[Freesurfer] standardize in asegstata2table

Hi all, I have a question. In the table created from asegstats2table, are the volumes standardized to Talairach space? or are they in their orig space? thank in advanced, anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr

RES: [Freesurfer] Cannot allocate memory / can't allocate region

Check ulimit -m That's the max mem per process. ulimit -m 0 Maybe will help. -- Pedro Paulo Jr E71 Nokia -Msg original- De: Jürgen Hänggi Enviada: 01/07/2009 02:36:36 Para: Freesurfer Mailinglist Assunto: [Freesurfer] Cannot allocate memory / can't allocate region Dear FS experts

Re: [Freesurfer] Cannot allocate memory / can't allocate region

Hi Juergen, how much ram do you have in the machine? Bruce On Wed, 1 Jul 2009, Jürgen Hänggi wrote: Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262

Re: [Freesurfer] standardize in asegstata2table

Hi Anita, no, they are in native space. cheers, Bruce On Wed, 1 Jul 2009, Anita di Iasio wrote: Hi all, I have a question. In the table created from asegstats2table, are the volumes standardized to Talairach space? or are they in their orig space? thank in advanced, anita ___

[Freesurfer] FreeSurfer: extracting regions from segmentation

Hi, We are trying to extract certain regions from FreeSurfer segmentation. There are couple of regions which are not found in the output files. We are currently searching for the regions in 13 output files. The regions are the following: right fornix (508), left fornix (558), right PLIC (158),

Re: [Freesurfer] FreeSurfer: extracting regions from segmentation

Hi Judit, the fornix is labeled in the aseg, not the parcellation, although this is not the default). If you rerun mri_cc with the -fornix option it will write a volume named mri/fornix.mgz with the fornix in it. cheers, Bruce On Wed, 1 Jul 2009, Judit Haasz wrote: Hi, We are trying to

Re: [Freesurfer] standardize in asegstata2table

Can I have the volumes in the standardize space? Thanks, anita 2009/7/1 Bruce Fischl > Hi Anita, > > no, they are in native space. > > cheers, > Bruce > > On Wed, 1 Jul 2009, Anita di Iasio wrote: > > Hi all, >> I have a question. >> In the table created from asegstats2table, are the volumes st

Re: [Freesurfer] fsaverage across versions

Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcella

[Freesurfer] mri_glmfit error

Hello, I am trying to run a cortical thickness analysis to look for an interaction between two continuous variables using mri_glmfit.  I created an fsgd file including only the two original CVs to investigate main effects and obtained the output.  When I added the interaction term (product of th

Re: [Freesurfer] Re: mkbrainmask not finding fslmaths

If you don't have FSL installed, then yes it will need to be. doug dah...@nmr.mgh.harvard.edu wrote: Perhaps I should have asked: Do I need to separately install FSL? Thanks Hi, I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsma

Re: [Freesurfer] mri_glmfit error

This can happen if the covariates have a very different scale (eg, age in years and something else in the range of 1-2). The product may have a different range as well. The product may be highly correlated with the first two CVs doug Susie Heo wrote: Hello, I am trying to run a cortical thic

[Freesurfer] Freesurfer FSL Dimensions

Hi: I am using Freesurfer and FSL together. My image dimensions initially are 256x256x128 in nii.gz format. I convert these images to .mgz using mri_convert and do cortical and subcoritcal segmentation in FreeSurfer. The outputs of the segmentation are the converted back into .nii.gz so I can use t

Re: [Freesurfer] Freesurfer FSL Dimensions

Try mri_vol2vol --interp nearest --mov aparc+aseg.mgz --regheader --targ rawavg.mgz --o aparc+aseg.native.nii.gz Natalia Sanchez wrote: Hi: I am using Freesurfer and FSL together. My image dimensions initially are 256x256x128 in nii.gz format. I convert these images to .mgz using mri_

[Freesurfer] Brain segmentation stats

Gurus, Looking over some stats recently I noticed that if you add up all of the freesurfer stats for ventricles, namely the left and right lateral ventricles plus 3rd, 4th, and 5th ventricles and subtract that from the "Number of Brain Segmentation Voxels" stat, you do not get the value of the

[Freesurfer] monte-carlo simulation question

Dear Freesurfers, I ran a monte carlo simulation for thickness analyses using mri_glmfit and found new files in the contrast subdirectory. I was able to figure out what the first two represent, but was wondering if any one could clarify what information the rest of the files show: mc-z.nega

Re: [Freesurfer] Brain segmentation stats

It's because "Brain Segmentation Volume Without Ventricles" stat is computed with partial volume correction but "Number of Brain Segmentation Voxels" stat is not. Please refer to this wiki for more info. https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume Sita On Wed, 1 Jul 2009, Jared