There are several things that will need to be done, and they can be quite tricky. Since you already have a registration between the fMRI and the MNI, you will have to create a rigid registration from the FS anatomical to the fMRI, then concatenate the registrations into a single registration. You can then apply the registration to the  FS segementation with mri_label2vol using the --seg option. It will not be easy to extract all these matrices, sorry, I don't know enough about SPM to help  you out much more.

On 6/13/2019 5:37 PM, Nelson, Eric A wrote:

        External Email - Use Caution        

Thanks for your response,

 

I believe CONN should be using SPM linear?

 

Best,

 

Eric

From: Greve, Douglas N.,Ph.D. [mailto:DGREVE@mgh.harvard.edu]
Sent: Wednesday, June 12, 2019 8:27 AM
To: Nelson, Eric A <eanelson@uab.edu>
Subject: Re: [Freesurfer] hippocampal subfield as CONN seeds

 

I meant how does CONN do the registration? SPM linear? FSL non-linear? That command definitely will not work. You have to do it in exactly the same way as CONN or else the segmentations won't align.


On 6/12/2019 2:39 PM, Nelson, Eric A wrote:

        External Email - Use Caution        

Hi,

 

Not sure I sent this correctly the last time. Im not sure I understand the question because I have not successfully registered the hippoSfLabels file to mni space. I can load the hippoSfLabels.mgz file into CONN at the subject level, but I have two problems. 1st it is not in MNI space. 2nd it is the whole hippocampus and I want to be able to use masks of the individual subfields. To try and convert the hippoSfLabels file to MNI space though I used the following.

 

mri_vol2vol --mov lh.hippoSfLabels-T1-T2.v10.mgz \

--targ $FREESURFER_HOME/average/mni305.cor.mgz \

--xfm transforms/talairach.xfm  \

--o test.mgz

 

Eric

 

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.