[Freesurfer] Cortical thickness measuring algo

[Saurabh Thakur]

Hello Freesurfer,

Laplacian based method for measuring Cortical thickness

Can u anyone help me to understand how freesurfer has implemented this algo
and where to find this algo for better understanding.


Thanks,

Saurabh Thakur,
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Re: [Freesurfer] Resting State Networks on Cortical Surface

[Douglas Greve]

I don't know of anything that will do this (or what a single object 
would mean in this case). If you have the overlay in a volume format 
(eg, mgz), you can use MRIread.m. This gives you a value for each 
vertex, not face, so you'd have to write something to assign the value 
to a face.


doug



On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into matlab 
without any issues using read_surf.m what I would like to have is the 
ICA overlay also imported into matlab as corresponding colors for each 
face on the cortical mesh. Thanks.





From: andrewz...@live.com.au
To: gr...@nmr.mgh.harvard.edu
Date: Tue, 11 Mar 2014 11:54:10 +1100
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface

Regarding matlab:

Currently, I have in freesurfer the surface extracted via recon-all. I 
also have the overlay from running mri_vol2surf on the ICA components.


I would like to export the pial surface + overlay into matlab together 
as a single object. Is there a matlab script for this, or do I need to 
do some further processing? Thanks.



> Date: Mon, 10 Mar 2014 11:25:23 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: andrewz...@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> > Hi Doug,
> >
> > To clarify my previous question:
> >
> > There is definitely some fuzziness when comparing with the mov,
> > whereas the target comparison looks very pristine. I was just
> > wondering if this is expected. The mov, as I scroll through the 
layers
> > seem to be also slightly offset in certain regions, I guess this 
again

> > may be due to the fuzziness of the mov fmri data.
> Yes this is somewhat expected. The target is the data the surface was
> generated from, so it should look perfect.
> >
> > Regarding my second q:
> >
> > I've got this working now- the segfault was due to me naively loading
> > the surface image as a surface, instead of using it as an overlay, I
> > can now successfully scroll through the various frames. However, I
> > noticed that in the documentation to load into matlab, say the left
> > pial surface (with the ICA components on it), I have to save it as a
> > mgz file and then use MRI_read. However, freeview doesn't seem to
> > offer this option once I load the pial surface and the the ICA 
components?

>
> Sorry, what has to be mgz? What matlab command? What instructions?
> doug
>
> >
> >
> > 


> > Date: Thu, 6 Mar 2014 10:19:25 -0500
> > From: gr...@nmr.mgh.harvard.edu
> > To: andrewz...@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/6/14 6:39 AM, Xuelong Zhao wrote:
> >
> > Hi Doug,
> >
> > A follow-up. I've gone back and re-done the registration using
> > nifti file with the ICA20 maps. I noticed in tkregister2 that when
> > I press on the TARGET tab there is extremely good alignment ( i
> > think it is to 'orig.mgz' in the mri folder of my subject which I
> > had processed using recon-all. While, when I switch to the
> > 'moveable' tab the green line seems to be slightly offset, but the
> > underlying image is very fuzzy too. Is this an issue?
> >
> > I don't know without seeing it. The mov is often lower resolution, so
> > some fuzziness is expected.
> >
> >
> > Also, when I load the surface image in freeview produced by
> > mri_vol2surf nothing seems to show up, even when I use the
> > registration file. In fact, if I have other volumes loaded it
> > causes freeview to segfault. When I do manage to load it
> > successfully with the anatomical template in talairach space, it
> > doesn't really show up and it seems that the anatomical template
> > is really small and I have to zoom in a lot. Maybe I didn't
> > process/register?
> >
> > Can you be more specific? What are your vol2surf and fv command 
lines?

> > Have you tried it in tksurfer?
> >
> >
> > Thanks again.
> >
> > 


> > Date: Tue, 4 Mar 2014 22:52:38 -0500
> > From: gr...@nmr.mgh.harvard.edu 
> > To: andrewz...@live.com.au 
> > CC: freesurfer@nmr.mgh.harvard.edu
> > 
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/4/14 7:18 PM, Xuelong Zhao wrote:
> >
> > Dear Doug,
> >
> > I've managed to get functional information onto the cortical
> > surface following your instructions.
> > But, there's a few issues that are still not resolved:
> >
> > 1/ wrt to registration I believe the supplied anatomical
> > template (in tailarach coords) is already aligned with the ica
> > maps 

Re: [Freesurfer] Resting State Networks on Cortical Surface

[Xuelong Zhao]

Should also add that I can import the cortical surface into matlab without any 
issues using read_surf.m what I would like to have is the ICA overlay also 
imported into matlab as corresponding colors for each face on the cortical 
mesh. Thanks.



From: andrewz...@live.com.au
To: gr...@nmr.mgh.harvard.edu
Date: Tue, 11 Mar 2014 11:54:10 +1100
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface




Regarding matlab:

Currently, I have in freesurfer the surface extracted via recon-all. I also 
have the overlay from running mri_vol2surf on the ICA components. 

I would like to export the pial surface + overlay into matlab together as a 
single object. Is there a matlab script for this, or do I need to do some 
further processing? Thanks.


> Date: Mon, 10 Mar 2014 11:25:23 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: andrewz...@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> 
> 
> On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> > Hi Doug,
> >
> > To clarify my previous question:
> >
> > There is definitely some fuzziness when comparing with the mov, 
> > whereas the target comparison looks very pristine. I was just 
> > wondering if this is expected. The mov, as I scroll through the layers 
> > seem to be also slightly offset in certain regions, I guess this again 
> > may be due to the fuzziness of the mov fmri data.
> Yes this is somewhat expected. The target is the data the surface was 
> generated from, so it should look perfect.
> >
> > Regarding my second q:
> >
> > I've got this working now- the segfault was due to me naively loading 
> > the surface image as a surface, instead of using it as an overlay, I 
> > can now successfully scroll through the various frames. However, I 
> > noticed that in the documentation to load into matlab, say the left 
> > pial surface (with the ICA components on it), I have to save it as a 
> > mgz file and then use MRI_read. However, freeview doesn't seem to 
> > offer this option once I load the pial surface and the the ICA components?
> 
> Sorry, what has to be mgz? What matlab command? What instructions?
> doug
> 
> >
> >
> > 
> > Date: Thu, 6 Mar 2014 10:19:25 -0500
> > From: gr...@nmr.mgh.harvard.edu
> > To: andrewz...@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/6/14 6:39 AM, Xuelong Zhao wrote:
> >
> > Hi Doug,
> >
> > A follow-up. I've gone back and re-done the registration using
> > nifti file with the ICA20 maps. I noticed in tkregister2 that when
> > I press on the TARGET tab there is extremely good alignment ( i
> > think it is to 'orig.mgz' in the mri folder of my subject which I
> > had processed using recon-all. While, when I switch to the
> > 'moveable' tab the green line seems to be slightly offset, but the
> > underlying image is very fuzzy too. Is this an issue?
> >
> > I don't know without seeing it. The mov is often lower resolution, so 
> > some fuzziness is expected.
> >
> >
> > Also, when I load the surface image in freeview produced by
> > mri_vol2surf nothing seems to show up, even when I use the
> > registration file. In fact, if I have other volumes loaded it
> > causes freeview to segfault. When I do manage to load it
> > successfully with the anatomical template in talairach space, it
> > doesn't really show up and it seems that the anatomical template
> > is really small and I have to zoom in a lot. Maybe I didn't
> > process/register?
> >
> > Can you be more specific? What are your vol2surf and fv command lines? 
> > Have you tried it in tksurfer?
> >
> >
> > Thanks again.
> >
> > 
> > Date: Tue, 4 Mar 2014 22:52:38 -0500
> > From: gr...@nmr.mgh.harvard.edu 
> > To: andrewz...@live.com.au 
> > CC: freesurfer@nmr.mgh.harvard.edu
> > 
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/4/14 7:18 PM, Xuelong Zhao wrote:
> >
> > Dear Doug,
> >
> > I've managed to get functional information onto the cortical
> > surface following your instructions.
> >  But, there's a few issues that are still not resolved:
> >
> > 1/ wrt to registration I believe the supplied anatomical
> > template (in tailarach coords) is already aligned with the ica
> > maps (which come from one individual). However, when I run
> > mri_vol2surf I need a registration.dat file so in such a
> > situation is the registration data from the anatomical
> > template sufficient?
> >
> > If the ica maps 

Re: [Freesurfer] applying Yeo atlas to individual brains

[Douglas Greve]

yes, that is the option. If you run it with --help, it will actually 
give you an example.
doug


On 3/10/14 7:23 PM, Thomas Yeo wrote:
> Hi Jeff,
>
> I am a little unsure myself since I usually work with data mapped to
> fsaverage space. I think you might want to use mri_surf2surf, since
> there's a "--sval-annot" option. It's hard for me to check now because
> I am away at a conference.
>
> Can someone chime in if mri_surf2surf is wrong?
>
> Thanks,
> Thomas
>
>
>
>
>
> On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen  wrote:
>> What I need are the ?h.Yeo.annot files for the individual subjects, similar 
>> to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will 
>> mri_label2labe give me that directly?
>>
>> Thanks,
>> -Jeff
>>
>>
>> -Original Message-
>> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, March 10, 2014 9:50 AM
>> To: Jeff Eriksen
>> Cc: 'freesurfer@nmr.mgh.harvard.edu'
>> Subject: Re: [Freesurfer] applying Yeo atlas to individual brains
>>
>> Hi Jeff
>>
>> you should be able to use mri_label2label to map the Yeo atlas from 
>> fsaverage to any subject.
>>
>> cheers
>> Bruce
>> On Mon, 10 Mar 2014, Jeff Eriksen wrote:
>>
>>> Our lab has a need to apply the Yeo atlas to individual brains. As I
>>> understand it, Yeo atlas is only currently available for the FSAverage
>>> brain. Any plans to incorporate Yeo on to the default FS segmentation,
>>> or have it available as an option?
>>>
>>>
>>>
>>> -Jeff Eriksen
>>>
>>>
>>>
>>>
>>>
>>
>> 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.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
>

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Re: [Freesurfer] applying Yeo atlas to individual brains

[Gregory Kirk]

problem with surf2surf is it deals with scalar fields ( data ) so don't think 
that will do it.

problem with label2label is that it deals with a single label which has a 
diferent structure than anot.

so a way to do it

1. mri_annotation2label ... to convert the yeo anotation file to individual 
labels

2. mri_label2label ... to map each label from the fsaverage space to the 
individual subject space

3. then the function that takes the labels on the individual subject space and 
makes a .annot of
it in indiv. subject space. you will need to supply a colormap table to, don't 
remember
the name ( google freesurfer make annotation file, or something like that)

seems like a lot of work but just make a little script and you only need to 
figure it out once.

if any problems i could dig in my notes, i did not find one function to map a 
.annot in
1one space to a .annot in another.

gref

On 03/10/14, Thomas Yeo  wrote:
> Hi Jeff,
> 
> I am a little unsure myself since I usually work with data mapped to
> fsaverage space. I think you might want to use mri_surf2surf, since
> there's a "--sval-annot" option. It's hard for me to check now because
> I am away at a conference.
> 
> Can someone chime in if mri_surf2surf is wrong?
> 
> Thanks,
> Thomas
> 
> 
> 
> 
> 
> On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen  wrote:
> > What I need are the ?h.Yeo.annot files for the individual subjects, similar 
> > to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will 
> > mri_label2labe give me that directly?
> >
> > Thanks,
> > -Jeff
> >
> >
> > -Original Message-
> > From: Bruce Fischl 
> > [mailto:fis...@nmr.mgh.harvard.edu](javascript:main.compose()
> > Sent: Monday, March 10, 2014 9:50 AM
> > To: Jeff Eriksen
> > Cc: 'freesurfer@nmr.mgh.harvard.edu'
> > Subject: Re: [Freesurfer] applying Yeo atlas to individual brains
> >
> > Hi Jeff
> >
> > you should be able to use mri_label2label to map the Yeo atlas from 
> > fsaverage to any subject.
> >
> > cheers
> > Bruce
> > On Mon, 10 Mar 2014, Jeff Eriksen wrote:
> >
> >>
> >> Our lab has a need to apply the Yeo atlas to individual brains. As I
> >> understand it, Yeo atlas is only currently available for the FSAverage
> >> brain. Any plans to incorporate Yeo on to the default FS segmentation,
> >> or have it available as an option?
> >>
> >>
> >>
> >> -Jeff Eriksen
> >>
> >>
> >>
> >>
> >>
> >
> >
> > 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.
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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Re: [Freesurfer] Resting State Networks on Cortical Surface

[Xuelong Zhao]

Regarding matlab:

Currently, I have in freesurfer the surface extracted via recon-all. I also 
have the overlay from running mri_vol2surf on the ICA components. 

I would like to export the pial surface + overlay into matlab together as a 
single object. Is there a matlab script for this, or do I need to do some 
further processing? Thanks.


> Date: Mon, 10 Mar 2014 11:25:23 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: andrewz...@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> 
> 
> On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> > Hi Doug,
> >
> > To clarify my previous question:
> >
> > There is definitely some fuzziness when comparing with the mov, 
> > whereas the target comparison looks very pristine. I was just 
> > wondering if this is expected. The mov, as I scroll through the layers 
> > seem to be also slightly offset in certain regions, I guess this again 
> > may be due to the fuzziness of the mov fmri data.
> Yes this is somewhat expected. The target is the data the surface was 
> generated from, so it should look perfect.
> >
> > Regarding my second q:
> >
> > I've got this working now- the segfault was due to me naively loading 
> > the surface image as a surface, instead of using it as an overlay, I 
> > can now successfully scroll through the various frames. However, I 
> > noticed that in the documentation to load into matlab, say the left 
> > pial surface (with the ICA components on it), I have to save it as a 
> > mgz file and then use MRI_read. However, freeview doesn't seem to 
> > offer this option once I load the pial surface and the the ICA components?
> 
> Sorry, what has to be mgz? What matlab command? What instructions?
> doug
> 
> >
> >
> > 
> > Date: Thu, 6 Mar 2014 10:19:25 -0500
> > From: gr...@nmr.mgh.harvard.edu
> > To: andrewz...@live.com.au
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/6/14 6:39 AM, Xuelong Zhao wrote:
> >
> > Hi Doug,
> >
> > A follow-up. I've gone back and re-done the registration using
> > nifti file with the ICA20 maps. I noticed in tkregister2 that when
> > I press on the TARGET tab there is extremely good alignment ( i
> > think it is to 'orig.mgz' in the mri folder of my subject which I
> > had processed using recon-all. While, when I switch to the
> > 'moveable' tab the green line seems to be slightly offset, but the
> > underlying image is very fuzzy too. Is this an issue?
> >
> > I don't know without seeing it. The mov is often lower resolution, so 
> > some fuzziness is expected.
> >
> >
> > Also, when I load the surface image in freeview produced by
> > mri_vol2surf nothing seems to show up, even when I use the
> > registration file. In fact, if I have other volumes loaded it
> > causes freeview to segfault. When I do manage to load it
> > successfully with the anatomical template in talairach space, it
> > doesn't really show up and it seems that the anatomical template
> > is really small and I have to zoom in a lot. Maybe I didn't
> > process/register?
> >
> > Can you be more specific? What are your vol2surf and fv command lines? 
> > Have you tried it in tksurfer?
> >
> >
> > Thanks again.
> >
> > 
> > Date: Tue, 4 Mar 2014 22:52:38 -0500
> > From: gr...@nmr.mgh.harvard.edu 
> > To: andrewz...@live.com.au 
> > CC: freesurfer@nmr.mgh.harvard.edu
> > 
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
> >
> >
> > On 3/4/14 7:18 PM, Xuelong Zhao wrote:
> >
> > Dear Doug,
> >
> > I've managed to get functional information onto the cortical
> > surface following your instructions.
> >  But, there's a few issues that are still not resolved:
> >
> > 1/ wrt to registration I believe the supplied anatomical
> > template (in tailarach coords) is already aligned with the ica
> > maps (which come from one individual). However, when I run
> > mri_vol2surf I need a registration.dat file so in such a
> > situation is the registration data from the anatomical
> > template sufficient?
> >
> > If the ica maps are in voxel-for-voxel alignment with the template
> > then yes (i,e they must have the same dimension and voxel size)
> >
> >
> > 2/ the nifti file for functional data actually contains 20 ICA
> > components. After I ran mri_vol2surf how do I view each
> > component independently? Currently it seems to only show one
> > particular ICA component in freeview.
> >
> > Bring up the overlay configuration window. Yo

Re: [Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

[Anastasia Yendiki]

Hi Colm - Note that the information in the tutorial (particularly the part 
where gradient tables can be formatted in 3 rows or 3 columns) pertains to 
the latest tracula update:

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

You're using an older version that only supports the 3-column format. I 
have no idea if this is what's causing the error without looking at your 
trac-all.log, but this would be a first guess.


a.y

On Mon, 10 Mar 2014, McGinnity, Colm wrote:


Dear Experts,
 
I am very new to TRACULA, I apologise for what is probably a silly question.
 
I’ve got the following error on running trac-all –prep (FreeSurfer 5.2.0):
 
awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or
directory)
mri_concat --i
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o
/home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
niiRead(): error opening file /home/k1193186/
FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
 
Can anyone tell me what this means and how to fix this, please?
I’m guessing I’ve set up my configuration wrong or have the files in the
wrong place?
 
Many thanks!
Best wishes,
Colm.
King's College London
 
 
 

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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.

Re: [Freesurfer] applying Yeo atlas to individual brains

[Thomas Yeo]

Hi Jeff,

I am a little unsure myself since I usually work with data mapped to
fsaverage space. I think you might want to use mri_surf2surf, since
there's a "--sval-annot" option. It's hard for me to check now because
I am away at a conference.

Can someone chime in if mri_surf2surf is wrong?

Thanks,
Thomas





On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen  wrote:
> What I need are the ?h.Yeo.annot files for the individual subjects, similar 
> to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will 
> mri_label2labe give me that directly?
>
> Thanks,
> -Jeff
>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Monday, March 10, 2014 9:50 AM
> To: Jeff Eriksen
> Cc: 'freesurfer@nmr.mgh.harvard.edu'
> Subject: Re: [Freesurfer] applying Yeo atlas to individual brains
>
> Hi Jeff
>
> you should be able to use mri_label2label to map the Yeo atlas from fsaverage 
> to any subject.
>
> cheers
> Bruce
> On Mon, 10 Mar 2014, Jeff Eriksen wrote:
>
>>
>> Our lab has a need to apply the Yeo atlas to individual brains. As I
>> understand it, Yeo atlas is only currently available for the FSAverage
>> brain. Any plans to incorporate Yeo on to the default FS segmentation,
>> or have it available as an option?
>>
>>
>>
>> -Jeff Eriksen
>>
>>
>>
>>
>>
>
>
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Re: [Freesurfer] Brain Segmentation blurred at the interhemisphere surface

[Louis Nicholas Vinke]

Hi Kaiming,
I'm almost certain you are right at the medial line and what you are 
seeing is the transition from one hemi to the other.  Most likely the 
brain is slightly oblique and so the sagittal slice does not perfectly 
bisect the two hemispheres.
-Louis

On Mon, 10 Mar 2014, Kaiming Yin wrote:

> Hi FreeSurfer guys,
> 
> Just want to ask a quick question. So I have been using freesurfer on the 
> analyses on my brain-
> however I have noticed in certain parts, there hasn't been any segmentations.
> 
> I have attached a picture, to show what I mean. Is there a reason for this? 
> The blurry part kind
> of sweeps across the whole brain. Is there anything then, that I can do in 
> freesurfer to still
> allow it to calculate the segmentation?
> 
> Many thanks,
> Kaiming
> 
>
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Re: [Freesurfer] vtk conversion

[Martin Reuter]

Hi ,

mris_convert has some functionality for VTK output.

Best, Martin

On 03/10/2014 09:51 AM, LAOUCHEDI MAKHLOUF wrote:

Hi all
 i am developping an application for neuronavigation, and i 
want to use freesurfer cortical parcellation and sub-cortical 
segmentation, is there any freesurfer command to convert surface files 
to vtk files ?


Thanks


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Re: [Freesurfer] applying Yeo atlas to individual brains

[Jeff Eriksen]

What I need are the ?h.Yeo.annot files for the individual subjects, similar to 
the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will mri_label2labe 
give me that directly?

Thanks,
-Jeff


-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Monday, March 10, 2014 9:50 AM
To: Jeff Eriksen
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] applying Yeo atlas to individual brains

Hi Jeff

you should be able to use mri_label2label to map the Yeo atlas from fsaverage 
to any subject.

cheers
Bruce
On Mon, 10 Mar 2014, Jeff Eriksen wrote:

> 
> Our lab has a need to apply the Yeo atlas to individual brains. As I 
> understand it, Yeo atlas is only currently available for the FSAverage 
> brain. Any plans to incorporate Yeo on to the default FS segmentation, 
> or have it available as an option?
> 
>  
> 
> -Jeff Eriksen
> 
>  
> 
> 
>


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Re: [Freesurfer] applying Yeo atlas to individual brains

[Bruce Fischl]

Hi Jeff

you should be able to use mri_label2label to map the Yeo atlas from 
fsaverage to any subject.


cheers
Bruce
On Mon, 10 Mar 2014, Jeff Eriksen wrote:



Our lab has a need to apply the Yeo atlas to individual brains. As I
understand it, Yeo atlas is only currently available for the FSAverage
brain. Any plans to incorporate Yeo on to the default FS segmentation, or
have it available as an option?

 

-Jeff Eriksen

 


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Re: [Freesurfer] project locations from template to individual MRIs

[peng]

Thanks Doug for your reply. In fact I need both. I do this mainly for
computation (in volume); and display (in surface) is also cool.

The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in volume
of the template (icbm152). This can be implemented as an Nx3 matrix S,
where S(n, :) = [nx, ny, nz] indicates the location of An in the volume.
RAS here I mean such a coordinate system that, [0 0 0] is AC and the 3
dimensions are taking right, anterior, superior as positive, e.g An([nx0
ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior and nz0 mm
superior of AC.
The above two systems can be easily transformed by a transformation matrix.

I wish to know the correspondent locations of An in individual subject(B),
as Bn. e.g. if A1 is center of V1 in the template, I wish to find the
center of V1 in the subject as B1.
So far, all the locations are represented in volume. However, I guess to
normalise the individual brain to the template, freesurfer will extract the
volumes to surfaces. I imagine the procedure will be like An (volume
representation of dots in template)  -> ASn (surface representation of dots
in template) -> BSn(surface representation of dots in individual) ->
Bn(volume representation of dots in individual). If this assumption is
correct, I would like to use Bn for my computation and ASn for display
later.

I hope I have made myself clearer.

best
Peng


On Mon, Mar 10, 2014 at 4:21 PM, Douglas N Greve
wrote:

>
> Do you mean you want to display them in the MRI volume or on the surface
> (or both)? When you say that they are in "RAS coordinates", what do you
> mean? How are the coords defined?
> doug
>
>
>
> On 03/08/2014 07:26 AM, peng wrote:
> > Dear freesurfers,
> >
> >I have a set of dot locations (300~400) in a template brain,
> > indicated by indices of a 3-D array of the template MRI data, which
> > can be easily transformed to RAS coordinates. I wish to project these
> > dot locations to individual MRIs, ideally also as indicated by indices
> > in the 3-D array of the individual MRI data. Is it possible to do it
> > in freesurfer? I guess the surface-based procedure shall work well for
> > this. It might be a very junior question, if it was documented
> > somewhere before, please let me know the link. Thank you very much for
> > help.
> >
> > best
> > Peng
> >
> >
> > ___
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> properly
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[Freesurfer] applying Yeo atlas to individual brains

[Jeff Eriksen]

Our lab has a need to apply the Yeo atlas to individual brains. As I understand 
it, Yeo atlas is only currently available for the FSAverage brain. Any plans to 
incorporate Yeo on to the default FS segmentation, or have it available as an 
option?

-Jeff Eriksen

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[Freesurfer] TRACULA preprocessing error, FreeSurfer 5.2.0

[McGinnity, Colm]

Dear Experts,

I am very new to TRACULA, I apologise for what is probably a silly question.

I've got the following error on running trac-all -prep (FreeSurfer 5.2.0):

awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or 
directory)
mri_concat --i 
/home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz --mean --o 
/home/k1193186/ FreeSurfer/TRACULA/ROLAND03A/dmri/lowb.nii.gz
niiRead(): error opening file /home/k1193186/ 
FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz
ninputs = 1
Checking inputs
ERROR: reading /home/k1193186/FreeSurfer/TRACULA/ROLAND03A/dmri/dwi_frame.nii.gz

Can anyone tell me what this means and how to fix this, please?
I'm guessing I've set up my configuration wrong or have the files in the wrong 
place?

Many thanks!
Best wishes,
Colm.
King's College London



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Re: [Freesurfer] primary auditory cortex ROI

[Ritobrato Datta]

Hi Doug,

Wow, telepathy…Just resent my email and got this reply. THanks. I need to 
compute the surface area of primary auditory cortex so was looking for an 
approach similar to the Hinds V1 approach and came across two papers by your 
group. So if I can demarcate A1 based on myelination patterns in T1 MPRAGE 
images from 3T, that will be the best solution. Please let me know if thats 
possible. 

Thanks

Rito


- Original Message -
From: Douglas N Greve 
To: freesurfer@nmr.mgh.harvard.edu
Sent: Mon, 10 Mar 2014 11:19:07 -0400 (EDT)
Subject: Re: [Freesurfer] primary auditory cortex ROI

We do have a label for transversetemporal. What do you want to do with 
it? You can extract it out of ?h.aparc.annot or aparc+aseg.mgz, 
depending on what you want to do with it
doug


On 03/08/2014 06:48 AM, Ritobrato Datta wrote:
> Hi All,
>
> I need to demarcate primary auditory cortex in a group of subjects 
> anatomically and I came across the following papers -
>
> https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf
>
> https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf
>
> Is there a script that I can use on my 3T MPRAGE images to get primary 
> auditory cortex ROI ?
>
> That will be very helpful.
>
> Best,
>
> Ri
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>

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Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] primary auditory cortex ROI

[Ritobrato Datta]

Hi All,

My email may have fallen through the cracks over the weekend so I am sending it 
again. 

I need to demarcate primary auditory cortex in a group of subjects anatomically 
and I came across the following papers -

https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf

https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf

Is there a script that I can use on my 3T MPRAGE images to get primary auditory 
cortex ROI ? 

That will be very helpful.

Best,

Ri
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Re: [Freesurfer] Group comparisons

[Douglas N Greve]

On 03/09/2014 05:24 PM, Tudor Popescu wrote:
> Hello,
>
> In addition to this last question, I'd also like to ask the following:
>
> 1) It's very hard to understand a group X gender interaction (age as 
> nuisance) on a graph that has age on the x axis, and with 4 regression 
> lines corresponding to the 4 possible combinations of group 
> (patient/control) and gender (m/f) - see screenshot. Is it possible to 
> only view the means for this interaction in a more standard e.g. SPSS 
> style 
> ,
>  
> either in QDEC or in tksurfer?
No, sorry.
>
> 2) Exactly what hypotheses consistute the "family" whose error rate 
> (FWER) the Monte-Carlo is controlling to a desired alpha (p) value?
The family of clusters.
>
> 3) In a group X gender X age DODS design, exactly which contrast 
> (interaction) has to be examined in order to see if the analysis 
> proceeds as DODS or as DOSS? And what would the course of action be 
> assuming there are significant clusters for that contrast?

group X gender X age, group X age, gender X age

I've had statisticians tell me that you cannot do anything more if there 
is a sig interaction. However, this kind of thing gets published all the 
time without people even checking. If you wanted to push ahead, you have 
to choose an age where you want to do the test (eg, age=0 which would be 
the default or age=mean age). But you have to be aware that a sig effect 
found betweeen groups will depend on the age that you test it.

doug

>
> Many thanks!
> Tudor
>
>
> On 8 March 2014 10:03, Tudor Popescu  > wrote:
>
> > Thanks Doug. I wasn't clear in my DOSS question, I meant to
> ask why
> > are categoricalXcontinuous interactions (e.g. such as the
> one probed
> > by the contrast "Does the thickness-age correlation differ
> between
> > group A and B?") still created in DOSS analyses, when by
> definition
> > DOSS imposes that (e.g.) thickness-age correlations have the
> same
> > slopes for all groups?
> Do not use DOSS with QDEC. There is a bug in it that causes the
> contrasts to be in error at times
>
> I am aware of the contrasts bug, and have noticed some contrasts
> that were wrong, but I was just wondering whether the said
> contrast ("Does the thickness-age correlation differ between group
> A and B?") was is in fact ever meant to be computed, as it seems
> it should not be there by virtue of the definition of DOSS.
>
>
> On 8 March 2014 00:04, Douglas N Greve  > wrote:
>
>
> On 03/07/2014 06:45 PM, Tudor Popescu wrote:
> > Thanks Doug. I wasn't clear in my DOSS question, I meant to
> ask why
> > are categoricalXcontinuous interactions (e.g. such as the
> one probed
> > by the contrast "Does the thickness-age correlation differ
> between
> > group A and B?") still created in DOSS analyses, when by
> definition
> > DOSS imposes that (e.g.) thickness-age correlations have the
> same
> > slopes for all groups?
> Do not use DOSS with QDEC. There is a bug in it that causes the
> contrasts to be in error at times.
> >
> > Two more questions:
> >
> > - If selecting the Volume-based radio-button in QDEC's
> Design tab, the
> > Measure drop-down list is replaced with "Not yet
> implemented", but
> > pressing Analyze still proceeds as normal and delivers the
> expected
> > contrasts. What does "Volume" exactly refer to, in those
> contrasts,
> > and how is that different to the "normalised volume" measured in
> > voxel-based morphometry (VBM)?
> It was supposed to be an analysis like a VBM where you are
> looking a
> volume-structured data instead of surface-structured.
> >
> > - (Bailey, Zatorre, and Penhune 2013) say that "The
> thickness maps
> > produced are not restricted to the voxel resolution of the
> original
> > data and thus are capable of detecting submillimeter differences
> > between groups". Is it really the case that the power of a
> > surface-based analysis is completely independent of the
> resolution of
> > the T1 images? Isn't the accuracy of the mesh dependent on the
> > volumetric (T1) resolution?
>
> Bruce may want to weigh in on this one, but it is not the case
> that any
> resolution will do. I think what they are saying is that the
> surface
> placement (and so thickness est) is better than the voxel size
> (subvox
> rsolution). This can be achieved because of smoothness
> constraints.
>
> doug
>
> 

Re: [Freesurfer] Resting State Networks on Cortical Surface

[Douglas N Greve]

On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> Hi Doug,
>
> To clarify my previous question:
>
> There is definitely some fuzziness when comparing with the mov, 
> whereas the target comparison looks very pristine. I was just 
> wondering if this is expected. The mov, as I scroll through the layers 
> seem to be also slightly offset in certain regions, I guess this again 
> may be due to the fuzziness of the mov fmri data.
Yes this is somewhat expected. The target is the data the surface was 
generated from, so it should look perfect.
>
> Regarding my second q:
>
> I've got this working now- the segfault was due to me naively loading 
> the surface image as a surface, instead of using it as an overlay, I 
> can now successfully scroll through the various frames. However, I 
> noticed that in the documentation to load into matlab, say the left 
> pial surface (with the ICA components on it), I have to save it as a 
> mgz file and then use MRI_read. However, freeview doesn't seem to 
> offer this option once I load the pial surface and the the ICA components?

Sorry, what has to be mgz? What matlab command? What instructions?
doug

>
>
> 
> Date: Thu, 6 Mar 2014 10:19:25 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: andrewz...@live.com.au
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 3/6/14 6:39 AM, Xuelong Zhao wrote:
>
> Hi Doug,
>
> A follow-up. I've gone back and re-done the registration using
> nifti file with the ICA20 maps. I noticed in tkregister2 that when
> I press on the TARGET tab there is extremely good alignment ( i
> think it is to 'orig.mgz' in the mri folder of my subject which I
> had processed using recon-all. While, when I switch to the
> 'moveable' tab the green line seems to be slightly offset, but the
> underlying image is very fuzzy too. Is this an issue?
>
> I don't know without seeing it. The mov is often lower resolution, so 
> some fuzziness is expected.
>
>
> Also, when I load the surface image in freeview produced by
> mri_vol2surf nothing seems to show up, even when I use the
> registration file. In fact, if I have other volumes loaded it
> causes freeview to segfault. When I do manage to load it
> successfully with the anatomical template in talairach space, it
> doesn't really show up and it seems that the anatomical template
> is really small and I have to zoom in a lot. Maybe I didn't
> process/register?
>
> Can you be more specific? What are your vol2surf and fv command lines? 
> Have you tried it in tksurfer?
>
>
> Thanks again.
>
> 
> Date: Tue, 4 Mar 2014 22:52:38 -0500
> From: gr...@nmr.mgh.harvard.edu 
> To: andrewz...@live.com.au 
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> On 3/4/14 7:18 PM, Xuelong Zhao wrote:
>
> Dear Doug,
>
> I've managed to get functional information onto the cortical
> surface following your instructions.
>  But, there's a few issues that are still not resolved:
>
> 1/ wrt to registration I believe the supplied anatomical
> template (in tailarach coords) is already aligned with the ica
> maps (which come from one individual). However, when I run
> mri_vol2surf I need a registration.dat file so in such a
> situation is the registration data from the anatomical
> template sufficient?
>
> If the ica maps are in voxel-for-voxel alignment with the template
> then yes (i,e they must have the same dimension and voxel size)
>
>
> 2/ the nifti file for functional data actually contains 20 ICA
> components. After I ran mri_vol2surf how do I view each
> component independently? Currently it seems to only show one
> particular ICA component in freeview.
>
> Bring up the overlay configuration window. You can control the
> frame/time point from there.
>
>
> 3/ using mri_vol2surf if I want .nii output do I specify thus:
> '--out_type nii' ? (i did this and it seemed to have worked,
> but just wanted to double check).
>
> You can just specify the output file with a .nii extension
> doug
>
>
>
> Thanks!
>
> > Date: Tue, 4 Mar 2014 10:37:19 -0500
> > From: gr...@nmr.mgh.harvard.edu
> 
> > To: andrewz...@live.com.au ;
> freesurfer@nmr.mgh.harvard.edu
> 
> > Subject: Re: [Freesurfer] Resting State Networks on Cortical
> Surface
> >
> >

Re: [Freesurfer] version 5.3 bug fix

[Douglas N Greve]

No, it was not a problem with negative thickness but an 
inaccuracy/inconsistency with the way the surfaces were computed. It is 
not something that is easy to notice (which is how it made it past our QA).
I would re-run them.
doug

On 03/08/2014 11:21 PM, Gregory Kirk wrote:
> In the release notes for 5.3 i find
>
> Stable release version 5.3.0 is a bug fix release to correct the problem with 
> pial and white surface creation affecting thickness and area measures.
>
>
>   
>
> Is this only related to netative thickness values, which i have never found. 
> I have 150 subjects * 3 timepoints that i ran
>
>
> on a cluster with condor linux and freesurfer version 5.1 i myself inspected 
> time point 1 and did analysis and did not
>
> find any unusual problems. i am preparing to do a longitudinal analysis of 
> all 3 timepoints and wondering if
>
> i should reprocess and reinspect everything, considering the bug fix and 
> improvements for longitudinal stream.
>
>
>
>
> thanks
>
>
>
>
> greg
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Re: [Freesurfer] project locations from template to individual MRIs

[Douglas N Greve]

Do you mean you want to display them in the MRI volume or on the surface 
(or both)? When you say that they are in "RAS coordinates", what do you 
mean? How are the coords defined?
doug



On 03/08/2014 07:26 AM, peng wrote:
> Dear freesurfers,
>
>I have a set of dot locations (300~400) in a template brain, 
> indicated by indices of a 3-D array of the template MRI data, which 
> can be easily transformed to RAS coordinates. I wish to project these 
> dot locations to individual MRIs, ideally also as indicated by indices 
> in the 3-D array of the individual MRI data. Is it possible to do it 
> in freesurfer? I guess the surface-based procedure shall work well for 
> this. It might be a very junior question, if it was documented 
> somewhere before, please let me know the link. Thank you very much for 
> help.
>
> best
> Peng
>
>
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Re: [Freesurfer] primary auditory cortex ROI

[Douglas N Greve]

We do have a label for transversetemporal. What do you want to do with 
it? You can extract it out of ?h.aparc.annot or aparc+aseg.mgz, 
depending on what you want to do with it
doug


On 03/08/2014 06:48 AM, Ritobrato Datta wrote:
> Hi All,
>
> I need to demarcate primary auditory cortex in a group of subjects 
> anatomically and I came across the following papers -
>
> https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al._-_NeuroImage.pdf
>
> https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf
>
> Is there a script that I can use on my 3T MPRAGE images to get primary 
> auditory cortex ROI ?
>
> That will be very helpful.
>
> Best,
>
> Ri
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Re: [Freesurfer] Group Analysis Age slopes

[Douglas N Greve]

On 03/07/2014 07:46 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks for your reply. Yes there were areas of significant difference
> reported in the age slopes maps, after the mri_glmfit command was run.
> However, I haven't checked to see yet whether there are surviving clusters
> after correction for multiple comparisons. I see, yes that definitely
> makes sense especially since the slopes have an opposite sign. However I
> still had a couple questions:
>
> 1) If I did want to look at what the age-corrected trait looked like when
> compared between the Diseased and Healthy groups at age=mean instead of
> age=0, what would I need to do?
Subtract the mean age (computed across all subjects regardless of group) 
from the age of each subject
>
> 2) When not including the age in the fsgd file and using a design matrix
> of [1 -1] I get the significant differences between the average trait in
> the diseased cases vs the average trait in the control cases. Is there a
> way to get a summary file with the actual averages along with the
> significance maps?
If you run mri_glmfit-sim it will produce a lot of summaries. Run it 
with --help to see if what you want is there
doug
>
> Thanks a lot for your help!
> Panos
>
>> Was the difference in the age slopes significant? Ie, and interaction
>> between age and group. If so, then you have to proceed with caution (at
>> least one statistician told me not to proceed at at:) because the
>> difference in the intercepts between the two groups will depend on age
>> making it very difficult to interpret. At the age where the lines
>> intercept, there will be no difference
>> doug
>>
>>
>> On 03/07/2014 02:57 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>> Hi Doug,
>>>
>>> I ran a group analysis comparing a trait between two groups (Diseased vs
>>> Controls) with one continuous variable (age), with the following design
>>> matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map
>>> and
>>> the descriptor file, the age slope of the trait in Controls was positive
>>> whereas the age slope of the trait in the Diseased cases was negative.
>>> Therefore, comparing the intercept between the two groups does not
>>> really
>>> give that much info, since the slopes are of opposite sign. What do you
>>> believe would be the best course of action in order to compare the
>>> age-corrected traits:
>>> 1) instead of age=0 maybe comparing the groups at age=mean?
>>> 2) or going with a DOSS model?
>>>
>>> Thank you for your time,
>>> Panos
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>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
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>>
>>
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MGH-NMR Center
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Fax: 617-726-7422

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Re: [Freesurfer] Looking for cortical thickness procedure

[Bruce Fischl]

Hi Saurabh

this is all done for you in recon-all (not tkmedit). Why not just run it?

Bruce
On 
Mon, 10 Mar 2014, Saurabh Thakur wrote:

> Hello freesurfer Expert,
> Steps for measuring cortical thickness are in tkmedit :
>  1.
>
> Intensity normalisation,
>
>  2.
>
> Registration to Talairach space,
>
>  3.
>
> Skull stripping,
>
>  4.
>
> Segmentation of white matter,
>
>  5.
>
> Tesselation of the WM boundary,
>
>  6.
>
> Smoothing of the tesselated surface and automatic topology correction
> 
> Can u help me to step no 5 and 6. How to do this steps.
> 
> Thanks,
> Saurabh Thakur,
> 
> 
> 
> 
> 
>
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[Freesurfer] vtk conversion

[LAOUCHEDI MAKHLOUF]

Hi all
 i am developping an application for neuronavigation, and i want to use 
freesurfer cortical parcellation and sub-cortical segmentation, is there any 
freesurfer command to convert surface files to vtk files ?

Thanks
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[Freesurfer] Looking for cortical thickness procedure

[Saurabh Thakur]

Hello freesurfer Expert,
Steps for measuring cortical thickness are in tkmedit :

   1.

   Intensity normalisation,
   2.

   Registration to Talairach space,
   3.

   Skull stripping,
   4.

   Segmentation of white matter,
   5.

   *Tesselation of the WM boundary, *
   6.

   *Smoothing of the tesselated surface and automatic topology correction*

Can u help me to step no 5 and 6. How to do this steps.

Thanks,
Saurabh Thakur,
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