---------- Forwarded message ---------- From: Rafael Huber rafael@huberworld.ch Date: 11.09.2007 09:19 Subject: Re: Re: [Freesurfer] Average Volume To: Doug Greve greve@nmr.mgh.harvard.edu
Hy Doug,
Thank you for your help. I tried to do it with your advice, but when i runned "mri_concat --i SUBJECTS*/surf/lh.volume.mgz --o lh.volume --mean" i always got an error message called "ERROR: dimension mismatch between SUBJECT1/surf/lh.volume.mgz and SUBJECT2/surf/lh.volume.mgz". I created all the volume.mgz files in the same way in matlab. Do you have an idea? Thanks in advance.
Best Regards Rafael
2007/9/4, Doug Greve greve@nmr.mgh.harvard.edu:
Try following the instructions for doing a thickness study, ie, run mris_preproc specifying lh.volume.mgz as the measure, then run either mri_glmfit with --osgm or run mri_concat with --mean.
doug
On Mon, 3 Sep 2007, Rafael Huber wrote:
Our goal is to get a file of average volume. As i understand the make average command it takes the whole information of e.g. ?h.thickness out of every /surf folder of every subject and creates an average ?h.thickness file and saves it to /average/surf. i try to do the same with the ?h.volume.mgz files, which we created with the matlab command you proposed us. we made it as far that we have two ?h.volume.mgz files in each subjects surf folder and we would like to continue the group analyses process.
Hi Rafael,
sorry, I don't understand. What do you mean " Problems appeared later on, because we didn't find a difference in the average folder compared to using the command without lh.volume.mgz files in the surf folder." What problems? What kind of differences are you looking for and how?
Bruce
On Mon, 3 Sep 2007, Rafael Huber wrote:
Dear freesurfer users
Do you have an idea how to create an average ?h.volume file?
Our goal is to create a file with average volumes for our subjects, to follow the group analysis. We know that the idea of using a volume measure isn't implemented in the freesurfer software. We runned the make_average_subject command in hope to find something like an ?h.volume file in the average folder as there are files for the other measures like thickness, area, curvature. Before we runned the make_average command we followed the advice of Bruce Fischl to create .mgh files in matlab with the following command:
[thickness, f] = read_curv('lh.thickness') ; [area, f] = read_curv('lh.area') ; volume = thickness .* area; save_mgh(volume, 'lh.volume.mgz', eye(4));
This functioned very well and we got our lh.volume.mgz files in the surf folder. Problems appeared later on, because we didn't find a difference in the average folder compared to using the command without lh.volume.mgz files in the surf folder. We're now not sure if we should continue like normal, or what exactly to do. Has somebody an idea.
Best regards
Rafael Huber _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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