Hi Martin,

Thanks for the help of glm, I also try the QDEC table for the 3 times points of 1 same subject k. k was scanned at Aug-2012, May-2013, and Jul-2013. A little confusion here is should I record the time as which one of these:
 (1) --time years   (2) --time months   (3) --time ages
      0                                 0               25.36
      0.77                            9               26.13
      0.92                            11             26.28
I used these three timing ways and find that the freeview overlay shreshold differ a lot. both the (1) --time years and (3) --time ages can use threshold range as 2, 5 which i think means p<0.01 and p>0.00001? but the (2) --time months fits the threshold only as 0.1, 0.5 (p<0.8 and p>0.3?). The shape of the histogram are all the same in all these three and the area covered are also the same. In the tutorial I see the example use the first timing way, i.e. --time years, which also use the threshold as 2,5.

Another question is when I call the long_stats_slopes command:

long_stats_slopes --qdec long.qdec.table.dat --stats aseg.stats --meas Area_mm2 --do-avg --do-rate --do-pc1 --do-spc --do-stack --time ages --sd ../..

long_stats_slopes --qdec long.qdec.table.dat --stats lh.aparc.stats --meas area --do-avg --do-rate --do-pc1 --do-spc --do-stack --time ages --sd ../..

the flag --meas uses two different but very similar measures for area, and not sure what is the difference there.

Thanks a lot,
Kaiming




On Thu, Jan 30, 2014 at 6:46 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Hi Kaiming,

thickness is not a surface, it is a function defined on a surface. Don't add it as a surface name to the command line.

Best, Martin



On 01/30/2014 11:12 AM, Kaiming Yin wrote:
Dear Martin,

Make sense now. thanks for this. Yes I only have one subject with 3 different time points, what about the longitudinal two stage model (QDEC)? will this work?
and one more question about the glm is when doing the thickness comparison, calling the mri_glmfit command, should I mention: mri_glmfit ... --surf fsaverage lh thickness? or just left it as ... --surf fsaverage lh? I saw the default <surfacename> is 'white'. But when I add this 'thickness' parameter it seems can not work either and reports like:
"
gdfReadHeader: reading rmanova.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 TP1-vs-TP2 0 0.816497
1 TP1-vs-TP3 0 0.816497
Class Means of each Continuous Variable
1 k   0.0000   0.0000 
INFO: gd2mtx_method is doss
Reading source surface /Freesurfer//k/surf/lh.thickness
nquads=5767172,  nvertices=569
ERROR: MRISread: file '/Freesurfer//k/surf/lh.thickness' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!

Invalid argument
"

Thanks for your patience,
Kaiming


On Thu, Jan 30, 2014 at 3:46 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Dear Kaiming,

how many subjects do you have? only 1? You need to have more data to run a glm (your degrees of freedom is 0 , see error message).

Your other question:
you can select any target for running your analysis. But usually people do not select one of the subjects from the study, because that may introduce a processing bias towards that subject (maybe the thickness changes of that subject will drive the results or bias it). That is why fsaverage is recommended.

Best, Martin


On 01/30/2014 06:13 AM, Kaiming Yin wrote:
Dear Martin,

Yes I think so, and I run the mri_glmfit with fsaverage as the subject like:
mri_glmfit --glmdir lh.thickness.rmanova --y lh.thickness.sm05.mgh --fsgd rmanova.fsgd doss --C tp1-vs-tp2.mtx --C tp1-vs-tp3.mtx --C tp2-vs-tp3.mtx --C tp-effect.mtx --C mean.mtx --surf fsaverage lh

it reports:

FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y    /Freesurfer/k/lh.thickness.sm05.mgh
logyflag 0
usedti  0
FSGD rmanova.fsgd
labelmask  /Freesurfer//fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.thickness.rmanova
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.thickness.rmanova
Loading y from /Freesurfer/k/lh.thickness.sm05.mgh
INFO: gd2mtx_method is doss
Saving design matrix to lh.thickness.rmanova/Xg.dat
Normalized matrix condition is 1.73205
Matrix condition is 1.73205
Found 149955 points in label.
Pruning voxels by thr: 0.000000
Found 149955 voxels in mask
Saving mask to lh.thickness.rmanova/mask.mgh
Reshaping mriglm->mask...
search space = 74612.965197
DOF = 0
ERROR: DOF = 0


It seems still something wrong was ignored.


Also if I call the preproc or surf2surf commands with the base subject, i.e. k, instead of fsaverage, will it work? or even better? 

mris_preproc --target k --hemi lh  --meas thickness --out lh.thickness.mgh  --fsgd rmanova.fsgd

mri_surf2surf --s k --hemi lh --fwhm 5  --sval lh.thickness.mgh  --tval lh.thickness.sm05.mgh


Thanks,
Kaiming


On Thu, Jan 30, 2014 at 3:18 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:
Your data was probably mapped to fsaverage when you call the preproc or surf2surf commands? If so you should specify fsaverage as the subject nane.
Best Martin


Sent via my smartphone, please excuse brevity.


-------- Original message --------
From: Kaiming Yin
Date:01/29/2014 9:07 PM (GMT-05:00)
To: FreeSurfer Mailing List
Subject: [Freesurfer] Longitudinal RepeatedMeasuresAnova mri_glmfit "--surf subject hemi"

Dear FreeSurfer guys,

I am using longitudinal processing stream and with the RepeatedMeasuresAnova.

my fsgd file is:

GroupDescriptorFile 1
Title k_longitudinal
Class k
Variables  TP1-vs-TP2 TP1-vs-TP3
Input k_1  k      1                1
Input k_2  k     -1                0 
Input k_3  k      0               -1


contrasts is:

tp1-vs-tp2.mtx  tp1-vs-tp3.mtx  tp2-vs-tp3.mtx  tp-effect.mtx  mean.mtx
0 1 0                0 0 1                0 -1 1             0 1 0              1 0 0
                                                                    0 0 1

I run the mris_preproc and mri_surf2surf commands as the same for left hemi thickness,

but when I run the mri_glmfit command it reports "ERROR: you must use '--surface subject hemi' with surface data". if i add the flag as: 
      mri_glmfit ...(as the same before)... --surface k lh
or                                                       --surface k lh thickness
or                                                       --surface k_1.long.k lh
or                                                       --surface k_1.long.k lh thickness
or                                                       --surface k_1 lh
or                                                       --surface k_1 lh thickness
it still goes wrong and even not make an output folder.

Any problems there?

thanks,
Kaiming 

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-- 
Martin Reuter, Ph.D.
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 


-- 
Martin Reuter, Ph.D.
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