Dear FreeSurfer team,
I am writing a paper about FreeSurfer's estimates of intracranial volume (eTIV), when using FreeSurfer version 5.3.0, and have two questions that I would be very grateful if you could answer.
My understanding is that the alignment (from which the atlas scaling factor is calculated) of the input MR images to the MNI305 atlas is done by the “Avi Snyders 4dfp suite” (see https://surfer.nmr.mgh.harvard.edu/fswiki/talairach and https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi), and using this suite FreeSurfer is trying to align the input images to the brain and about a two cm thick layer around the brain in the MNI305 atlas (see https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-September/008370.... guess that FreeSurfer uses the function imgreg_4dfp (in the 4dfp suite, see https://searchcode.com/codesearch/view/39432481/) for the alignment with the following arguments: 1) the MNI305 atlas (as the target image), 2) a target image mask (so that the adoption/evaluation of the alignment only will be done towards the brain and the two cm thick layer around the brain), and 3) the input MR images (as the object image).
My questions are:
1) Is my understanding and/or guess correct?
2) Is there any paper or manual available that you know of that describe the alignment procedure used in the 4dfp suite?
Thanks in advance!
Best regards,
Niklas
Hi Niklas,
I cannot answer your question on the 4dfp suite, but want to point you at http://www.freesurfer.net/fswiki/eTIV It says that newer version in FreeSurfer "use the atlas $FREESURFER_HOME/average/711-2C_as_mni_average_305.4dfp.img and the registration to that atlas is found in $SUBJECTS_DIR/subjid/mri/transforms/talairach.xfm (created by talairach_avi http://www.freesurfer.net/fswiki/talairach_avi, a script which calls imgreg_4dfp). Note that the '711-2C' target image includes skull. "
In earlier version (4.2 and earlier) mri_em_register was used to create talairach_with_skull.lta, registerting to the RB_all_withskull_2008-03-26.gca atlas. We got a slightly better fit into manual TIV estimates using the talairach.xfm, so we switched to that (documented on the wiki above).
Best, Martin
On 01/20/2016 10:18 AM, Niklas Klasson wrote:
Dear FreeSurfer team,
I am writing a paper about FreeSurfer's estimates of intracranial volume (eTIV), when using FreeSurfer version 5.3.0, and have two questions that I would be very grateful if you could answer.
My understanding is that the alignment (from which the atlas scaling factor is calculated) of the input MR images to the MNI305 atlas is done by the “Avi Snyders 4dfp suite” (see _https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_ and https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi https://surfer.nmr.mgh.harvard.edu/fswiki/talairach_avi), and using this suite FreeSurfer is trying to align the input images to the brain *and about a two cm thick layer around the brain* in the MNI305 atlas (see _https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-September/008370.... guess that FreeSurfer uses the function imgreg_4dfp (in the 4dfp suite, see https://searchcode.com/codesearch/view/39432481/ https://searchcode.com/codesearch/view/39432481/) for the alignment with the following arguments: 1) the MNI305 atlas (as the target image), 2) a target image mask (so that the adoption/evaluation of the alignment only will be done towards the brain and the two cm thick layer around the brain), and 3) the input MR images (as the object image).
My questions are:
1)Is my understanding and/or guess correct?
2)Is there any paper or manual available that you know of that describe the alignment procedure used in the 4dfp suite?
Thanks in advance!
Best regards,
Niklas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Martin Reuter -
Niklas Klasson