Hi Bruce, Thanks for the reply. By "coordinates" I mean all the voxels that belong to a certain structure. I think it's called "labels"? I interest in the main structures like Hippocampus, Thalamus, Cerebellum, Amygdala, corpus callosum, etc. If the standard segmentation segments in that specificity only the lobes, it can be good enough... I see the .mgz files, but can not extract them... How should I do that?

Thank for the patience.. Adiel

2017-07-23 18:09 GMT+03:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

Hi Adiel

what kind of coordinates do you mean, and which brain structures are you interested in? Our standard segmentation is sampled into the volume in files named aparc*+aseg.mgz, but the Brodmann area estimates are on the surface.

cheers Bruce

On Sun, 23 Jul 2017, עדיאל חרבש wrote:

Hi,

...

I'm very new to Freesurfer, and actually work with some exist results of other people. The results are from the call of "-recon all -autorun". I try to get all the coordinates of each of the structures of the brain, that segmented. I can find on files only the volumes of some structures and something that look like detailed coordinates of Brodman Areas only. But I can't find the detailed coordinates of all structures in brain.

I'll be grateful if someone can guide me where can I find it, or what should I do to get these results.

Thanks, Adiel

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Hi Adiel

in matlab you could do something like:

cd $SUBJECTS_DIR/<subject id>/mri matlab

...

[v,M,mr] = load_mgh('aseg.mgz'); left_hippo_indices = find(v == 17);

where the '17' comes from $FREESURFER_HOME/FreeSurferColorLUT.txt and is the index for left hippocampus.

Is that would you mean? Or you could use mri_extract_labels to build volumes that have only the labels you want in them.

cheers Bruce

On Mon, 24 Jul 2017, עדיאל חרבש wrote:

Hi Bruce, Thanks for the reply. By "coordinates" I mean all the voxels that belong to a certain structure. I think it's called "labels"? I interest in the main structures like Hippocampus, Thalamus, Cerebellum, Amygdala, corpus callosum, etc. If the standard segmentation segments in that specificity only the lobes, it can be good enough... I see the .mgz files, but can not extract them... How should I do that?

Thank for the patience.. Adiel

2017-07-23 18:09 GMT+03:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Adiel

  what kind of coordinates do you mean, and which brain structures
  are you interested in? Our standard segmentation is sampled into
  the volume in files named aparc*+aseg.mgz, but the Brodmann area
  estimates are on the surface.

  cheers
  Bruce


  On Sun, 23 Jul 2017, עדיאל חרבש wrote:

        Hi,
        I'm very new to Freesurfer, and actually work with
        some exist results of
        other people. The results are from the call of
        "-recon all -autorun".
        I try to get all the coordinates of each of the
        structures of the brain,
        that segmented. I can find on files only the volumes
        of some structures and
        something that look like detailed coordinates of
        Brodman Areas only. But I
        can't find the detailed coordinates of all
        structures in brain.

        I'll be grateful if someone can guide me where can I
        find it, or what should
        I do to get these results.

        Thanks,
        Adiel

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HI Adiel

we distribute all our matlab scripts as part of FreeSurfer

cheers Bruce On Mon, 24 Jul 2017, עדיאל חרבש wrote:

Hi Bruce, It may really help to shorten and ease the procedure, thanks. I see that I should clone all your matlab repository to use this function?

I will look over mri_extract_labels as well.

Best, Adiel

2017-07-24 17:02 GMT+03:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Adiel

  in matlab you could do something like:

  cd $SUBJECTS_DIR/<subject id>/mri
  matlab
              [v,M,mr] = load_mgh('aseg.mgz');
              left_hippo_indices = find(v == 17);



  where the '17' comes from
  $FREESURFER_HOME/FreeSurferColorLUT.txt and is the index for
  left hippocampus.

  Is that would you mean? Or you could use mri_extract_labels to
  build volumes that have only the labels you want in them.

  cheers
  Bruce




  On Mon, 24 Jul 2017, עדיאל חרבש wrote:

        Hi Bruce,
        Thanks for the reply.
        By "coordinates" I mean all the voxels that belong
        to a certain structure. I
        think it's called "labels"? I interest in the main
        structures like
        Hippocampus, Thalamus, Cerebellum, Amygdala, corpus
        callosum, etc. If the
        standard segmentation segments in that specificity
        only the lobes, it can be
        good enough...
        I see the .mgz files, but can not extract them...
        How should I do that?

        Thank for the patience..
        Adiel


        2017-07-23 18:09 GMT+03:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              Hi Adiel

              what kind of coordinates do you mean, and
        which brain structures
              are you interested in? Our standard
        segmentation is sampled into
              the volume in files named aparc*+aseg.mgz, but
        the Brodmann area
              estimates are on the surface.

              cheers
              Bruce


              On Sun, 23 Jul 2017, עדיאל חרבש wrote:

                    Hi,
                    I'm very new to Freesurfer, and actually
        work with
                    some exist results of
                    other people. The results are from the
        call of
                    "-recon all -autorun".
                    I try to get all the coordinates of each
        of the
                    structures of the brain,
                    that segmented. I can find on files only
        the volumes
                    of some structures and
                    something that look like detailed
        coordinates of
                    Brodman Areas only. But I
                    can't find the detailed coordinates of
        all
                    structures in brain.

                    I'll be grateful if someone can guide me
        where can I
                    find it, or what should
                    I do to get these results.

                    Thanks,
                    Adiel



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If you want all the coordinates for a given segment (eg, left hippo), then you can run mri_cor2label --i aparc+aseg.mgz --id 17 --l file.label

17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt

The coordinates will be in "tkregister space" which you can convert to MNI305 using the info from here:

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

using case #2

On 7/24/17 2:11 AM, עדיאל חרבש wrote:

Hi Bruce, Thanks for the reply. By "coordinates" I mean all the voxels that belong to a certain structure. I think it's called "labels"? I interest in the main structures like Hippocampus, Thalamus, Cerebellum, Amygdala, corpus callosum, etc. If the standard segmentation segments in that specificity only the lobes, it can be good enough... I see the .mgz files, but can not extract them... How should I do that?

Thank for the patience.. Adiel

2017-07-23 18:09 GMT+03:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:

Hi Adiel

what kind of coordinates do you mean, and which brain structures
are you interested in? Our standard segmentation is sampled into
the volume in files named aparc*+aseg.mgz, but the Brodmann area
estimates are on the surface.

cheers
Bruce



On Sun, 23 Jul 2017, עדיאל חרבש wrote:

    Hi,
    I'm very new to Freesurfer, and actually work with some exist
    results of
    other people. The results are from the call of "-recon all
    -autorun".
    I try to get all the coordinates of each of the structures of
    the brain,
    that segmented. I can find on files only the volumes of some
    structures and
    something that look like detailed coordinates of Brodman Areas
    only. But I
    can't find the detailed coordinates of all structures in brain.

    I'll be grateful if someone can guide me where can I find it,
    or what should
    I do to get these results.

    Thanks,
    Adiel



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I would put the spm and fs analysis into the same space

On 07/25/2017 10:19 AM, עדיאל חרבש wrote:

Hi Douglas, Thank you, works perfectly. But, I need to know first which structures id's are inside each file. I preferred to extract all the brain map with Matlab, as Bruce commented.

Now I try to match the coordinates, according to the linked you posted. The brain space in results is of 256x256x256 voxels. What are the dimensions of each voxel here? If I need to compare that results to another analysis that come from SPM, so case #2 is the way? And then, I'll need in fact the coordinates from mri_cor2label?

Thanks for the fast and useful replies. Adiel

2017-07-24 22:11 GMT+03:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:

If you want all the coordinates for a given segment (eg, left
hippo), then you can run mri_cor2label --i aparc+aseg.mgz --id 17
--l file.label

17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt

The coordinates will be in "tkregister space" which you can
convert to MNI305 using the info from here:

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
<https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems>

using case #2


On 7/24/17 2:11 AM, עדיאל חרבש wrote:

...

Hi Bruce,
Thanks for the reply.
By "coordinates" I mean all the voxels that belong to a certain
structure. I think it's called "labels"? I interest in the main
structures like Hippocampus, Thalamus, Cerebellum, Amygdala,
corpus callosum, etc. If the standard segmentation segments in
that specificity only the lobes, it can be good enough...
I see the .mgz files, but can not extract them... How should I do
that?

Thank for the patience..
Adiel


2017-07-23 18:09 GMT+03:00 Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>:

    Hi Adiel

    what kind of coordinates do you mean, and which brain
    structures are you interested in? Our standard segmentation
    is sampled into the volume in files named aparc*+aseg.mgz,
    but the Brodmann area estimates are on the surface.

    cheers
    Bruce



    On Sun, 23 Jul 2017, עדיאל חרבש wrote:

        Hi,
        I'm very new to Freesurfer, and actually work with some
        exist results of
        other people. The results are from the call of "-recon
        all -autorun".
        I try to get all the coordinates of each of the
        structures of the brain,
        that segmented. I can find on files only the volumes of
        some structures and
        something that look like detailed coordinates of Brodman
        Areas only. But I
        can't find the detailed coordinates of all structures in
        brain.

        I'll be grateful if someone can guide me where can I find
        it, or what should
        I do to get these results.

        Thanks,
        Adiel



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finding coordinates is the same problem as putting the results into the same space (except probably harder). There is not a simple formula for converting one to the other. Eg, fsaverage uses MNI305 space. What is SPM using? You have to figure out all these things to convert

On 07/26/2017 04:10 AM, עדיאל חרבש wrote:

Oh, sure you are right. But each analysis is done on different protocols, and also, for now I already have many of analysis results that has been run on the SPM and on Freesurfer, and has a difference in coordinates. So- for now, what is the right way to treat that? the link that you gave up here? And for future- how can I set the dimensions for the results in freesurfer? For example, my data is 432x432x150, but the segmentation results are 256x256x256.

Thank you. Adiel

2017-07-25 20:51 GMT+03:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:

I would put the spm and fs analysis into the same space


On 07/25/2017 10:19 AM, עדיאל חרבש wrote:
> Hi Douglas,
> Thank you, works perfectly.
> But, I need to know first which structures id's are inside each
file.
> I preferred to extract all the brain map with Matlab, as Bruce
commented.
>
> Now I try to match the coordinates, according to the linked you
posted.
> The brain space in results is of 256x256x256 voxels. What are the
> dimensions of each voxel here?
> If I need to compare that results to another analysis that come from
> SPM, so case #2 is the way? And then, I'll need in fact the
> coordinates from mri_cor2label?
>
> Thanks for the fast and useful replies.
> Adiel
>
> 2017-07-24 22:11 GMT+03:00 Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>:
>
>     If you want all the coordinates for a given segment (eg, left
>     hippo), then you can run mri_cor2label --i aparc+aseg.mgz
--id 17
>     --l file.label
>
>     17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt
>
>     The coordinates will be in "tkregister space" which you can
>     convert to MNI305 using the info from here:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
<https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems>
>     <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
<https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems>>
>
>     using case #2
>
>
>     On 7/24/17 2:11 AM, עדיאל חרבש wrote:
>>     Hi Bruce,
>>     Thanks for the reply.
>>     By "coordinates" I mean all the voxels that belong to a certain
>>     structure. I think it's called "labels"? I interest in the main
>>     structures like Hippocampus, Thalamus, Cerebellum, Amygdala,
>>     corpus callosum, etc. If the standard segmentation segments in
>>     that specificity only the lobes, it can be good enough...
>>     I see the .mgz files, but can not extract them... How
should I do
>>     that?
>>
>>     Thank for the patience..
>>     Adiel
>>
>>
>>     2017-07-23 18:09 GMT+03:00 Bruce Fischl
>>     <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>>:
>>
>>         Hi Adiel
>>
>>         what kind of coordinates do you mean, and which brain
>>         structures are you interested in? Our standard segmentation
>>         is sampled into the volume in files named aparc*+aseg.mgz,
>>         but the Brodmann area estimates are on the surface.
>>
>>         cheers
>>         Bruce
>>
>>
>>
>>         On Sun, 23 Jul 2017, עדיאל חרבש wrote:
>>
>>             Hi,
>>             I'm very new to Freesurfer, and actually work with some
>>             exist results of
>>             other people. The results are from the call of "-recon
>>             all -autorun".
>>             I try to get all the coordinates of each of the
>>             structures of the brain,
>>             that segmented. I can find on files only the volumes of
>>             some structures and
>>             something that look like detailed coordinates of
Brodman
>>             Areas only. But I
>>             can't find the detailed coordinates of all
structures in
>>             brain.
>>
>>             I'll be grateful if someone can guide me where can
I find
>>             it, or what should
>>             I do to get these results.
>>
>>             Thanks,
>>             Adiel
>>
>>
>>
>>         _______________________________________________
>>         Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>         <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>
>>
>>
>>         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
<http://www.partners.org/complianceline>
>>         <http://www.partners.org/complianceline
<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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>     The information in this e-mail is intended only for the
person to
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Phone Number: 617-724-2358
Fax: 617-726-7422

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