points is 1, which is not true in my case (the time difference
between TP1 and TP2 is around six months, and between TP2 and TP3, as well as
TP3 and TP4 is one year). This indicates that there should be some difference
in the result.
Am I doing something wrong or misunderstood anything, or maybe there are some
temporary files from the first running of the command that are used also in the
second one (without --generic-time flag)?
Best, Katarina
Katarina Trojacanec, M.Sc.
Teaching and research assistant
Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
________________________________
From: Katarina Trojacanec
Sent: Monday, September 12, 2016 10:01:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Analysis of rates or percent changes
Hi Martin,
Thanks a lot.
Best, Katarina
Katarina Trojacanec, M.Sc.
Teaching and research assistant
Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Martin Reuter
<mreu...@nmr.mgh.harvard.edu>
Sent: Monday, September 12, 2016 7:58:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Analysis of rates or percent changes
Hi Katarina,
different time spacing is OK (not optimal, but OK). This 2-stage procedure
first fits a line in each subject, independent on how many time points the
subject has. Of course a linear fit from 4 time points will be more reliable
than one from just 2 time points. This is not taken into consideration and
therefore we usually recommend the Linear Mixed Effects modeling (where it is
considered in the model). If most of your subjects have 4 time points and the
spacing is similar (across subjects) you should be fine.
Other things I noticed:
- you should drop the --generic-time flag. I probably should change the help
text to be more specific, but what it does it assigns a time of 1 2 3 4 to the
time points (this is if you do repeated measures and there is no real time). So
don't pass it.
- you can drop some of the --do... flags. Probably you are interested in the
rate and one of the pct change flags. The average is just the average thickness
(across time) for each subject. Not sure you want to analyze that. The
--do-stack is a subject-specific stack of the time points, usually only used
for debugging.
- the -stack-avg is not needed unless you want to analyze average thickness for
each subject, rather you may want to create a stack for the rate or the pc1 or
whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or
whatever you use).
Best, Martin
On 09/12/2016 12:40 PM, Katarina Trojacanec wrote:
Hi,
I have a question about the analysis of rates or percent changes.
I use data with available scans at baseline (TP1) and the 6-month (TP2),
12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of
some of the data in the appropriate qdec table is given below:
fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr
MMSE_TotScr FAQ_TotScr visit1_2_3_4
ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc
ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06
ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12
ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24
ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc
ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06
ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12
ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24
The base is constructed using all four time points. The time variable is given
in years. I am using long_stats_slopes for aseg.stats as follows:
long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit
--do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg
./qdec/long_AD_NL_TP1_2_3_4
(similarly for ?h.aparc.stats)
Having in mind that TP1 and TP2, as well as TP2 and TP3 are separated
approximately 6 months and TP3 and TP4 are separated approximately 12 months,
are the annualized percent change or atrophy rates using this scenario
reasonable (statistically?). Is it maybe more reasonable to apply the same
scenario using three time points (for example TP1, TP3 and TP4 from the
previous example and the template based only on these time points with the same
approximate difference between all of them of 12 months, or TP1, TP2 and TP3
from the previous example and the template based only on these time points with
the same approximate difference between all of them of 6 months)?
Best Regards,
Katarina Trojacanec, M.Sc.
Teaching and research assistant
Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia
_______________________________________________
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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