Hi Andreia, I've done this before using information in the spectroscopy header, then synthesizing an MRI "volume" with one voxel that covers the size of your spectroscopy voxel, then registering that to the FS anatomical, then computing the partial volume fractions from the anatomical. The hard part is the first step, which I can't really advise you on.

doug

_andreia_@sapo.pt wrote:

Dear list,

I am performing single-voxel and multivoxel spectroscopy analysis and I need to do partial volume correction. I found a thread on the list of someone asking if it possible to achieve this using Freesurfer (see below), but there is no answer saying how it is done. My question is how can I define the voxel (for single-voxel) and the chosen voxels (for multivoxel) in the anatomical data set to use the segmentation of only that defined voxel? I'm using a Siemens TrioTim 3T. All acquisitions are in the same session. The anatomical dataset is an average of 2 MPRAGEs which I've already processed using FS, and the spectra files are .rda. The header of the MRS data has info on vectors, but I don't know how to use them.

"Re: [Freesurfer] need info for beginner

Bruce Fischl Thu, 26 Apr 2007 11:17:01 -0700

Hi Pom,

yes, people here are using it for spectroscopy and for partial volume correction (also for voxel placement).

cheers, Bruce

On Thu, 26 Apr 2007 [EMAIL PROTECTED] wrote:

Hi,

I am about to install FREE SURFER for my Spectroscopy work. I want to use the software to perform GM/WM segmentation on my single voxel data sets.

I am wondering if any one on this mailing list is currently doing this task. I would like to get comments.

My study is on a GE 3T scanner.

thank you,

Pom"

Any advice, please?

Thank you!

Andreia

--

Andreia Pereira, MSc student Visual Neuroscience Laboratory IBILI-Faculdade de Medicina Azinhaga de Santa Comba 3000-354 Coimbra Portugal Phone +(351) 239480220 Fax +(351) 239480280

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi, Thank you for your help! I think there might be something wrong just with the display, as in fact more brains looked strange. I have re-run the concatenation with the same commands after killing many processes on my computer and now all brains look correct and in the expected order.

Cheers, Aga

On 7/19/11 10:19 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:

Hi Aga, that does sound strange. mri_concat does no processing at all, so if that subject looks ok before you run mri_concat, it should look fine afterwards. Try running just that subject through mri_concat (so there's no real concatenation). Also, make sure that the bad subject in the mri_concat output is the same subject that you are looking at individually; you could be off by 1.

doug

Agnieszka Burzynska wrote:

...

Dear experts, I used mri_concat to concatenate sig.mgh files from fixed-level analysis (combining runs within each subject). All input files when viewed as initial single frame images look correct. For one person, however, in the multiframe image the sig.mgh looks just like noise (see attached picture). I used only --i and --o in the mri_concat command line. What could have happened? I get no error messages and everything else looks ok.

Thank you for your help, Aga

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

I hope this attachement works. I also noticed that some heterotopias are classified as WM, other as GM and sometimes are outlined by the yellow line and sometimes are not.

Best regards,

Carolina

2011/7/19 Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Carolina,

can you gzip it or use compression? Usually people can send a few images to the list.

cheers Bruce

On Tue, 19 Jul 2011, Carolina Valencia wrote:

Dear FS experts,

...

I'm trying to analyse a case of cortical dysplasia, but after recon-all I see some errors in tkmedit that I don't know what to edit. I found some errors in cortical and subcortical segmentation, I don't find in the failure mode presentation a way to solve this. I saw the pial surface (yellow line) with acceptable accuracy but the GM (the red one) in some regions are misplaced (WM classified as GM and some GM not classified (empty color)) I tried to attached an image to illustrate the problem but I don't succeed, because the mailing list reject my email. How I can send you an image of ~700kb?

Thanks a lot,

Carolina

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