OK, got it. The problem is that your images are aligned in physical coordinates, but not in voxel coordinates. FreeView handles that nicely, but I don’t know about FSLview. The subfield code also generates files named *.FSvoxelSpace.mgz, which are in the same voxel coordinates as the recon-all files. You can try using those instead. Regarding the voxel size of your T1s: the volumes are always in cubic millimeters ;-) Cheers, /Eugenio

-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon erikohanlon@rcsi.ie Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 12 January 2018 at 15:13 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] making masks with subfields etc

Hello Eugenio,

Thanks for your reply. When I'm in freeview, the hippocampus and even the amgydala from the aseg align nicely with my input T1 image. I suspect that it could be an issue when export ing them from freeview. I just saved the hippocampus etc as nii volumes and then tried to open them in FSL view with my T1 which has my DWI image aligned but it complains about image size and dimensions etc which made me think that the hippocampus volumes etc weren't in the same space as my T1. So my files in the subject/mri dir (T1, aseg and hippo etc) are all in native space (the same space that my initial T1 image fed into reconall is in)?

Sorry for the confusion on my part.

Also as an aside, teh hippocampal subfield measures in the txt files giving the volume for each subfield, are they in mm3 or if my T1 is 0.89mm3 do I need to adjust for that.

Thanks again for any help.

Best regards

Erik ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk] Sent: 12 January 2018 14:21 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E

-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon erikohanlon@rcsi.ie Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 12 January 2018 at 13:07 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] making masks with subfields etc

Hi FS experts,

I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus and amygdala as volume ROI masks for tractography. 1. My diffusion data is registered to my T1 data. Just wondering is it the rawavg.mgz file I need to register the ROI's to? 2. I'm using freeview and 3D rendererd the Hippocampus (203-226) and saved that as a volume. Do I use the mri_vol2vol command to align my roi's to the rawavg image for correctly map onto my T1 native space image because when I try that it seems that the ROI volume image can't be opened. I think I must be missing a step when creating the mask perhaps? 3. If I also wish to generate additional masks from the aseg.mgz, will that be done via the same steps used for the hippocampus or do I need to use the fslmaths <input imgae> -thr LUT number of the subcorical structure -uthr lut number again <output filename> first and then regsiter them to the rawavg.mzg?

Thanks for any guidance which is always greatly appreciated.

Best regards

Erik

Erik O'Hanlon Postdoctoral researcher

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RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie/

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