Hi Doug, Ok. Thank you! :)
Andreia Citando Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > Yes, that should work. You will need a registration matrix to give to > mri_compute_volume_fractions. You can get this from tkregister2: > > tkregister2 --mov mrs.vol.nii --s subject --regheader --reg register.dat > > when you run this, hit the compare button to make sure that the mrs box > falls on the part of the anatomical you think it should be. Then hit > "Save" to save the registration. > > doug > > _andre...@sapo.pt wrote: >> Hi Doug, >> >> This already sheds some light on the issue! I didn't know >> mri_volsynth, I'm a begginer in FS. Lets see if I got it right. I have >> the anatomical and the MRS data acquired in the same session, so I >> won't need the EPI. If I manage to create the MRS volume using the >> header info and mri_volsynth I only need to coregister my anatomical >> with the synthetised volume and then run mri_compute_volume_fractions >> through the synthesed volume and the identity matrix (?) (since my >> data are from the same session) to get the % of the different tissue >> types only inside the voxel. Of course I'll need more advice on this >> later, but one thing at a time. >> >> Thanks! >> Andreia >> >> >> >> Citando Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >> >>> Sorry, I don't know anyone who can help with that. As you note, people >>> do it, so there must be people around who can extract the relevant >>> information out of the header. The information you need are the >>> direction cosines and RAS of the corner of the voxel. You can feed this >>> into mri_volsynth. >>> >>> To register to FS, you'll need to have a whole-brain volume collected >>> during the same session. If you collected the anatomical analyzed in FS >>> at the same time, then you don't need another. If you did not, you can >>> literally use any whole brain acquisition, eg, a single TR of an EPI >>> (less than 10 sec to acquire). You can then register the EPI to the >>> anatomical with bbregister. This gives you a "register.dat". You can >>> then concatenate that with the EPI-MRS registration (I can show you >>> how). After that, you can run mri_compute_volume_fractions passing it >>> the synthesized volume and the register.dat (or identity matrix if same >>> session). >>> >>> Another alternative is to collect an actual MRI volume that spans your >>> MRS volume. You can then substitute that for the synthetic volume. Note >>> that the actual pixel content of this volume is irrelevant -- it's just >>> used to get geometry information out of it. This will be the easiest if >>> you can do it. >>> >>> doug >>> >>> _andre...@sapo.pt wrote: >>>> Hi Doug, >>>> >>>> Do you know who can help me with this? That's exactly what I think >>>> that I need to do... The thing is that, unfortunately, I can't find >>>> anyone who can describe how the creation of an MRI "volume" from the >>>> MRS voxel is done, although this approach is present in many many >>>> papers. >>>> >>>> About the second part, how do I register the synthetized MRI "volume" >>>> to the FS anatomical? And how can I get the volumes of only that >>>> "volume"? >>>> >>>> (Hopefully I'll find a way to do the first part...) >>>> >>>> Thanks, >>>> Andreia >>>> >>>> >>>> >>>> >>>> Citando Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>>> >>>>> 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 >>>>> >>>>> _andre...@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 >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> gr...@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> 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. >>>>> >>>>> >>>> >>>> >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
