Re: [Freesurfer] dcm2nii and recon all

2011-09-02 Thread Alfredo Damasceno
I am also using dcm2nii and running recon-all with the original image. It is working ok so far. Alfredo > Date: Fri, 2 Sep 2011 12:30:26 -0400 > From: gr...@nmr.mgh.harvard.edu > To: cvalen...@linkdx.com.co > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] dcm2nii and recon all >

Re: [Freesurfer] what is thalamus-proper and clusters-table related question

2011-09-02 Thread Douglas N Greve
I don't think it does. Jean manually labeled LGN in a few cases for me a few years ago, and I vaguely remember that LGN did not overlap with our thalamus seg (but I could be wrong). doug Bruce Fischl wrote: > I dint think it does, but maybe jean or David can confirm > > > On Sep 2, 2011, at 1:07

[Freesurfer] Regarding Segmentation of Hippocampal Subfield

2011-09-02 Thread mohan boddu
Hello, When I segmented the Hippocampal Subfields (using the process stated in http://www.freesurfer.net/fswiki/HippocampalSubfieldSegmentation ) it generated two files by name *"posterior_Left-Hippocampus.mgz"* and * "posterior_Right-Hippocampus.mgz*". I would like to know what actually are those

Re: [Freesurfer] what is thalamus-proper and clusters-table related question

2011-09-02 Thread Bruce Fischl
I dint think it does, but maybe jean or David can confirm On Sep 2, 2011, at 1:07 PM, Ritobrato Datta wrote: > Actually I have the same question - does the thalamus proper include LGN ? > > - Original Message - > From: "Douglas N Greve" > To: "Tetiana Dadakova" > Cc: freesurfer@nmr.

Re: [Freesurfer] what is thalamus-proper and clusters-table related question

2011-09-02 Thread Bruce Fischl
Yes, not sure why the CMA called it that On Sep 2, 2011, at 12:28 PM, Douglas N Greve wrote: > I'm not sure about #1, maybe BF can chime in. > > Tetiana Dadakova wrote: >> Dear FS list, >> >> 1. What does a label Thalamus Proper include? Is it the same as thalamus? >> >> 2. After correcting

[Freesurfer] Surface analysis FSL GFEAT results for multiple subjects with 4 runs each

2011-09-02 Thread Michelle Umali
Hi Freesurfers, I've been looking at the wiki for information on doing an surface analysis using GFEAT results for within subject, across multiple runs. On the wiki, a fixed effects analysis was used because there were only two runs. I have four runs and FSL uses FLAME 1 and FLAME 1+2. 1. Shoul

Re: [Freesurfer] what is thalamus-proper and clusters-table related question

2011-09-02 Thread Ritobrato Datta
Actually I have the same question - does the thalamus proper include LGN ? - Original Message - From: "Douglas N Greve" To: "Tetiana Dadakova" Cc: freesurfer@nmr.mgh.harvard.edu Sent: Friday, September 2, 2011 12:28:45 PM Subject: Re: [Freesurfer] what is thalamus-proper and clusters-tab

Re: [Freesurfer] Grad_Unwarp question

2011-09-02 Thread Nick Schmansky
The grad_unwarp_tables directory is not distributed with the public release of freesurfer, as the files are under Siemens license to the NMR Center only. So I suppose you could check with Siemens to see if they can supply you with those data tables for your scanner. N. > Hello, > > We used to r

Re: [Freesurfer] dcm2nii and recon all

2011-09-02 Thread Douglas N Greve
I have no idea, but probably the original. doug Carolina Valencia wrote: > Dear FS' users, > > I have a 3D T1 from a GE scanner which I convert with dcm2nii to use > it with recon-all, but I got 3 images: > o -- original > oo -- orthogonal > co -- cropped image > > Which I should use to run the

Re: [Freesurfer] what is thalamus-proper and clusters-table related question

2011-09-02 Thread Douglas N Greve
I'm not sure about #1, maybe BF can chime in. Tetiana Dadakova wrote: > Dear FS list, > > 1. What does a label Thalamus Proper include? Is it the same as thalamus? > > 2. After correcting for multiple comparisons, I get a table of > clusters. I have several questions regarding this table: What do

[Freesurfer] what is thalamus-proper and clusters-table related question

2011-09-02 Thread Tetiana Dadakova
Dear FS list, 1. What does a label Thalamus Proper include? Is it the same as thalamus? 2. After correcting for multiple comparisons, I get a table of clusters. I have several questions regarding this table: What do the columns Max, CWPLow, and CWPHigh represent? Regarding the NVtxs column: is it

Re: [Freesurfer] Longitudinal aseg errors

2011-09-02 Thread Martin Reuter
Hi Jeff, after editing anything in the cross, you usually need to rerun the base (and then all longs). Also you need to edit the base (brainmask, talairach) as that is where the long processes take the information from. It is more important to fix the base than the cross in many cases. More on lo

[Freesurfer] dcm2nii and recon all

2011-09-02 Thread Carolina Valencia
Dear FS' users, I have a 3D T1 from a GE scanner which I convert with dcm2nii to use it with recon-all, but I got 3 images: o -- original oo -- orthogonal co -- cropped image Which I should use to run the command recon-all? thanks! Carolina ___ Freesu

[Freesurfer] Ventricular structures - exact definitions

2011-09-02 Thread mschwei1
Hello, as I am interested in the volume of ventricular structures in the brain, I would like to more precisely understand the labels given by /stats/aseg.stats in Freesurfer. Most importantly, what is the precisely defined difference between Left-Lateral-Ventricle and Left-Inf-Lat-Vent? Would you

[Freesurfer] WM Parcellation - lobe mapping

2011-09-02 Thread Brainiac .
Hi All, I need to classify WM into different lobes (temporal, parietal, frontal, occipital). I tried to do the lobe mapping using parcellations from wmparc.mgz. http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation My problem is the "unsegmented white matter" in wmparc.mgz. My understandi