Hi Paola, please remember to post to the list and not to us personally. thanks! I would still use the xhemi tools for this. If you have N subjects, you will get 2*N surfaces aligned to the fsaverage_sym atlas. You can then just pick the ones you want to analyze further doug
On 04/22/2014 08:34 AM, Paola Valsasina wrote:
Dear Doug,
We have followed your suggestion and we performed the recon-all analysis for all study subjects (till autorecon3) on non-flipped images.
I am now reading the instructions on the wiki about the xhemi tool, but I am not 100% sure they apply to our case.
The wiki instructions describe a comparison between LH and RH within subjects (i.e., an analysis of cortical asymmetry), whereas we would like simply to L-R flip the final surfaces of patients having a RH damage, so that all patients have the damage in the LH. Then, we would like to compare them with control subjects.
For this purpose, is it sufficient to register the patients lesioned in the RH to the symmetric template with the --xhemi option?
(i.e. surfreg --s subject_name --t fsaverage_sym --xhemi --rh --lh)
Then, how do we perform final statistical analysis?
Thank you in advance for any suggestion! Kind regards Paola
Paola Valsasina, MSc Research Fellow Neuroimaging Research Unit (Director Prof. M. Filippi) Institute of Experimental Neurology, Division of Neuroscience, Scientific Institute and University "Vita-Salute" San Raffaele Via Olgettina 60, 20132 Milan, Italy
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-----Messaggio originale----- Da: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Per conto di Douglas N Greve Inviato: giovedì 13 febbraio 2014 21.50 A: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] Filipping issue
Definitely #2. You should use the xhemi tools http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi First run them through recon-all as normal, then follow the steps on the wiki. Contact the list again to get instructions for the final analysis.
doug
On 02/13/2014 08:23 AM, Paola Valsasina wrote:
Dear List,
we are starting the analysis of cortical thickness for a group of patients who have only one side affected. The majority of patients have the left hemisphere affected, but some patients have the right hemisphere affected. In order to do a group analysis, we would like to flip the images of some patients, so that the affected side is left for all subjects.
Which is the best way to do this:
1)flip the 001.mgz volume and perform the entire recon-all pipeline with flipped images;
or
2)perform the recon-all pipeline with the non-flipped volumes and flip only the final surfaces for statistical purposes?
Thank you for any suggestion
Kind regards
Paola
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