Re: [Freesurfer] cotical surface labeling...

Hi again, I am trying to convert a surface segmentation into a volume file, here is the command I am using:   mri_surf2vol --surfval (???) --hemi lh --surf orig --volregidentity c2 --template ../mri/rawavg.mgz --outvol orig.img  now my question is what should go to surface value argument. My unders

Re: [Freesurfer] cotical surface labeling...

Look in $FREESURFER_HOME/FreeSurferColorLUT.txt Behrang Nosrat Makouei wrote: Hi, thanks for help. That was the segmentation i was looking for. Now the question is what is the look up table Freesurfer uses to assign values to different labels? in other words, if I want to segment the " G_

Re: [Freesurfer] cotical surface labeling...

Hi, thanks for help. That was the segmentation i was looking for. Now the question is what is the look up table Freesurfer uses to assign values to different labels? in other words, if I want to segment the " G_postcentral" (for e.g.) what value should i look for? bets   On 9/25/06, Doug Greve <[EM

Re: [Freesurfer] processing steps

Claudia -- With your line of questioning, you may also might like to look at: http://grahamwideman.com/gw/brain/fs/index.htm ... particularly ... http://grahamwideman.com/gw/brain/fs/fsunderstanding2006/processvsdata2006.htm Graham At 9/25/2006 10:29 AM, you wrote: Hi,   I have just started t

Re: [Freesurfer] processing steps

Claudia, I'll try to answer some of your questions, in each section below: On Mon, 2006-09-25 at 18:29 +0100, claudia wheeler-kingshott wrote: > Hi, > > I have just started to look at freesurfer and decided to run each step > to try to understand what recon-all does. Some resources to learn th

[Freesurfer] processing steps

Hi,   I have just started to look at freesurfer and decided to run each step to try to understand what recon-all does.   Well, after a bit of teething to put the data in the right orientation, we managed to start, but we have a few questions :-)   First of all, our SPGR data is 1.2x1.2x1.2mm^

Re: [Freesurfer] Getting PET statistics using the subcortical segmentation

Hi Jorge, The register.dat maps the PET of an individual to the subject's anatomical? If so, then use mri_label2vol to map the aseg.mgz or aparc+aseg.mgz or ?h.aparc.annot to the native PET space for each subject, then use mri_segstats to average the intensities in each ROI -- this produces a

Re: [Freesurfer] cotical surface labeling...

Have you looked at the aparc+aseg.mgz? It has cortical and subcortical labelings. You can convert it to analyze with mri_convert. Behrang Nosrat Makouei wrote: Hi,   I actually had the some extra question in addition to the question Shahab had. So i thought to put the questions in th

Re: [Freesurfer] anonymizing dicom files

Hi Inge, here is a WEB page for BIRNDUP distribution. http://wiki.na-mic.org/Wiki/index.php/MBIRN:BIRNDUP:Distribution Silvester > Hi Inge, > > no, certainly not all the info in the dicoms is preserved (there's a > ton), and patient name is not. We have an anonymization procedure that > we've

Re: [Freesurfer] anonymizing dicom files

Hi Inge, no, certainly not all the info in the dicoms is preserved (there's a ton), and patient name is not. We have an anonymization procedure that we've developed through the morphometry birn that both fuzzifies dates and such in the patient header and removed identifying features in the MRI

Re: [Freesurfer] anonymizing dicom files

Is all info from the the dicom headers included in the mgz's throughout the processing stream (eg. Patientname and such)? Najmeh: Have you found a solution for anonymizing dicoms you are satified with? Thanks Inge Amlien > > sorry about nonstop posting! > > I'm trying to remove the patient name

Re: [Freesurfer] Performance

well, you could buy a faster machine :). The 6 days I don't think is normal. The subcortseg can take a long time, although on current opterons it's more like 15 hours I think. Check to make sure that you don't have a cerebellum attached in your filled volume (or ?h.orig surfaces), and that the

[Freesurfer] Getting PET statistics using the subcortical segmentation

Hello all I have PET images corregistered in spm with their corresponding MRI images obtained by converting brain.mgz to analyze. I have created in freesurfer the file register.dat for each one of them, so i can use tksurfer and tkmedit. Now I would like to compute for each PET image t

[Freesurfer] Performance

Hello   We are running freesurfer on a Power Mac G4 with a 1.25 GHz processor and 1 GB Ram.   The subcortical segmentation procedure recon-all subcortseg –s ran for 49 hours.   The rest of autorecon2 (recon-all –autorecon2-cp –s ) has been running for 6 days and is still working on t