[Freesurfer] Cuda 8, Centos 7, FreeSurfer 6

[neuroimage analyst]

Hello.

We recently installed Centos 7 with cuda 8 and tried to build the
FreeSurfer 6.0 using the wiki instructions but were unsuccessful to do so.
Has anyone successfully built FreeSurfer 6 on Cuda 8 (Centos 7) and willing
to share the binaries with us or share their steps with us? We will greatly
appreciate that.

Thanks

Regards

V
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[Freesurfer] 3D conversion of Desikan-Killiany Atlas

[Kwangyeol Baek]

Hi, all.

Is there a 3D MNeI space version of Desikan-Killiany Atlas? (e.g. a sample
3D parcellation using MNI152 brain)
Please let me know where I can find it or how I can get it in using
Freesurfer.

Thank you very much!



Sincerely,
Kwangyeol Baek
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[Freesurfer] Grey matter misclassified as white matter

[Maryam Kouchakidivkolaei]

Dear experts,
I am using freesurfer V5.3. I am trying to fix some error in freesurfer outputs.
The issue is that grey matter misclassified as white matter in temporal lobe 
(lh). I tried to edit Wm.mgz and re-run with -autorecon2-wm, but it did not 
work.
Looking at the brainmask.mgz, white matter boundary includes area with 
intensity normalization less than 60-50. Any suggestion?

I appreciate any help,
Maryam

 
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[Freesurfer] help

[Aditya P Singh]

> On May 18, 2017, at 11:29 AM, freesurfer-requ...@nmr.mgh.harvard.edu wrote:
> 
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> 
> Today's Topics:
> 
>   1. Re: Freesurfer white matter outer edge to volume (Gamaliz)
>   2. Re: Freesurfer white matter outer edge to volume (Gamaliz)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 18 May 2017 12:16:46 -0400
> From: Gamaliz 
> Subject: Re: [Freesurfer] Freesurfer white matter outer edge to volume
> To: Freesurfer support list 
> Message-ID:
>

[Freesurfer] Questions about FreeSurfer

[Alliey-Rodriguez, Ney [PSY]]

Dear FreeSurfers,

I received FreeSurfer structural MRI brain data to analyze, but there are some 
questions about specific FreeSurfer variables that I could not find answered on 
your wiki or in the mail archive:

1.- "Non-White Matter hypointensities":
1.a - Are these the same thing as "gray matter hyperintensities"?
1.b - Are these scanned from the whole brain gray matter or only sub-cortical?
1.c - Are these also considered traumatic markers? (literature would be 
appreciated)

2.- 5th Ventricle:  is this variable encompassing the Cavum Septum Pellucidum 
only, or does it also include the Cavum Vergae?

3.- Are there published analysis about FreeSurfer accuracy for CSF volumes?


Thanks and will look forward,


Ney


__
Ney Alliey-Rodriguez, M.D.
Research Assistant Professor - Gershon Lab
Department of Psychiatry and Behavioral Neuroscience
University of Chicago
5841 S Maryland Ave Room M344 (MC3077)
Chicago, IL 60637
Phone: 1(773)702-0599


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Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

[Bruce Fischl]

Hi Karteek

the aseg isn't surface based, sorry, but the watershed that we use to do 
the skull stripping is and does use smoothness constraints. If it is 
leaving dura around try using mri_gcut.

cheers
Bruce

On Thu, 18 May 2017, Karteek Popuri 
wrote:

> Hi,
> My goal is to use the best possible skull-stripped version of the input MRI. 
> Is brainmask.mgz the one? or I was wondering if anyone has tried improving 
> the brainmask.mgz further by masking it out using the aseg.mgz. Will that 
> help with regards to getting rid of the dura in the brainmask.mgz. My 
> intuition is because the generation of aseg.mgz includes a surface-based 
> algorithm, the smoothing constraints of the surface evolution should minimize 
> the "leakage" of the GM surface into the dura, hence the aseg might have some 
> dura but not as much as the brainmask. Will be thankful for any 
> suggestions/comments.
> Karteek
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Re: [Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

[Douglas N Greve]

You can use the aseg.mgz (in v6) or aparc+aseg.mgz in any version.


On 05/18/2017 10:42 AM, Karteek Popuri wrote:
> Hi,
> My goal is to use the best possible skull-stripped version of the input MRI. 
> Is brainmask.mgz the one? or I was wondering if anyone has tried improving 
> the brainmask.mgz further by masking it out using the aseg.mgz. Will that 
> help with regards to getting rid of the dura in the brainmask.mgz. My 
> intuition is because the generation of aseg.mgz includes a surface-based 
> algorithm, the smoothing constraints of the surface evolution should minimize 
> the "leakage" of the GM surface into the dura, hence the aseg might have some 
> dura but not as much as the brainmask. Will be thankful for any 
> suggestions/comments.
> Karteek
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gr...@nmr.mgh.harvard.edu
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[Freesurfer] Improving the brainmask.mgz using aseg.mgz for getting rid of dura

[Karteek Popuri]

Hi,
My goal is to use the best possible skull-stripped version of the input MRI. Is 
brainmask.mgz the one? or I was wondering if anyone has tried improving the 
brainmask.mgz further by masking it out using the aseg.mgz. Will that help with 
regards to getting rid of the dura in the brainmask.mgz. My intuition is 
because the generation of aseg.mgz includes a surface-based algorithm, the 
smoothing constraints of the surface evolution should minimize the "leakage" of 
the GM surface into the dura, hence the aseg might have some dura but not as 
much as the brainmask. Will be thankful for any suggestions/comments.
Karteek
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Re: [Freesurfer] mri_mcsim for individual subjects and references {Disarmed}

[Douglas N Greve]

I don't know of a tool that would do it. I could imagine measuring the 
spatial autocorrelation function, then running the MC simulation using 
that instead of a gaussian (AFNI added this, but it only runs in the 
volume). Getting a particular ACF on the surface would be hard.


On 05/16/2017 08:00 PM, Kevin Aquino wrote:
> Hi Doug,
>
> Thanks for that! with regards to your last point
>
> Unfortunately, it does not help much. Much was made of the bug
> that Eklund, et al, found in the alphasim program (the AFNI mc
> simulator), but even after fixing it, the volume-based analyses
> still had very high false positive rates. This is because the
> problem is that the smoothness in the data is not Gaussian, so any
> method that assumes Gaussianity will be inaccurate.
>
>
> From what I read, the MC simulations on the surface uses this Gaussian 
> assumption. Do you have any ideas (or something in the works) on how 
> to handle these issues on a single subject level? - since the 
> permutation test won't be applicable.
>
>
> Cheers,
>
>
> *Dr Kevin Aquino*
> Research fellow,
> Sir Peter Mansfield Magnetic Resonance Center, The University of 
> Nottingham.
>
> Honorary Research Fellow
> School of Physics, Faculty of Science, University of Sydney
>
> *E* kevin.aqu...@nottingham.ac.uk 
> , aqu...@physics.usyd.edu.au 
>  | *W* *MailScanner has detected a 
> possible fraud attempt from "www.physics.usyd.edu.au" claiming to be* 
> https://kevinaquino.github.io 
>
> --
>
> The brain is a wonderful organ. It starts working the moment you get 
> up and does not stop until you get into the office.
> -
> Robert Frost
>
> CRICOS 00026A
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>
> On Wed, May 17, 2017 at 1:18 AM, Douglas Greve 
> > wrote:
>
>
>
> On 5/15/17 10:34 PM, Kevin Aquino wrote:
>> Hi all,
>>
>> First of all, Freesurfer V6 is working like a dream, my 0.7 mm
>> segmentations are running really well and in comparisons to
>> hi-resrecon in 5.3 and early beta, I'm having to do fewer manual
>> corrections!
>>
>>
>> Now for my questions,
>>
>> 1. I'm running mri_mcsim in order to correct for multiple
>> comparisons via the FS-FAST stream. I'm wondering how many
>> iterations are advised, and how can one check for convergence in
>> an automatic fashion.
>>
>> I've run the simulations with 1000 and 10,000 iterations on a 1mm
>> segmentation with the FWHM simulations at 8mm. (i.e.
>> using mri_mcsim --o . --base mc-z --save-iter  --surf subject
>> lh/rh --nreps 1 --fwhm 8) and I can't see many differences
>> between the two when correcting for multiple comparisons (i.e.
>> using cluster-sess -analysis  myanalysis -thresh 3 -cwp .05 -s
>> SESSION -sign pos).
> For the tables hat we distribute I ran it to 10,000, but there
> will probably not be much difference with 1000. If you look in the
> cluster summary file, it will actually give the 95% confidence
> intervals on the cluster p-values. If the worst is ok, then you
> don't really need to run it more.
>>
>> 2. I'm trying to find some references that detail the simulations
>> and form the corrections, does anyone have advice which list I
>> can read/start off with, as well as some key papers that use it
>> (esp on a single subject level).
> You can check out "Smoothing and cluster thresholding for cortical
> surface-based group analysis of fMRI data" by Don Hagler
>> I really like this approach and It does look to circumvent (I
>> think...) a lot of the problems of cluster-wise corrections
>> described with Eklund et al. (Cluster failure paper).
> Unfortunately, it does not help much. Much was made of the bug
> that Eklund, et al, found in the alphasim program (the AFNI mc
> simulator), but even after fixing it, the volume-based analyses
> still had very high false positive rates. This is because the
> problem is that the smoothness in the data is not Gaussian, so any
> method that assumes Gaussianity will be inaccurate.
> doug
>>
>> Cheers,
>>
>>
>> *Dr Kevin Aquino*
>> Research fellow,
>> Sir Peter Mansfield Magnetic Resonance Center, The University of
>> Nottingham.
>>
>> Honorary Research Fellow
>> School of Physics, Faculty of Science, University of Sydney
>>
>> *E* kevin.aqu...@nottingham.ac.uk
>> ,
>> aqu...@physics.usyd.edu.au  |
>> *W* 

Re: [Freesurfer] Freesurfer white matter outer edge to volume

[Douglas N Greve]

how were you examining the registration? When I run the command, the 
rh.white.mgz aligns perfectly with the T1.mgz


On 05/16/2017 05:38 PM, Gamaliz wrote:
> Douglas,
>
> The previous message had an images attached that seemed to be too big. 
> it was "bounced" automatically. I guess too many images were attached.
>
> I ran the command for the rh.white and lh.white and the image is not 
> perfectly registered. I tried a lot of things, but nothing worked. I 
> ended up using the idea from Bruce. I Binarized the aseg+aparc file, 
> extracting the wm regions, eroded, and subtracted. That gave me a 
> surface as a volumen. This also can be done with only the images (no 
> need to extract the whole freesurfer output)  The image from 
> mri_surf2vol had better quality, but I couldn't get it to register. If 
> by any chance someone figures this registration problem out, I will 
> use certainly use it.
>
> Thanks for all your help.
>
> Gabriel
>
>
> previous message:
>
> Douglas,
>
> I extracted the whole directory and ran:
>
> mri_surf2vol --mkmask --surf white --hemi rh --o rh.white.mgz 
> --template ../subjects/subject/mri/T1.mgz --sd ../subjects --subject 
> subject --identity subject
> gdiagno = -1
> Using identity matrix for registration
> Overriding reg subject subject with subject
> Qa2v: SurfXYZ to VolCRS: --
> -1.000   0.000   0.000   128.000;
>  0.000   0.000  -1.000   128.000;
>  0.000   1.000   0.000   128.000;
>  0.000   0.000   0.000   1.000;
> --
> subjects dir   ../subjects
> hemi rh
> mksurfmask 1
> projfrac 0
> outvol path  rh.white.mgz
> template path  ../subjects/subject/mri/T1.mgz
> --- Anat2Vol Registration (TkReg)
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> -
> height = 256
>  width = 256
>  depth = 256
>  xsize = 1.00
>  ysize = 1.00
>  zsize = 1.00
>   cdc  = -1.00 0.00 0.00
>   rdc  = 0.00 0.00 -1.00
> sdc  = 0.00 1.00 0.00
> xyz0 = 3.373505 20.515587 -6.721008
> Gdiag_no -1
> Reading surface ../subjects/subject/surf/rh.white
> Done reading source surface
> surf nframes = 1
> INFO: mapping vertices to closest voxel
> INFO: resampling surface to volume
> INFO: sampled 84160 voxels in the volume
> INFO: writing output volume to rh.white.mgz
> done
>
> I did both hemispheres, they are not registered. I tried using as 
> template the T1.mgz, and T1 converted to nifti. I also tried output as 
> mgz and then mri_convert to nifti, the also output to nifti. I always 
> obtained the same volumes, and they were always unregistered.
>
>
> both hemispheres, they are not registered. I tried using as
> template the T1.mgz, and T1 converted to nifti. I also tried
> output as mgz and then mri_convert to nifti, the also output to
> nifti.
>
> Inline image 2
>
>
>
>
>
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-- 
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] manuel edits

[Bruce Fischl]

1. No, we usually do wm edits/control points first as this can fix the 
pial problems.


2. You can put control points in any voxel that is clearly WM with no other
   tissue class partial-volumed into it. The intensity threshold depends on
   the MR sequence, where you are in the brain and possible
   pathology/developmental/aging effects


cheers
Bruce

On Thu, 18 May 2017, Caroline Beelen wrote:



Dear FS team,

 

I have two questions regarding manuel editing. We were looking at
inter-rater reliability, but noticed it was not too high... However, during
editing we used different criteria. Therefore I would like to ask:

 

1.  Does the order of pial correction, topological deficit, wm
corrections and control points editing matters? You seem to assume on your
website for instance that pial corrections would come before wm
corrections/control points, but is this necessarily the case?

 

2.  When the wm intensity value is below 110, voxel inclusions might be
needed. On the website is written: “when you feel like there is wm
underneath you can add control points (…)”. How to make a decision on this
matter: based on sight or on wm intensity values?

For instance, often the WM values are either 0 or 80 or above... Would it be
good to assume that wm intensity values above 80 are actually wm, regardless
of how it visually would look like? Likewise, would it be good to assume
that areas where it says the wm intensity value is 0, that these areas are
actually not wm, regardless of whether it might look like wm?  So,
basically, it is correct to make your decision only based on wm intensity
values?

 

Thank you for your reply.

 

Kind regards,

 

Caroline Beelen


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Re: [Freesurfer] Mean gray-white contrast for each ROI

[Douglas N Greve]

You will want the "Mean" column. The value is

  100*(W-G)
   GWC = -
  0.5*(W+G)

The area is the surface area of the label. The "SNR" is the spatial mean 
gwc divided by the spatial stddev gwc, probably not very useful



On 05/17/2017 01:43 PM, Yaakub, Siti Nurbaya wrote:
> Hi,
>
> I read from a previous post that the "{lh,rh}.w-g.pct.stats files in 
> $SUBJECTS_DIR/subject/stats … will have the mean gray-white contrast 
> for each ROI in the aparc."
>
> I've looked at the lh.w-g.pct.stats file and am not sure which values 
> I should be looking at if I am interested in the ratio of grey to 
> white matter averaged over each of the ROIs? What are the area in mm2 
> and the SNR in this w-g context?
>
> Thank you,
> Siti
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Question of longitudinal processing

[jahanvi patel]

Hi Martin,

Thanks a lot.
So it is uncorrected. Can one use the following cmd to do multiple
comparison correction?

mri_glmfit-sim \
  --glmdir lh.testretest.thickness-pc1.fwhm15  \
  --cache 4 neg \
  --cwp  0.05\
  --2spaces

I tried to run above cmd, it shows

ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
done

Not sure if there is a bug or if my input is wrong.

Any suggestions is appreciated!

Best,
Jahanvi

On Thu, May 18, 2017 at 9:46 AM, Martin Reuter 
wrote:

> Hi Jahanvi,
>
> there should be a way to display the bar, but I don’t know how (others
> will know)!
>
> sig is not FDR corrected.
>
> Best, Martin
>
> On 18 May 2017, at 08:56, jahanvi patel  wrote:
>
> Hi Martin,
>
> Thanks a lot for the reply. Is there a way to display the bar in effect
> size?
> And is this sig.mgh already statistically corrected? (FDR?)
>
> Best,
> Jahanvi
>
> On Thu, May 18, 2017 at 1:55 AM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Jahanvi,
>>
>> I think red is positive (some people invert the colors, then
>> red=hot=dangerous ). But I think default is blue negative, red positive, so
>> there is an average increase in thickness. You should also look at the
>> effect size (gamma).
>> The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.1
>>
>> Best, Martin
>>
>> On 17 May 2017, at 22:17, jahanvi patel 
>> wrote:
>>
>> Hi Martin,
>>
>> Thanks a lot. It had worked nicely.
>> I got one question about this following cmd
>>
>> tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw
>> hm15/osgm/sig.mgh
>>
>> I got a red to yellow sig.mgh, does it mean I got a increased percent
>> thickness change (pc1)? and the color bar showing 2 to 5 means?
>>
>> Best,
>> Jahanvi
>>
>>
>>
>> On Sun, May 14, 2017 at 10:11 PM, Martin Reuter <
>> mreu...@nmr.mgh.harvard.edu> wrote:
>>
>>> Hi Jahanvi,
>>>
>>> 1. yes, you need to create this table to then perform the stats
>>> 2. no, the format is as I described it below
>>> fsidfsid-base
>>> tp1_subA  templatesubA
>>> tp2_subA  templatesubA
>>> tp1_subB  templatesubB
>>> tp2_subB  templatesubB
>>>
>>> this is assuming that you called your base templatesubA and templatesubB
>>> for the two subjects. It will automatically look in the
>>> tp1_subA.long.templatesubA etc. directories.
>>>
>>> Best, Martin
>>>
>>> On 12 May 2017, at 16:55, jahanvi patel 
>>> wrote:
>>>
>>>
>>> Hi Martin,
>>>
>>> Do you mean by creating this long.testretest.qdec file, one can then
>>> perform the stats for the longitudinal2StageModel?
>>>
>>> So for a 2 timepoints analysis, eg. TP1 & TP2.
>>>  the long.testretest.qdec will be looking like this  ?
>>>
>>>
>>> fsid fsid-base
>>>
>>> tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA
>>> tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB
>>> tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC
>>>
>>> .
>>> .
>>> .
>>>
>>>
>>> Thanks,
>>>
>>> Jahanvi
>>>
>>>
>>>
>>> tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw
>>> hm15/osgm/sig.mgh
>>>
>>>
>>> Hi Jahanvi,

 long.testretest.qdec is a qdec table in the longitudional format (with
 the fsid-base as the second column).

 For test-retest (e.g. same session with subject removal), you usually
 don't need a time column, that is why --generic-time is specified. the qdec
 table would just look like

 fsid fsid-base

 me me_test

 me me_retest

 you you_test

 you you_retest

 ...


 Best, Martin


 On 05/08/2017 04:10 PM, jahanvi patel wrote:
 Hello list,

 I have a simple question about the LongitudinalTwoStageModel tutorials
 on freesurfer website.

 It is from this link
 https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel


 long_mris_slopes --qdec long.testretest.qdec \
   --meas thickness \
   --hemi lh \
   --sd $SUBJECTS_DIR \
   --do-pc1 --do-label \
   --generic-time \
   --fwhm 15 \
   --qcache fsaverage \
   --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \
   --isec-labels lh.testretest.fsaverage.cortex.label

 My question is, what is the content of  long.testretest.qdec ?
 I understood till 1st stage was done, we got only one file which is
 long.qdec.table.dat.

 Could anyone help to clarify my question?

 Thanks a lot
 Jahanvi




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 Freesurfer@nmr.mgh.harvard.edu
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>>>
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>>> 

[Freesurfer] manuel edits

[Caroline Beelen]

Dear FS team,

I have two questions regarding manuel editing. We were looking at inter-rater 
reliability, but noticed it was not too high... However, during editing we used 
different criteria. Therefore I would like to ask:



1.  Does the order of pial correction, topological deficit, wm corrections 
and control points editing matters? You seem to assume on your website for 
instance that pial corrections would come before wm corrections/control points, 
but is this necessarily the case?


2.  When the wm intensity value is below 110, voxel inclusions might be 
needed. On the website is written: "when you feel like there is wm underneath 
you can add control points (...)". How to make a decision on this matter: based 
on sight or on wm intensity values?
For instance, often the WM values are either 0 or 80 or above... Would it be 
good to assume that wm intensity values above 80 are actually wm, regardless of 
how it visually would look like? Likewise, would it be good to assume that 
areas where it says the wm intensity value is 0, that these areas are actually 
not wm, regardless of whether it might look like wm?  So, basically, it is 
correct to make your decision only based on wm intensity values?

Thank you for your reply.

Kind regards,

Caroline Beelen
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[Freesurfer] Postdoctoral position in psychosis studies - Oslo, Norway

[Tiril Pedersen Gurholt]

Dear All,

At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre 
of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo 
University Hospital and Diakonhjemmet Hospital, Norway, there is a position 
available as a postdoctoral student with employment at Diakonhjemmet hospital. 
The research area is psychiatric neuroimaging with focus on obstetric 
complications and the analysis of structural and functional, DTI and ASL MR 
imaging datasets with regard to developmental trajectories and genetic, 
environmental and phenotypic variation. Applicants should have a doctoral 
degree (PhD) in psychiatry or a related medical discipline, neuroimaging, 
computer science, bioinformatics, psychology, or equivalent. Applicants who 
have handed in their dissertation for evaluation are also encouraged to apply, 
caveat the dissertation is approved. Application deadline is June 15th, 2017. 
For further information and to submit an application please see the website of 
Diakonhjemmet Hospital, Oslo, Norway:
https://www.webcruiter.no/WcMain/advertviewpublic.aspx?oppdragsnr=3420277973_id=201412_source_id=0_position_site_header=0_id=NB-NO

Best regards,

Tiril Gurholt
---
Tiril Gurholt
Postdoctoral Fellow
Psychosis Research Centre, NORMENT
Institute of Clinical Medicine, University of Oslo, Norway

http://www.med.uio.no/norment/


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Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

[Matthieu Vanhoutte]

Hi Martin,

Thank you this helps !

Please find last question below inline.

Best,
Matthieu

Le 18 mai 2017 10:33 AM, "Martin Reuter"  a
écrit :

Hi Matthieu,


1) you would put a column of score and a column of score X time.  The first
allows you to test if the intercept changes based on scores (e.g. if
hippocampal volume is affected by the score, controlling for whatever else
you included, e.g. age and gender etc) and the second interaction allows
you to test if the the slopes are affected by score (so if atrophy rates
are different at different score levels).

2) if your effect for that interaction column is positive, there is a
positive correlation (higher score, slower atrophy (or even brain growth),
and lower score with faster atrophy - this is what you would expect) if
there is a negative effect, it would mean the opposite.

How do you deduce this from combination of atrophy, score and time ?
I know that positive leads to positive correlation and when group X time is
negative means that cortical thickness decreases with time.
However I can't manage to understand relation between cortical thickness
and score X time. Could you explain me ?

Best, Martin


On 05/17/2017 11:12 PM, Matthieu Vanhoutte wrote:

Hi Martin,

I will read up on interpretation of time varying covariates.

If initially I use score as variable fixed across time, and define a
variable for 'score x time' interaction:
1) Would putting only 1 to 'score x time' column (for contrast) test for
progression of correlation patterns between atrophy and score ?
2) How to interpret this according to sign  of contrast (knowing that
decrease in score means worse performance) ?

Many thanks for your time and lights !

Best,
Matthieu

Le 17 mai 2017 1:46 PM, "Martin Reuter"  a
écrit :

Hi Matthieu,

replacing time by score is very different from adding score as a covariate.
Often scores are crude and often they are constant in controls (always full
score), and only vary slightly in diseased. In those cases it may not be
good to use score as a time variable.

I would either add avg. score as a variable (fixed across time - would
probably do this for intial testing anyway) or score as time-varying
covariate, but would read up on how to interpret results in the presence of
time-varying-covariates. I am not a statistician.
Best, Martin


On 05/16/2017 08:09 PM, Matthieu Vanhoutte wrote:

Hi Martin,

Thank you for this detailed answer.

Are replacing time by score or include score as time-varying covariate
leading to the same result because of looking at the same effect ?

My willing would be to find patterns of atrophy rate/progression correlated
with cognitive score. In context of AD which method would be the best for
you ?

Best,
Matthieu


Le 16 mai 2017 11:17 AM, "Martin Reuter"  a
écrit :

Hi Matthieu,

one option is to replace time with score in the model. That should be
straight forward.

The other option is to include score as a time-varying covariate. If your
score is not varying much across time and you are more interested if the
average score (or baseline score) affects atrophy rates, you can also
include is as a standard (fixed across time) co-variate (such as baseline
age) with a time (and a group  etc) interaction.

Sorry, but I cannot do your design. Ultimately the model is the research
question that you are asking and it is important that this is done
correctly. Maybe there is a local biostats person that you can talk to?

Best, Martin



On 05/15/2017 08:20 PM, Matthieu Vanhoutte wrote:

Hi Martin,

Thank you. How should this variable be coded ? Should it be as age
covariate where age at baseline is used along all time points of each
subject ?

Could you provide me an example of design matrix, I don't manage to see
what does it look like to.

Best regards,
Matthieu


Le 14 mai 2017 8:08 PM, "Martin Reuter"  a
écrit :

Hi Matthieu,

yes, that is possible. Instead of group, you use a variable for your score
(and interaction etc). Sometimes it may also makes sense to use score
instead of time.

Best, Martin


> On 12 May 2017, at 10:51, Matthieu Vanhoutte 
wrote:
>
> Dear Freesurfer's experts,
>
> I have searched through the mailing list but haven't found any answer to
my question.
>
> Is it possible with LME model to make correlations between for example
cortical thickness surface data and cognition scores along time ? As it is
possible to test for interaction of group X time, is this also in the same
way feasible to test for coognition score X time on cortical thickness ?
>
> Many thanks for your advice !
>
> Best regards,
> Matthieu
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Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

[Martin Reuter]

Hi Matthieu,


1) you would put a column of score and a column of score X time. The 
first allows you to test if the intercept changes based on scores (e.g. 
if hippocampal volume is affected by the score, controlling for whatever 
else you included, e.g. age and gender etc) and the second interaction 
allows you to test if the the slopes are affected by score (so if 
atrophy rates are different at different score levels).


2) if your effect for that interaction column is positive, there is a 
positive correlation (higher score, slower atrophy (or even brain 
growth), and lower score with faster atrophy - this is what you would 
expect) if there is a negative effect, it would mean the opposite.


Best, Martin


On 05/17/2017 11:12 PM, Matthieu Vanhoutte wrote:

Hi Martin,

I will read up on interpretation of time varying covariates.

If initially I use score as variable fixed across time, and define a 
variable for 'score x time' interaction:
1) Would putting only 1 to 'score x time' column (for contrast) test 
for progression of correlation patterns between atrophy and score ?
2) How to interpret this according to sign  of contrast (knowing that 
decrease in score means worse performance) ?


Many thanks for your time and lights !

Best,
Matthieu

Le 17 mai 2017 1:46 PM, "Martin Reuter" > a écrit :


Hi Matthieu,

replacing time by score is very different from adding score as a
covariate. Often scores are crude and often they are constant in
controls (always full score), and only vary slightly in diseased.
In those cases it may not be good to use score as a time variable.

I would either add avg. score as a variable (fixed across time -
would probably do this for intial testing anyway) or score as
time-varying covariate, but would read up on how to interpret
results in the presence of time-varying-covariates. I am not a
statistician.

Best, Martin


On 05/16/2017 08:09 PM, Matthieu Vanhoutte wrote:

Hi Martin,

Thank you for this detailed answer.

Are replacing time by score or include score as time-varying
covariate leading to the same result because of looking at the
same effect ?

My willing would be to find patterns of atrophy rate/progression
correlated with cognitive score. In context of AD which method
would be the best for you ?

Best,
Matthieu


Le 16 mai 2017 11:17 AM, "Martin Reuter"
> a écrit :

Hi Matthieu,

one option is to replace time with score in the model. That
should be straight forward.

The other option is to include score as a time-varying
covariate. If your score is not varying much across time and
you are more interested if the average score (or baseline
score) affects atrophy rates, you can also include is as a
standard (fixed across time) co-variate (such as baseline
age) with a time (and a group  etc) interaction.

Sorry, but I cannot do your design. Ultimately the model is
the research question that you are asking and it is important
that this is done correctly. Maybe there is a local biostats
person that you can talk to?

Best, Martin



On 05/15/2017 08:20 PM, Matthieu Vanhoutte wrote:

Hi Martin,

Thank you. How should this variable be coded ? Should it be
as age covariate where age at baseline is used along all
time points of each subject ?

Could you provide me an example of design matrix, I don't
manage to see what does it look like to.

Best regards,
Matthieu


Le 14 mai 2017 8:08 PM, "Martin Reuter"
> a écrit :

Hi Matthieu,

yes, that is possible. Instead of group, you use a
variable for your score (and interaction etc). Sometimes
it may also makes sense to use score instead of time.

Best, Martin


> On 12 May 2017, at 10:51, Matthieu Vanhoutte
> wrote:
>
> Dear Freesurfer's experts,
>
> I have searched through the mailing list but haven't
found any answer to my question.
>
> Is it possible with LME model to make correlations
between for example cortical thickness surface data and
cognition scores along time ? As it is possible to test
for interaction of group X time, is this also in the
same way feasible to test for coognition score X time on
cortical thickness ?
>
> Many thanks for your advice !
>
> Best regards,
 

Re: [Freesurfer] Question of longitudinal processing

[Martin Reuter]

Hi Jahanvi, 

there should be a way to display the bar, but I don’t know how (others will 
know)!

sig is not FDR corrected. 

Best, Martin

> On 18 May 2017, at 08:56, jahanvi patel  wrote:
> 
> Hi Martin,
> 
> Thanks a lot for the reply. Is there a way to display the bar in effect size?
> And is this sig.mgh already statistically corrected? (FDR?)
> 
> Best,
> Jahanvi
> 
> On Thu, May 18, 2017 at 1:55 AM, Martin Reuter  > wrote:
> Hi Jahanvi, 
> 
> I think red is positive (some people invert the colors, then 
> red=hot=dangerous ). But I think default is blue negative, red positive, so 
> there is an average increase in thickness. You should also look at the effect 
> size (gamma). 
> The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.1
> 
> Best, Martin
> 
>> On 17 May 2017, at 22:17, jahanvi patel > > wrote:
>> 
>> Hi Martin,
>> 
>> Thanks a lot. It had worked nicely.
>> I got one question about this following cmd 
>> 
>> tksurfer fsaverage lh pial -overlay 
>> lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh
>> 
>> I got a red to yellow sig.mgh, does it mean I got a increased percent 
>> thickness change (pc1)? and the color bar showing 2 to 5 means?
>> 
>> Best,
>> Jahanvi
>> 
>> 
>> 
>> On Sun, May 14, 2017 at 10:11 PM, Martin Reuter > > wrote:
>> Hi Jahanvi, 
>> 
>> 1. yes, you need to create this table to then perform the stats
>> 2. no, the format is as I described it below
>> fsidfsid-base
>> tp1_subA  templatesubA
>> tp2_subA  templatesubA
>> tp1_subB  templatesubB
>> tp2_subB  templatesubB
>> 
>> this is assuming that you called your base templatesubA and templatesubB for 
>> the two subjects. It will automatically look in the
>> tp1_subA.long.templatesubA etc. directories. 
>> 
>> Best, Martin
>> 
>>> On 12 May 2017, at 16:55, jahanvi patel >> > wrote:
>>> 
>>> 
>>> Hi Martin,
>>> 
>>> Do you mean by creating this long.testretest.qdec file, one can then 
>>> perform the stats for the longitudinal2StageModel?
>>> 
>>> So for a 2 timepoints analysis, eg. TP1 & TP2.
>>>  the long.testretest.qdec will be looking like this  ?
>>> 
>>> 
>>> fsid fsid-base
>>> 
>>> tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA
>>> tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB
>>> tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC
>>> 
>>> .
>>> .
>>> .
>>> 
>>> 
>>> Thanks,
>>> 
>>> Jahanvi
>>> 
>>> 
>>> 
>>> tksurfer fsaverage lh pial -overlay 
>>> lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh
>>> 
>>> 
>>> Hi Jahanvi,
>>> 
>>> long.testretest.qdec is a qdec table in the longitudional format (with the 
>>> fsid-base as the second column).
>>> 
>>> For test-retest (e.g. same session with subject removal), you usually don't 
>>> need a time column, that is why --generic-time is specified. the qdec table 
>>> would just look like
>>> 
>>> fsid fsid-base
>>> 
>>> me me_test
>>> 
>>> me me_retest
>>> 
>>> you you_test
>>> 
>>> you you_retest
>>> 
>>> ...
>>> 
>>> 
>>> Best, Martin
>>> 
>>> 
>>> On 05/08/2017 04:10 PM, jahanvi patel wrote:
>>> Hello list,
>>> 
>>> I have a simple question about the LongitudinalTwoStageModel tutorials on 
>>> freesurfer website.
>>> 
>>> It is from this link
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel 
>>> 
>>> 
>>> 
>>> long_mris_slopes --qdec long.testretest.qdec \
>>>   --meas thickness \
>>>   --hemi lh \
>>>   --sd $SUBJECTS_DIR \
>>>   --do-pc1 --do-label \
>>>   --generic-time \
>>>   --fwhm 15 \
>>>   --qcache fsaverage \
>>>   --stack-pc1 lh.testretest.thickness-pc1.st 
>>> ack.mgh \
>>>   --isec-labels lh.testretest.fsaverage.cortex.label
>>> 
>>> My question is, what is the content of  long.testretest.qdec ?
>>> I understood till 1st stage was done, we got only one file which is 
>>> long.qdec.table.dat.
>>> 
>>> Could anyone help to clarify my question?
>>> 
>>> Thanks a lot
>>> Jahanvi
>>> 
>>> 
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@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 
>>> 
>> 
>> The information in this e-mail is intended only for 

Re: [Freesurfer] Question of longitudinal processing

[jahanvi patel]

Hi Martin,

Thanks a lot for the reply. Is there a way to display the bar in effect
size?
And is this sig.mgh already statistically corrected? (FDR?)

Best,
Jahanvi

On Thu, May 18, 2017 at 1:55 AM, Martin Reuter 
wrote:

> Hi Jahanvi,
>
> I think red is positive (some people invert the colors, then
> red=hot=dangerous ). But I think default is blue negative, red positive, so
> there is an average increase in thickness. You should also look at the
> effect size (gamma).
> The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.1
>
> Best, Martin
>
> On 17 May 2017, at 22:17, jahanvi patel  wrote:
>
> Hi Martin,
>
> Thanks a lot. It had worked nicely.
> I got one question about this following cmd
>
> tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.
> fwhm15/osgm/sig.mgh
>
> I got a red to yellow sig.mgh, does it mean I got a increased percent
> thickness change (pc1)? and the color bar showing 2 to 5 means?
>
> Best,
> Jahanvi
>
>
>
> On Sun, May 14, 2017 at 10:11 PM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Jahanvi,
>>
>> 1. yes, you need to create this table to then perform the stats
>> 2. no, the format is as I described it below
>> fsidfsid-base
>> tp1_subA  templatesubA
>> tp2_subA  templatesubA
>> tp1_subB  templatesubB
>> tp2_subB  templatesubB
>>
>> this is assuming that you called your base templatesubA and templatesubB
>> for the two subjects. It will automatically look in the
>> tp1_subA.long.templatesubA etc. directories.
>>
>> Best, Martin
>>
>> On 12 May 2017, at 16:55, jahanvi patel 
>> wrote:
>>
>>
>> Hi Martin,
>>
>> Do you mean by creating this long.testretest.qdec file, one can then
>> perform the stats for the longitudinal2StageModel?
>>
>> So for a 2 timepoints analysis, eg. TP1 & TP2.
>>  the long.testretest.qdec will be looking like this  ?
>>
>>
>> fsid fsid-base
>>
>> tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA
>> tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB
>> tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC
>>
>> .
>> .
>> .
>>
>>
>> Thanks,
>>
>> Jahanvi
>>
>>
>>
>> tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw
>> hm15/osgm/sig.mgh
>>
>>
>> Hi Jahanvi,
>>>
>>> long.testretest.qdec is a qdec table in the longitudional format (with
>>> the fsid-base as the second column).
>>>
>>> For test-retest (e.g. same session with subject removal), you usually
>>> don't need a time column, that is why --generic-time is specified. the qdec
>>> table would just look like
>>>
>>> fsid fsid-base
>>>
>>> me me_test
>>>
>>> me me_retest
>>>
>>> you you_test
>>>
>>> you you_retest
>>>
>>> ...
>>>
>>>
>>> Best, Martin
>>>
>>>
>>> On 05/08/2017 04:10 PM, jahanvi patel wrote:
>>> Hello list,
>>>
>>> I have a simple question about the LongitudinalTwoStageModel tutorials
>>> on freesurfer website.
>>>
>>> It is from this link
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel
>>>
>>>
>>> long_mris_slopes --qdec long.testretest.qdec \
>>>   --meas thickness \
>>>   --hemi lh \
>>>   --sd $SUBJECTS_DIR \
>>>   --do-pc1 --do-label \
>>>   --generic-time \
>>>   --fwhm 15 \
>>>   --qcache fsaverage \
>>>   --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \
>>>   --isec-labels lh.testretest.fsaverage.cortex.label
>>>
>>> My question is, what is the content of  long.testretest.qdec ?
>>> I understood till 1st stage was done, we got only one file which is
>>> long.qdec.table.dat.
>>>
>>> Could anyone help to clarify my question?
>>>
>>> Thanks a lot
>>> Jahanvi
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>
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>>
>>
>>
>> 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.
>>
>
>
>
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