Re: [Freesurfer] GLM design question

[Martijn Steenwijk]

Hi Doug,

Thanks for your reply again. It's getting more and more clear now.

I've however one question remaining, which is regarding the correction for
sex. What I did not tell (my fault ;-) ), is that 75% of the cohort is
female. Comparing the sex-corrected results with male-only and female-only
results, it appears to me that the relatively small male-group partly
'drives' the results in the sex-corrected results. I guess this is because
the males and females are currently equally weighted in the contrast
matrices. Shouldn't the differences in sex also be represented in the
contrast matrices, like
[.25 .75 -.25 -.75 0 0 0 0 0 0 0 0]
[0 0 .25 .75 -.25 -.75 0 0 0 0 0 0]
[ .25  .75 0 0 -.25 -.75 0 0 0 0 0 0]

? Or am I wrong?

Best,
Martijn


On Wed, Dec 21, 2011 at 5:45 PM, Douglas N Greve
wrote:

>
> Hi Martijn, sorry for  the delay. Your contrast matrices look correct. The
> differences between demeaning and not demeaning is somewhat expected. When
> you do not demean, you are testing whether there is a difference between
> groups at age=0 (ie, birth). When you demean, you are testing for a
> difference at age=MeanAge. If the slope of each group with respect to age
> is the same, then this will yield the same result since the regression
> lines will be parallel and the distance between parallel lines will always
> be the same. If the slopes differ, then the distance will change with age.
> For example, there will be an age where the lines cross. If you test at
> this age, you are assured not to see a difference! For this reason, it is
> better to test for a difference in the slopes, and, if there is no
> difference, then reanalyze with DOSS which forces the lines to be parallel.
> In your case, you found that there is some difference in insula. If this is
> not the area that you are interested in, then I would not worry about it.
> You should just keep in mind that you should not try to draw conclusions
> from this area.
> doug
>
> Martijn Steenwijk wrote:
>
>> Dear Doug,
>>
>> Thanks again for your reply. Based on that I did some further work.
>>
>> I first demeaned the age of all subjects. Actually, I have a third group
>> which I would like to compare to, so my contrast matrices will be [.5 .5
>> -.5 -.5 0 0 0 0 0 0 0 0]
>> [0 0 .5 .5 -.5 -.5 0 0 0 0 0 0]
>> [.5 .5 0 0 -.5 -.5 0 0 0 0 0 0]
>> to test for CT differences between all the groups while correcting for
>> age and sex. Surprisingly, I'm observing a big difference in the results
>> compared to the results without demeaning. Could you explain the reson for
>> this? In the FSGD-examples (eg http://surfer.nmr.mgh.harvard.**
>> edu/fswiki/FsgdFormat),
>> age is also not normalized. Does normalizing the variance to 1 also
>> influence the results?
>> Given this big difference, I started wondering whether it would maybe be
>> better to analyze the data in pairs of two groups (and then demean by the
>> mean of the two groups). Would this be a better approach?
>>
>> Concerning your second suggestion: if I test the data for differences in
>> group slope, a number of small area's are significantly different. Regions
>> popping up are especially in the neighborhood of the insula. Unfortunately
>> this suggests that I cannot use the DOSS model, or am I wrong?
>>
>> Looking forward to your reply,
>> With best regards,
>> Martijn
>>
>>
>> On Sat, Dec 10, 2011 at 7:16 PM, Douglas Greve 
>> > gr...@nmr.mgh.harvard.**edu >> wrote:
>>
>>Yes, that is correct, though I think your matrix should be [.5 .5
>>-.5 -.5 0 0 0 0]. You should also remove the mean from the age
>>(mean computed from all subjects). Or even better, first test
>>whether there is a group difference in age slope with [0 0 0 0 .5
>>.5 -.5 -.5]. If there is nothing that is significant, then re-run
>>your analysis using the Different Offset Same Slope (DOSS) model
>>with this contrast [.5 .5 -.5 -.5 0].
>>
>>doug
>>
>>
>>On 12/10/11 4:15 AM, Martijn Steenwijk wrote:
>>
>>>
>>>Dear all,
>>>
>>>
>>>I’m relatively new with Freesurfer, but slowly getting more and
>>>more used to it’s great possibilities. To be ‘sure’, I’ve a
>>>question about the design of a GLM.
>>>
>>>
>>>I want to compare CT in Healthy Controls vs Diseased, and control
>>>for age and sex. It appears to me that factors (eg sex) cannot be
>>>used as covariate/variable, which forces me to model them as a
>>>separate class although I’m not interested in sex differences.
>>>This brings me to the following FSGD file:
>>>
>>>
>>># HcDis.fsgd
>>>
>>>GroupDescriptorFile 1
>>>
>>>Title HcDis
>>>
>>>Class Hc_Male
>>>
>>>Class Hc_Female
>>>
>>>Class Dis_Male
>>>
>>>Class Dis_Female
>>>
>>>Variables Age
>>>
>>>Input subjid1 Hc_Male 35
>>>
>>>Input subjid2 Dis_Female 30
>>>
>>>….
>>>
>>>
>>>Then the difference between Hc and Dis, corrected for age and sex
>>>is given by th

[Freesurfer] SPGR compressed files

[Cat Chong]

Hi Experts,

We wanted to run clinical scans that underwent some compression at the scanner 
through freesurfer.

I just wanted to seek confirmation that SPGR sequences that have undergone 
slight compression can not be run through freesurfer, is that correct?

thank you,
catherine
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[Freesurfer] Building from source without GUIs

[Malcolm Tobias]

I'm attempting to build the development branch of the source code.
To reduce dependencies, I'm trying to build without any of the GUI support 
using the flags:

--disable-all-apps
--disable-gl-apps

It's complaining about a missing dependency:

configure: error: FATAL: libBLT not found. Check config.log. Set LDFLAGS or --
with-BLT-dir.

but the instructions imply that BLT is only necessary for GUIs.

Are there additional arguments that I need to pass to configure?

Malcolm

-- 
Malcolm Tobias
314.362.1594

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[Freesurfer] Group Analysis for non-FA data

[Antonella Kis]

Dear Lilla,

I wonder if I can use my results from the mri_cvs_register to do a non_FA group 
study analysis, more exactly I am interested on the mean diffusivity (adc.nii 
from dt_recon).
I hope I don't need to run again the registration again.

Since from the significant map I can only find/ tells only about about the p 
values how can I see if there is an increase or decrease in FA values or how 
can I do an FA comparison between two groups?

Thank you very much for your time and help.
Antonella
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Re: [Freesurfer] SPGR compressed files

[Bruce Fischl]

Hi Catherine

can you explain what you mean by compression?

Bruce

On Fri, 6 Jan 2012, Cat Chong 
wrote:

> Hi Experts,
> 
> We wanted to run clinical scans that underwent some compression at the
> scanner through freesurfer.
> I just wanted to seek confirmation that SPGR sequences that have undergone
> slight compression can not be run through freesurfer, is that correct?
> 
> thank you,
> catherine
> 
>
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Re: [Freesurfer] SPGR gadolinium contrast

[Bruce Fischl]

Hi Catherine,

yes, we have run post-enhancement datasets through FS with few problems. 
The only inaccuracies are in the choroid and dura which are a lot 
brighter than we expect them to be. Still, it typically works fine.

cheers
Bruce

p.s. what do you mean by compressed?


On Thu, 
5 Jan 2012, Cat Chong wrote:

> Hello Experts:
> 
> Is is possible to run 3D SPGR's with contrast (gadolineum) through
> freesurfer?
> 
> Also, in a separate dataset, we have 3D SPGR's that have unfortunately been
> compressed. Can they still be run?
> 
> Thanks,
> catherine
> 
>
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Re: [Freesurfer] Reviewer request

[Bruce Fischl]

Hi Jürgen

in some ways you can think of it as a partial volume correction. We know 
the cortex is smooth at the spatial scale of a couple of mm, and so 
impose this constraint to estimate the location of the surface with 
subvoxel accuracy. In addition, if a given voxel is darker than it's 
neighboring gray matter voxels it probably contains more CSF so the surface 
should be a bit further in than if the voxel were brighter.


I hope that helps
Bruce



On Thu, 5 Jan 2012, Jürgen Hänggi wrote:


Dear FS experts

We have the following request from one reviewer:

"Provide more detail and more discussion on why the thickness maps produced
by FreeSurfer are not limited to the voxel resolution of the image. This is
not obvious to everybody who is not an expert in cortical thickness
measurements using the free-surfer approach, since it is not so easy to
comprehend that differences can be found that are beyond the resolution of
the acquisition."

I can provide the references that provide this statement, but I do not
really have a sound explanation why this is possible.

Any idea is welcome and appreciated

Thanks in advance
Jürgen



Jürgen Hänggi, Ph.D.
Division Neuropsychology
Institute of Psychology
University of Zurich
Binzmuehlestrasse 14, PO Box 25
8050 Zurich, Switzerland
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Re: [Freesurfer] Segmentation Problem

[Bruce Fischl]

Hi Markus

can you send us an example of where you think the volume is far too low? 
Tar and gzip the entire subject dir and put it on our filedrop

cheers
Bruce
On Thu, 5 Jan 
2012, Markus Savli wrote:

> Dear Freesurfer Community!
> Recently I started working with Freesurfer and had a number of subjects
> processed through the pipeline (recon-all -autorecon-all -subjid subjname)
> without error.
> So far I am mainly interested in the outcome of the segmentation of
> subcortical regions found in ../stats/aseg.stats. However, of about 20% of
> the scans the calculated volumes were far below the normal range. I couldnt
> figure out why it sometimes doesnt work properly. All scans came from the
> same scanner, protocol, had same orientation, etc. Perhaps I need some
> "finetuning"? How can I manage to make the segmentation work correctly
> though? thanx in advance!
> Markus
> 
>
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