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.edumailto: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
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