[Freesurfer] subcortical segmentation

Hi, I am a new user of freesurfer. Is it possible to do just the volumetric processing stages without the surface processing stages? In fact what I want is to segment the subcortical structures. Is there a command line for this purpose only or should we run all the recon-all steps? Thank you

[Freesurfer] RV: FREESURFER

> Good morning,I am working on brain segmentation using freesurfer program. > I wonder if it is possible to turn an initial image with some tool freesurfer. Because my problem is that when I start to perform segmentation in freesurfer, I get an error and I think that is because dicom image format

Re: [Freesurfer] subcortical segmentation

Hi Salem, yes, you can run any individual options in recon-all. See the -help output and run it through step 11 if you want. Note that we do use the surfaces to improve the aseg accuracy at the very end, so you'll be giving that up. cheers Bruce On Wed, 7 Jul 2010, Hannoun wrote: > > > Hi,

Re: [Freesurfer] RV: FREESURFER

Hi Santiago, if the talairach is correct (you can verify this in tkmedit or tkregister2) then you can just turn the auto checking of the tal transform off in recon-all. cheers Bruce On Wed, 7 Jul 2010, SANTIAGO GONZALEZ CALERO wrote: > >> Good morning,I am working on brain segmentation using

Re: [Freesurfer] Qdec - problem with the Generate Stats Data Import button.

Hi Krish, Thank you for your reply. Unfortunately none of these did work (but now I've an up-to-date environment at least). But the IT/research engineer in the lab found that it was "just" my environment PYTHONHOME and PYTHONPATH which were pointing at a bad directory. After unsetting these two en

Re: [Freesurfer] subcortical segmentation

I have used: recon-all -s -subcortseg which runs through step 11 (-calabel), with the understanding re: accuracy that Bruce pointed out. -Julie On 7/7/10 8:07 AM, "Bruce Fischl" wrote: > Hi Salem, > > yes, you can run any individual options in recon-all. See the -help output > and run it th

[Freesurfer] Help on QDEC: Obtainign mean, sd and p-values from glm result

Hello, I've just started using freesurfer. I've reading the mail list wich helps me a lot, but I can't find how I can obtain a table with the values of my glm analysis. For exemple, in the Qdec's tutorial I have a surface that answer the question "Does the correlation between thickness and age di

[Freesurfer] manual corregistration...

Hi: How can I do a manual corresistration with freesurfer ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___

Re: [Freesurfer] manual corregistration...

co-registration of what with what? tkregister2 is for function/diffusion to structure On Wed, 7 Jul 2010, Gonzalo Rojas wrote: > Hi: > > How can I do a manual corresistration with freesurfer ?... > > Sincerely, > > > ___ Freesurfer mailing list Free

Re: [Freesurfer] Help on QDEC: Obtainign mean, sd and p-values from glm result

If you just want a mean and sd over a region you can run mri_segstats with the --annot option. What do you mean by a p-value for a region? doug Fernanda Palhano wrote: > > Hello, > > > I've just started using freesurfer. I've reading the mail list wich > helps me a lot, but > I can't find how I

Re: [Freesurfer] entorhinal surface and wm intensity

Hi Derin, that is odd, not sure what's going on either with your wrinkles or the loss of surface after editing. Can you upload the pre and post edited datasets for us to look at? Bruce On Thu, 1 Jul 2010, Derin Cobia wrote: > I have questions regarding two issues we've run into processing dem

[Freesurfer] editing labels in tksurfer

Hi Everyone, I remember a post in March when Allison referred someone to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit and I think this will be really helpful for me if I can figure out how to make it work. I have a scan with corpus callosum bleeding into the caudalant

[Freesurfer] probabilistic white matter mask

Hi Folks, I believe that I can create a binary white matter mask using "mri_wmfilter". I was wondering if there is a way to create a probabilistic white matter mask ? (for each voxel, I would like to obtain the probability of it being white matter) I did a search on the mailing list and found th

[Freesurfer] Freesurfer file

Hello, Freesurfer experts I'v got a work with the freesurfer files. As we all know, there are many files in the freesurfer subject directory, and each file has its usage. My question is, what's the particular usage for each of these files and how can I read these files using Matlab or any other so

[Freesurfer] ERROR selxavg-sess

Hi,Freesurfers I'm going to analyze the functional data. By now I finished reconstruction of anatomical data and maiking hierarchy, mc-sess,spatialsmooth-sess,inorm-sess,mkanalysis-sess and fslregister. But selxavg-sess output following ERROR. please tell me about -ipr. Keta ke...@localhost[r

Re: [Freesurfer] ERROR selxavg-sess

Hi Keta, this is a pretty old version. Are you sure you don't want to upgrade? The ipr is the "in-plane resolution" stored in the seq.info file in the bold directory. Newer versions don't use this anymore. doug On Thu, 8 Jul 2010, ±¬ÌÂÀ wrote: Hi,Freesurfers I'm going to analyze the fun