Re: [Freesurfer] [Fsdev] [PATCH] fix ups for DESTDIR

[Z K]

Hello Yaroslav,

It the case when "some subdirs makefiles do not care about DESTDIR, 
which is generally respected by autotools" an autotools version issue? 
Or related to something else completely?

I see that making the change on my end does not produce any ill effects, 
but I would like to observe the behavior before committing the "fix".

-Zeke

On 02/22/2016 11:33 PM, Yaroslav Halchenko wrote:
> Dear FS Developers,
>
> Per ZK's blessing I am moving my "whining"... khe khe... dialogue over
> to fsdev mailing list.  And would like to begin with this patch which
> have got buried in the users' mailing list:
>
> I have got into a problem that currently some subdirs makefiles do not
> care about DESTDIR, which is generally respected by autotools...
> attached patch should help to make FS 'installable' e.g. via
>
> make install DESTDIR=$PWD/INSTALL-DIR/
>
> NB in the future, it would be a nice "test" to add to .travis.yml
> upon successful build, without system wide installation with sudo ;)
>
> Please review/adopt/accept.
>
> With best regards,
>
>
>
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[Freesurfer] mri_label2vol projfrac missing voxels

[dgw]

Hi,

I am having trouble with the projfrac option in mri_label2vol (on the
current dev freesurfer environment). When I use the following command:

mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o
lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1
.01

I get many missed voxels from the gray matter (see the attached image,
with the yellow representing the label overlaid on the ribbon.mgz). I
have tried more extreme delta values and this doesn't help. (note
scrolling to nearby slices indicates the neighboring voxels are
included, so it isn't from the angle projecting oddly (that is why I
took a slice from the middle of this large label)). Is there a better
way to convert the annotation to a volume just in the gray matter, but
including all of the relevant voxels?

Is there a fundamental algorithmic difference between mris_volmask and
mri_label2vol?

If yes, why?

Thanks,
D
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[Freesurfer] -qcache of v5.0 data with newer versions

[Daniel Ferreira]

Dear experts,

Can I do -qcache with FS 5.3.0 or FS 5.1.0 on images that have been
recon-all -all with FS 5.0.0?

Thanks

Dani
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

I changed the directory and it ran, but with errors. I had to change the
last part --surf lh.seghead --surf-smooth 10 because it does not recognise
--surf. When I change this to --o, it runs but with errors.

On Tue, Feb 23, 2016 at 2:42 PM, Douglas Greve 
wrote:

>
>
> On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
>
> It seems to be giving me an error and saying it cannot read the
> seghead.mgz file.
>
> Is it in the same directory where you are running the command? If so, what
> is the terminal output?
>
>
> From my earlier question; do you know how to check if lh.seghead is
> corrupted?
>
> If you can view it in tksurfer/freeview, then it is probably not
> corrupted. I vaguely remember that there was some problem reading this file
> in matlab, but I don't remember every coming up with a fix
>
>
> On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve 
> wrote:
>
>> you can try
>>
>> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
>>
>>
>>
>>
>> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>>
>> Is it possible to use a different function? Can I use mri_vol2surf on the
>> seghead.mgz file? Or do you think that mkheadsurf is the right one to be
>> using?
>>
>> Thanks!!
>>
>> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> Can you load it in tksurfer or freeview?
>>>
>>>
>>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>>
>>> Hi FreeSurfer users,
>>>
>>> I have used the "mkheadsurf" command to create a head surface for my
>>> subject. However when I try to use "read_surf" to read the "lh.seghead"
>>> file that is created, the magic number is not one that is recognised.
>>>
>>> Having read some previous posts/questions with similar problem/error, I
>>> think the problem is probably within the "lh.seghead" file. I think someone
>>> wrote that incompatibility of the magic number means that the surface is
>>> corrupted. Is there a way to check errors of mkheadsurf? Or whether
>>> something is wrong? It looked fine in freeview.
>>>
>>> Does anybody have any advice?
>>>
>>> Thanks,
>>>
>>> Maheen
>>>
>>>
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>>>
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>>> properly
>>> dispose of the e-mail.
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>>>
>>
>>
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Bruce Fischl]

the magic # 16777213 means it's a quad file, not a triangle file. I still 
would have thought we could read it fine. Do you want to email us the 
surface file and someone will take a look?


On Tue, 23 Feb 2016, Douglas Greve wrote:


Can you load it in tksurfer or freeview?

On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
  Hi FreeSurfer users, 
I have used the "mkheadsurf" command to create a head surface for my subject. However 
when I try to use "read_surf" to
read the "lh.seghead" file that is created, the magic number is not one that is 
recognised. 

Having read some previous posts/questions with similar problem/error, I think 
the problem is probably within the
"lh.seghead" file. I think someone wrote that incompatibility of the magic 
number means that the surface is corrupted. Is
there a way to check errors of mkheadsurf? Or whether something is wrong? It 
looked fine in freeview. 

Does anybody have any advice?

Thanks,

Maheen 


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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas Greve]

On 2/23/16 9:39 AM, Maheen Siddiqui wrote:
It seems to be giving me an error and saying it cannot read the 
seghead.mgz file.
Is it in the same directory where you are running the command? If so, 
what is the terminal output?


From my earlier question; do you know how to check if lh.seghead is 
corrupted?
If you can view it in tksurfer/freeview, then it is probably not 
corrupted. I vaguely remember that there was some problem reading this 
file in matlab, but I don't remember every coming up with a fix


On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve 
> wrote:


you can try

mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead
--surf-smooth 10




On 2/23/16 9:22 AM, Maheen Siddiqui wrote:

Is it possible to use a different function? Can I use
mri_vol2surf on the seghead.mgz file? Or do you think that
mkheadsurf is the right one to be using?

Thanks!!

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve
> wrote:

Can you load it in tksurfer or freeview?


On 2/23/16 8:58 AM, Maheen Siddiqui wrote:

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head
surface for my subject. However when I try to use
"read_surf" to read the "lh.seghead" file that is created,
the magic number is not one that is recognised.

Having read some previous posts/questions with similar
problem/error, I think the problem is probably within the
"lh.seghead" file. I think someone wrote that
incompatibility of the magic number means that the surface
is corrupted. Is there a way to check errors of mkheadsurf?
Or whether something is wrong? It looked fine in freeview.

Does anybody have any advice?

Thanks,

Maheen


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Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

[Douglas Greve]

Run mri_mcsim --help and look at Example 2
doug

On 2/23/16 4:52 AM, Silas wrote:


Dear FS team,


I followed the BuildYourOwnMonteCarlo guide and received an error 
running mri_glmfit-sim. This might be a simple problem but I have 
troubles finding the flaw. Hopefully you can help me out.



*Commands:*

% step 1: If not done already - create the label:
mri_annotation2label --subject fsaverage --hemi rh --outdir labeldir

% step 2: mri_mcsim using my own label on the fsaverage surface:
mri_mcsim --o .../S1M1_GroupAnalysis/S1M1 --base mc-z --save-iter 
 --surf fsaverage rh --nreps 1 --label 
.../S1M1_GroupAnalysis/S1M1.label


% step 3: mri_glmfit investigating the correlation between an AUC 
value and t1t2ratio
mri_glmfit --y rh.t1t2ratio_fmed_3sm_decurv.fsavg.5.mgh --fsgd 
AUC.fsgd --surf fsaverage rh --C intercept.mtx --C slope.mtx --label 
S1M1.label --o t1t2vsAUC_S1M1.5.glmdir


% step 4: mris_glmfit-sim
mri_glmfit-sim --glmdir t1t2vsAUC_S1M1.5.glmdir --cache-dir 
.../S1M1_GroupAnalysis/S1M1  --cache 2 pos --cwp 0.05


*Error:*

ERROR: cannot find 
.../S1M1_GroupAnalysis/S1M1/fsaverage/rh/*cortex*/fwhm09/pos/th20/mc-z.csd

*
*
*
*
*
*Question:*
*
Is there any obvious flaws in my commands?
In the guide I'm suggested to place my results into 
$FREESURFER_HOME/... is this a necessity?
How does mri_glmfit-sim recognizes that I'm investigating the label 
S1M1 and not cortex?
Could i simply just copy-paste my results from mri_mcsim into 
.../S1M1_GroupAnalysis/S1M1/fsaverage/rh/*cortex*/ ?


Best, Silas


*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 


*Sent:* Monday, February 8, 2016 4:35 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim


On 2/7/16 1:34 PM, Silas wrote:


Dear FS team,


I'm currently making a group analysis using the "command-line" group 
analysis stream in freesurfer.


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng



FsTutorial/GroupAnalysisDng - Free Surfer Wiki 


surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the 
"command-line" group analysis stream in FreeSurfer (as opposed to 
QDEC which is GUI-driven), including ...



1) I would like to do a surface based analysis where i'm only 
investigating a certain area or label - instead of doing a 
whole brain analysis. This can be done by introducing --label 
surface_area_of_interest.label when running mri_glmfit. Would this 
(in theory) give me different results from doing a whole brain 
analysis - or would it just exclude the results from outside the label?


No. However, if your activation is near the boundary of the ROI, then 
you may want to constrain the spatial smoothing to be within the ROI.


And how about after clusterwise correction for multiple comparisons?

If your new ROI is much smaller than whole hemisphere, then you will 
need to generate new correction tables (otherwise it won't help to 
constrain it to an ROI). To do this, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo


-> is there a better way to do this than following the command-line 
group analysis stream in freesurfer?



No



2) When running mri_glmfit-sim i'm investigating the output ending 
with -voxel.mgh - how do i interpret the results of this file? When 
investigating the file in freeview what is the meaning of the units 
when configuring the overlay?


This is the voxel-wise correction for multiple comparisons. The value 
of the voxel (and overlay config units) are -log10(p), where p is the 
p-value corrected for multiple comparisons. So p=.01 means 2.



Best, Silas



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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

It seems to be giving me an error and saying it cannot read the seghead.mgz
file.

>From my earlier question; do you know how to check if lh.seghead is
corrupted?

On Tue, Feb 23, 2016 at 2:30 PM, Douglas Greve 
wrote:

> you can try
>
> mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10
>
>
>
>
> On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
>
> Is it possible to use a different function? Can I use mri_vol2surf on the
> seghead.mgz file? Or do you think that mkheadsurf is the right one to be
> using?
>
> Thanks!!
>
> On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
> wrote:
>
>> Can you load it in tksurfer or freeview?
>>
>>
>> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>>
>> Hi FreeSurfer users,
>>
>> I have used the "mkheadsurf" command to create a head surface for my
>> subject. However when I try to use "read_surf" to read the "lh.seghead"
>> file that is created, the magic number is not one that is recognised.
>>
>> Having read some previous posts/questions with similar problem/error, I
>> think the problem is probably within the "lh.seghead" file. I think someone
>> wrote that incompatibility of the magic number means that the surface is
>> corrupted. Is there a way to check errors of mkheadsurf? Or whether
>> something is wrong? It looked fine in freeview.
>>
>> Does anybody have any advice?
>>
>> Thanks,
>>
>> Maheen
>>
>>
>> ___
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Re: [Freesurfer] Convert spm volume to fresurfer surface

[Douglas Greve]

It depends on the space you used for your SPM analysis. If you used the 
mni152, then you should run recon-all on that, the use mri_vol2surf with 
--regheader, probably specifying --projfrac-max 0 1 .1
Then use mri_surf2surf to map it to fsaverage space, then use 
mri_binarize to binarize it at the threshold you want. Finally use the 
result of that as the --mask option to mri_glmfit. You will need to 
build your own monte carlo simulation

https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

doug


On 2/23/16 5:50 AM, Daniel Baena Pérez wrote:


Dear Fresurfer users,

I would like to analyze group differences in cortical thickness in 
fresurfer by using as a mask a volumetric SPM activity image. Which 
command should be used for this purpose?


Thanks a lot and best wishes,

Sofia



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Re: [Freesurfer] Still age corrected?

[Douglas Greve]

Where are you getting the mean value for each subject? Only the 
gamma.mgh file will be corrected.


On 2/23/16 7:43 AM, Daniel Baena Pérez wrote:

Dear Freesurfer user,

We have performed group contrasts on cortical thickness correcting by 
age. Now we want to use the mean cortical thickness of one of the 
significant clusters as a regressor in other analysis, but we do 
not know whether the mean cortical thickness value for each subject 
within this ROI is corrected by age or not.


Best regards and thank you


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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas Greve]

you can try

mri_binarize --i seghead.mgz --min 0.5 --surf lh.seghead --surf-smooth 10



On 2/23/16 9:22 AM, Maheen Siddiqui wrote:
Is it possible to use a different function? Can I use mri_vol2surf on 
the seghead.mgz file? Or do you think that mkheadsurf is the right one 
to be using?


Thanks!!

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
> wrote:


Can you load it in tksurfer or freeview?


On 2/23/16 8:58 AM, Maheen Siddiqui wrote:

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head surface for
my subject. However when I try to use "read_surf" to read the
"lh.seghead" file that is created, the magic number is not one
that is recognised.

Having read some previous posts/questions with similar
problem/error, I think the problem is probably within the
"lh.seghead" file. I think someone wrote that incompatibility of
the magic number means that the surface is corrupted. Is there a
way to check errors of mkheadsurf? Or whether something is wrong?
It looked fine in freeview.

Does anybody have any advice?

Thanks,

Maheen


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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Is it possible to use a different function? Can I use mri_vol2surf on the
seghead.mgz file? Or do you think that mkheadsurf is the right one to be
using?

Thanks!!

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
wrote:

> Can you load it in tksurfer or freeview?
>
>
> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>
> Hi FreeSurfer users,
>
> I have used the "mkheadsurf" command to create a head surface for my
> subject. However when I try to use "read_surf" to read the "lh.seghead"
> file that is created, the magic number is not one that is recognised.
>
> Having read some previous posts/questions with similar problem/error, I
> think the problem is probably within the "lh.seghead" file. I think someone
> wrote that incompatibility of the magic number means that the surface is
> corrupted. Is there a way to check errors of mkheadsurf? Or whether
> something is wrong? It looked fine in freeview.
>
> Does anybody have any advice?
>
> Thanks,
>
> Maheen
>
>
> ___
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Hi,

Yes I can load it in freeview.

On Tue, Feb 23, 2016 at 2:18 PM, Douglas Greve 
wrote:

> Can you load it in tksurfer or freeview?
>
>
> On 2/23/16 8:58 AM, Maheen Siddiqui wrote:
>
> Hi FreeSurfer users,
>
> I have used the "mkheadsurf" command to create a head surface for my
> subject. However when I try to use "read_surf" to read the "lh.seghead"
> file that is created, the magic number is not one that is recognised.
>
> Having read some previous posts/questions with similar problem/error, I
> think the problem is probably within the "lh.seghead" file. I think someone
> wrote that incompatibility of the magic number means that the surface is
> corrupted. Is there a way to check errors of mkheadsurf? Or whether
> something is wrong? It looked fine in freeview.
>
> Does anybody have any advice?
>
> Thanks,
>
> Maheen
>
>
> ___
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> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Corrupted head surface with mkheadsurf?

[Douglas Greve]

Can you load it in tksurfer or freeview?

On 2/23/16 8:58 AM, Maheen Siddiqui wrote:

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head surface for my 
subject. However when I try to use "read_surf" to read the 
"lh.seghead" file that is created, the magic number is not one that is 
recognised.


Having read some previous posts/questions with similar problem/error, 
I think the problem is probably within the "lh.seghead" file. I think 
someone wrote that incompatibility of the magic number means that the 
surface is corrupted. Is there a way to check errors of mkheadsurf? Or 
whether something is wrong? It looked fine in freeview.


Does anybody have any advice?

Thanks,

Maheen


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[Freesurfer] Corrupted head surface with mkheadsurf?

[Maheen Siddiqui]

Hi FreeSurfer users,

I have used the "mkheadsurf" command to create a head surface for my
subject. However when I try to use "read_surf" to read the "lh.seghead"
file that is created, the magic number is not one that is recognised.

Having read some previous posts/questions with similar problem/error, I
think the problem is probably within the "lh.seghead" file. I think someone
wrote that incompatibility of the magic number means that the surface is
corrupted. Is there a way to check errors of mkheadsurf? Or whether
something is wrong? It looked fine in freeview.

Does anybody have any advice?

Thanks,

Maheen
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Re: [Freesurfer] Still age corrected?

[Bruce Fischl]

how do you obtain it? If you just create an roi/label and use it as input 
to mris_anatomical_stats it will not be corrected


cheers
Bruce
On Tue, 23 Feb 2016, 
Daniel Baena Pérez wrote:



Dear Freesurfer user,
 

We have performed group contrasts on cortical thickness correcting by age.
Now we want to use the mean cortical thickness of one of the significant
clusters as a regressor in other analysis, but we do not know whether the
mean cortical thickness value for each subject within this ROI is corrected
by age or not. 

 
Best regards and thank you
 

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Re: [Freesurfer] Convert spm volume to fresurfer surface

[Bruce Fischl]

Hi Sofia

you will need to use mri_vol2surf to sample the mask onto the surface. Do 
you have one for each subject? Or some type of average? We will need more 
details about what you are trying to do


cheers
Bruce
On Tue, 23 Feb 2016, Daniel Baena 
Pérez wrote:




Dear Fresurfer users,

I would like to analyze group differences in cortical thickness in fresurfer
by using as a mask a volumetric SPM activity image. Which command should be
used for this purpose?

Thanks a lot and best wishes,

Sofia

 

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Re: [Freesurfer] Regarding: 1.5T images

[Bruce Fischl]

Hi Sampada

you need to identify why you are getting  excessive topologic defects. 
Can you send an image of one of your acquisitions?

Bruce
On Tue, 23 Feb 2016, Dr 
Sampada Sinha wrote:

> Hello freesurfer experts,
> 
> I am trying to do T1w analysis using freesurfer. The raw images are in dicom
> format. However, when I view those raw dicom images, some of the brain areas
> are missing. I just wanted to ask if there is any tool to reconstruct those
> missing brain areas in the raw images using freesurfer or I need to discard
> those participants scan altogether?
> 
> Also, because the resolution is not good with 1.5T, I have seen that skull
> stripping is not good with a large chunk of skull tissue coming in the
> processed images. I tried to adjust the watershed parameters and somehow it
> worked, but it wasn't satisfactory. I tried to run it through fsl bet and
> got a good skull strip. However, after running the recon-all followed by
> auorecon11 no skull strip command the with autorecon2 and autorecon3 I am
> getting excessive topologic defect. I am attaching the log file with this
> email for your perusal
> 
> Will greatly appreciate if I can be helped regarding these two problems I am
> presently facing with the analysis.
> 
> Thanks and regards,
> 
> Sampada
> Pre-doctoral student
> India
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] control points function

[Bruce Fischl]

Hi Kiersten

at its heart it is a region-growing algorithm followed by soap bubble 
smoothing. That is, the detected control points become fixed points in the 
soap bubble (which amounts to iterative averaging of all the non-fixed 
points). We use a Voronoi diagram to initialize the soap bubble for speed. 
There are lots of other things in it (e.g. robust histogramming, peak 
detection, outlier detection), but that is the core of it

Bruce


On Mon, 22 Feb 2016, Kiersten Snyder wrote:


Hello,I am new to using Freesurfer and am currently using it for a
biomedical image processing class. I am working on a project and would like
to know the image processing technique behind the Control Points function. 
Is it region growing, or what other process?

Thanks for the help!
Kiersten 

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Re: [Freesurfer] Ris: eTIV question

[angela . favaro]

yes, I agree. I will explore both
thank you!
Angela

>
> That is, going back to your earlier post, I personally don’t find it all
> that interesting whether a given brain area is atrophic relative to head
> size, especially in the situation where many regions are atrophic (i.e.,
> global atrophy).  I’m more interested in knowing whether the atrophy in a
> given region is greater (or less than) what would be predicted based on
> the global atrophy.
>
> cheers,
> -MH
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 2/22/16, 10:19 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Harms, Michael"  mha...@wustl.edu> wrote:
>
> Even assuming one had a true measure of TIV, if you get meaningfully
> different results when using TIV vs. brain size as a covariate, isn’t that
> a rather important thing to point out?
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 2/22/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Bruce Fischl"  fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Angela
>
> yes, although if the eTIV is (incorrectly) correlated with atrophy you
> may be removing some of your effect (and slightly reducing your power)
>
> cheers
> Bruce
> On
> Mon, 22 Feb 2016, angela.fav...@unipd.it wrote:
>
>> Hi Bruce,
>> this is true, but I noticed that many papers used TIV as a covariate. In
>> addition, in my samples (both pathological and healthy) there is a
>> moderate positive correlation between gyrification and TIV (and brain
>> volume). For the hemispheric overall gyrification index the correlation
>>is
>> 0.3-0.35 with TIV and 0.35-0.4 with total brain volume.
>> I think that in pathological samples with possible brain atrophy, this
>> is
>> a way to control for a possible bias effect. Am I wrong?
>>
>> Thank you
>> Angela
>>
>>> Hi Angela
>>>
>>> gyrification is the ratio of areas and hence dimensionless, so I would
>>> think it wouldn't be much affected by TIV.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote:
>>>
 In the case of a gyrification analysis, does correction for total
 brain
 volume make sense?

 Angela

 Inviato dal mio dispositivo Huawei

  Messaggio originale 
 Oggetto: Re: [Freesurfer] eTIV question
 Da: Bruce Fischl
 A: Freesurfer support list
 CC:


   yes, it's a somewhat different and more conservative test. I
   guess you
   could check the talairach transforms of some of your subjects
   with eTIVs
   that don't make sense (or change the most over time) to try to
   see why
   this is happening. Or take Mike's suggestion and test a
   different (but
   probably still interesting) hypothesis

   On Sun, 21 Feb 2016, Angela Favaro wrote:

  > Hi, thank you
  > I think this would test something different: 'how much a brain
   area is
  > atrophic controlling for the average brain atrophy' and not
   'how much
  > a brain area is atrophic controlling for the individual
   differences in
  > head size'. Doesn't it?
  >
  > Angela
  >
  >
  > "Harms, Michael" ha scritto:
  >
  >> Hi,
  >> Why not use a measurement of brain size rather than “eTIV”?
  >>
  >> cheers,
  >> -MH
  >>
  >> --
  >> Michael Harms, Ph.D.
  >>
  >> ---
  >> Conte Center for the Neuroscience of Mental Disorders
  >> Washington University School of Medicine
  >> Department of Psychiatry, Box 8134
  >> 660 South Euclid Ave.Tel: 314-747-6173
  >> St. Louis, MO 63110Email: mha...@wustl.edu
  >>
  >>
  >>
  >>
  >> On 2/21/16, 6:06 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
   on behalf of
  >> Angela Favaro" >> angela.fav...@unipd.it> wrote:
  >>
  >> there is a mistake in the graph, hippocampal volume is TIV2
  >> I apologize for that!
  >>
  >> Angela Favaro ha scritto:
  >>
  >>> Hi Bruce,
  >>> please find attached the 

[Freesurfer] Convert spm volume to fresurfer surface

[Daniel Baena Pérez]

Dear Fresurfer users, 

I would like to analyze group differences in cortical thickness in
fresurfer by using as a mask a volumetric SPM activity image. Which
command should be used for this purpose? 

Thanks a lot and best wishes, 

Sofia

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Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

[Silas]

Dear FS team,


I followed the BuildYourOwnMonteCarlo guide and received an error running 
mri_glmfit-sim. This might be a simple problem but I have troubles finding the 
flaw. Hopefully you can help me out.


Commands:

% step 1: If not done already - create the label:
mri_annotation2label --subject fsaverage --hemi rh --outdir labeldir

% step 2: mri_mcsim using my own label on the fsaverage surface:
mri_mcsim --o .../S1M1_GroupAnalysis/S1M1 --base mc-z --save-iter  --surf 
fsaverage rh --nreps 1 --label .../S1M1_GroupAnalysis/S1M1.label


% step 3: mri_glmfit investigating the correlation between an AUC value and 
t1t2ratio
mri_glmfit --y rh.t1t2ratio_fmed_3sm_decurv.fsavg.5.mgh --fsgd AUC.fsgd --surf 
fsaverage rh --C intercept.mtx --C slope.mtx --label S1M1.label --o 
t1t2vsAUC_S1M1.5.glmdir

% step 4: mris_glmfit-sim
mri_glmfit-sim --glmdir t1t2vsAUC_S1M1.5.glmdir --cache-dir 
.../S1M1_GroupAnalysis/S1M1  --cache 2 pos --cwp 0.05


Error:

ERROR: cannot find 
.../S1M1_GroupAnalysis/S1M1/fsaverage/rh/cortex/fwhm09/pos/th20/mc-z.csd

Question:

Is there any obvious flaws in my commands?
In the guide I'm suggested to place my results into $FREESURFER_HOME/... is 
this a necessity?
How does mri_glmfit-sim recognizes that I'm investigating the label S1M1 and 
not cortex?
Could i simply just copy-paste my results from mri_mcsim into 
.../S1M1_GroupAnalysis/S1M1/fsaverage/rh/cortex/ ?

Best, Silas


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Monday, February 8, 2016 4:35 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim



On 2/7/16 1:34 PM, Silas wrote:

Dear FS team,


I'm currently making a group analysis using the "command-line" group analysis 
stream in freesurfer.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng

[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]

FsTutorial/GroupAnalysisDng - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Introduction. This tutorial is designed to introduce you to the "command-line" 
group analysis stream in FreeSurfer (as opposed to QDEC which is GUI-driven), 
including ...



1) I would like to do a surface based analysis where i'm only investigating a 
certain area or label - instead of doing a whole brain analysis. This can be 
done by introducing --label surface_area_of_interest.label when running 
mri_glmfit. Would this (in theory) give me different results from doing a whole 
brain analysis - or would it just exclude the results from outside the label?

No. However, if your activation is near the boundary of the ROI, then you may 
want to constrain the spatial smoothing to be within the ROI.

And how about after clusterwise correction for multiple comparisons?

If your new ROI is much smaller than whole hemisphere, then you will need to 
generate new correction tables (otherwise it won't help to constrain it to an 
ROI). To do this, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

-> is there a better way to do this than following the command-line group 
analysis stream in freesurfer?

No


2) When running mri_glmfit-sim i'm investigating the output ending with 
-voxel.mgh - how do i interpret the results of this file? When investigating 
the file in freeview what is the meaning of the units when configuring the 
overlay?

This is the voxel-wise correction for multiple comparisons. The value of the 
voxel (and overlay config units) are -log10(p), where p is the p-value 
corrected for multiple comparisons. So p=.01 means 2.


Best, Silas



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