Dear Bruce

Thank you for your answer. I tried to analyze these data both with FS 4.5 and with FS 5.0. Outputs are similar and bad in both cases. I think that the major problem is the quality of the starting sequence (3D FFE acquired on a Philips 3T), because I am running FS on another dataset (MP-RAGE from Siemens Avanto) and outputs are much better. Before starting FS pipeline, I also tried to segment starting images with SPM8, which produces as output also non-uniformity corrected images. I used these corrected images as input for FS, but outputs are bad also in this case. I would like that you look at my images, in order to have an expert opinion about feasibility of FS on these data. My original image (001.mgz) is 30 MB, whereas brainmask.mgz image is 10 MB. Can I send brainmask.mgz image by attachment? Or can I load the original image somewhere? Thank you in advance Best regards, Paola

Paola Valsasina Research Fellow to Prof. M. Filippi Neuroimaging Research Unit Institute of Experimental Neurology Hospital San Raffaele via Olgettina 60 20132 Milan - ITALY

-----Messaggio originale----- Da: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Inviato: martedì 28 dicembre 2010 14.01 A: Valsasina Paola Cc: freesurfer@nmr.mgh.harvard.edu Oggetto: Re: [Freesurfer] bad output of autorecon2 - is there any way to adjust it?

Hi Paola, that looks pretty bad. What version are you running? You can try using rhe expert opts to set the g/w intensities, or drop the dataset on our site and we'll take a look. cheers Bruce

On Tue, 28 Dec 2010, Paola Valsasina wrote:

Dear Freesurfer experts,

I have tried to analyze with Freesurfer a dataset of images acquired with

a

3D T1 sequence without inversion pulse (unfortunately, it is simply a FFE sequence and not a MP-RAGE). Contrast between grey and white matter is not optimal in this image, and when I run -autorecon2 step I obtain a very bad output (attached). "white/grey" surface seems to be where the pial

surface

is expected to be, and pial surface is in the middle of csf.

In your opinion, is it possible to obtain meaningful results with these images or not? Is there any setting of post-processing that I can change

in

order to obtain better surfaces?

Thank you for any suggestion

Kind regards,

Paola

---------------------------------------------------------------------------- -------

SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San

Raffaele.

Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

----------------------------------------------------------------------------------- SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE. NON C'E' CURA SENZA RICERCA. Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus del San Raffaele. Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org