glad it worked out :) On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

Hi Bruce,

thanks for a quick reply! mri_surf2surf worked fine just with specifying the target and source subjects, no registration file needed - much appreciated :)

Best regards, Patrycja

2017-04-26 22:51 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Patrycja

  the standard transform we use to fsaverage coordinates is
  surface-based (spherical). If you sample your EPI onto the
  surface, I believe you can use mri_surf2surf to transfer it from
  subject to fsaverage

  cheers
  Bruce
  On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

        Hello FS experts,

        I have a question regarding FS-Fast processing. I
        have performed
        (successfully!)  an FS-Fast single subject analysis.
        The results look fine
        in the fsaverage space, but I'm interested in
        viewing them in the subject
        space.

        Are the registration files used along the processing
        pipeline
        (EPI->T1->fsaverage) stored anywhere (so far I only
        found the EPI->T1 and
        T1->talairach files), so I can use them? Or do I
        need to create new
        registration files (bbregister/tkregister2)?

        Best regards,
        Patrycja

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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.

If you just want to view the result on the native anatomy, you can use tkmedit-sess with the -self option. You can do the same thing with tksurfer-sess to view the surface-based data on the subject's own surface instead of fsaverage. If this is something you want to do in general, you can analyze directly in the subject's space (most people are doing group analysis, so this does not make sense in general)

On 04/27/2017 08:15 AM, Patrycja Naumczyk wrote:

Hi everyone again,

I transformed the surfaces from fsaverage to subject's space fine but I got stuck on the subcortical volume transformation. I apologize, as this is probably basic, still I run out of ideas...

So, my problem is to transform the 'sig.nii.gz' map (of the subcortical activations from standard FS-Fast pipeline) from the mni305 to the orig space of the subject. I found the 'talairach.xfm' transform from the orig->MNI space, but I didn't find the reversed registration file (if it exists anywhere, please let me know). So I created the back-registration file with bbregister: /bbregister --s Sub001 --mov ~/Freesurfer/subjects/fsaverage/mri/mni305.cor.mgz --T1 --init-fsl --reg mni2subject.dat/

I checked both with the tkregister2 and with the freeview that the orig.mgz and the mni305 with applied registration align. So I tried to apply this registration parameters to the sig.nii.gz with mri_vol2vol: /mri_vol2vol --mov sig.nii.gz --targ ~/Freesurfer/subjects/Sub001/mri/orig.mgz --reg mni2subject.dat --o sig.native.nii.gz/ But the output 'sig.native.nii.gz' does not align with the 'orig.mgz' of the subject.

What's more, the prompt on the terminal suggests to check for the registration with: /tkregister2 --mov sig.native.nii.gz --targ /home/pati/Freesurfer/subjects/Sub001/mri/orig.mgz --reg sig.native.nii.gz.reg/

as if it was the output file (sig.native...) being moved with the registration parameters. So I assume that I've messed up something?

So all in end I have a strange situation when sig.nii aligns with MNI, MNI with registration aligns with orig.mgz, but sig.nii with registration does not align with orig.mgz. I will appreciate any ideas of - how to deal with the problem. Also, as it is highly possible, maybe there's an easier way of transforming the volume output of fs-fast back to orig subject space?

I'm running Freesurfer 5.3 on Gentoo Linux.

Best regards, Patrycja

2017-04-26 23:20 GMT+02:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>:

glad it worked out :)

On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

    Hi Bruce,

    thanks for a quick reply! mri_surf2surf worked fine just with
    specifying the
    target and source subjects, no registration file needed - much
    appreciated
    :)

    Best regards,
    Patrycja

    2017-04-26 22:51 GMT+02:00 Bruce Fischl
    <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>:
          Hi Patrycja

          the standard transform we use to fsaverage coordinates is
          surface-based (spherical). If you sample your EPI onto the
          surface, I believe you can use mri_surf2surf to transfer
    it from
          subject to fsaverage

          cheers
          Bruce
          On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:

                Hello FS experts,

                I have a question regarding FS-Fast processing. I
                have performed
                (successfully!)  an FS-Fast single subject analysis.
                The results look fine
                in the fsaverage space, but I'm interested in
                viewing them in the subject
                space.

                Are the registration files used along the processing
                pipeline
                (EPI->T1->fsaverage) stored anywhere (so far I only
                found the EPI->T1 and
                T1->talairach files), so I can use them? Or do I
                need to create new
                registration files (bbregister/tkregister2)?

                Best regards,
                Patrycja


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On 4/29/17 8:51 AM, Patrycja Naumczyk wrote:

Hi Douglas,

thanks for the tip - as a new FS user I didn't mastered tkmedit yet, so it's good to know that this viewer supports MNI->orig transformation automatically.

In v6, tkmedit-sess actually calls freeview, and tkmedit-sess will apply all the necessary transforms, so you should not need to do anything once the image comes up

I understand it's unusual to perform a single subject fMRI in freesurfer. It's just that we came across a very interesting case study of pure alexia, in which presenting fMRI results in patient space is crucial for further interpretation. I thought of re-runing the analyses in subject space (as You suggested), and probably will end up doing so. Just for the record and expanding my FS skills, I would very much liked to know - where is my mistake in the process of transforming the 'sig.nii.gz' volumes from MNI to orig space. I suppose that's an issue I may came across in future as well (even if with different files/spaces). So - any help in that matter is still very much appreciated!

It is a little tricky, but if you look in tkmedit-sess you will find the code that creates the matrix and applies the transform

And also, even though not designed for the purpose of case studies, I have to admit - Freesurfer is so incredible! I processed this very same subject through SPM's fMRI stream, and didn't got even partly as conclusive and precise statistical maps. I've become a huge fan of surface-based analyses :) You're doing amazing job with developing this software!

Glad to have another happy customer!

Best regards, Patrycja

2017-04-27 17:14 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:

If you just want to view the result on the native anatomy, you can use
tkmedit-sess with the -self option. You can do the same thing with
tksurfer-sess to view the surface-based data on the subject's own
surface instead of fsaverage. If this is something you want to do in
general, you can analyze directly in the subject's space (most people
are doing group analysis, so this does not make sense in general)



On 04/27/2017 08:15 AM, Patrycja Naumczyk wrote:
> Hi everyone again,
>
> I transformed the surfaces from fsaverage to subject's space
fine but
> I got stuck on the subcortical volume transformation. I
apologize, as
> this is probably basic, still I run out of ideas...
>
> So, my problem is to transform the 'sig.nii.gz' map (of the
> subcortical activations from standard FS-Fast pipeline) from the
> mni305 to the orig space of the subject.
> I found the 'talairach.xfm' transform from the orig->MNI space,
but I
> didn't find the reversed registration file (if it exists anywhere,
> please let me know). So I created the back-registration file with
> bbregister:
> /bbregister --s Sub001 --mov
> ~/Freesurfer/subjects/fsaverage/mri/mni305.cor.mgz --T1 --init-fsl
> --reg mni2subject.dat/
>
> I checked both with the tkregister2 and with the freeview that the
> orig.mgz and the mni305 with applied registration align. So I
tried to
> apply this registration parameters to the sig.nii.gz with
mri_vol2vol:
> /mri_vol2vol --mov sig.nii.gz --targ
> ~/Freesurfer/subjects/Sub001/mri/orig.mgz --reg mni2subject.dat --o
> sig.native.nii.gz/
> But the output 'sig.native.nii.gz' does not align with the 'orig.mgz'
> of the subject.
>
> What's more, the prompt on the terminal suggests to check for the
> registration with:
> /tkregister2 --mov sig.native.nii.gz --targ
> /home/pati/Freesurfer/subjects/Sub001/mri/orig.mgz --reg
> sig.native.nii.gz.reg/
>
> as if it was the output file (sig.native...) being moved with the
> registration parameters. So I assume that I've messed up something?
>
> So all in end I have a strange situation when sig.nii aligns
with MNI,
> MNI with registration aligns with orig.mgz, but sig.nii with
> registration does not align with orig.mgz.
> I will appreciate any ideas of - how to deal with the problem. Also,
> as it is highly possible, maybe there's an easier way of
transforming
> the volume output of fs-fast back to orig subject space?
>
> I'm running Freesurfer 5.3 on Gentoo Linux.
>
> Best regards,
> Patrycja
>
> 2017-04-26 23:20 GMT+02:00 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>>>:
>
>     glad it worked out :)
>
>     On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:
>
>         Hi Bruce,
>
>         thanks for a quick reply! mri_surf2surf worked fine just
with
>         specifying the
>         target and source subjects, no registration file needed
- much
>         appreciated
>         :)
>
>         Best regards,
>         Patrycja
>
>         2017-04-26 22:51 GMT+02:00 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 Patrycja
>
>               the standard transform we use to fsaverage
coordinates is
>               surface-based (spherical). If you sample your EPI
onto the
>               surface, I believe you can use mri_surf2surf to
transfer
>         it from
>               subject to fsaverage
>
>               cheers
>               Bruce
>               On Wed, 26 Apr 2017, Patrycja Naumczyk wrote:
>
>                     Hello FS experts,
>
>                     I have a question regarding FS-Fast
processing. I
>                     have performed
>                     (successfully!)  an FS-Fast single subject
analysis.
>                     The results look fine
>                     in the fsaverage space, but I'm interested in
>                     viewing them in the subject
>                     space.
>
>                     Are the registration files used along the
processing
>                     pipeline
>                     (EPI->T1->fsaverage) stored anywhere (so far
I only
>                     found the EPI->T1 and
>                     T1->talairach files), so I can use them? Or do I
>                     need to create new
>                     registration files (bbregister/tkregister2)?
>
>                     Best regards,
>                     Patrycja
>
>
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