[Freesurfer] How to extract subjects' volume based on mask from spm?

Dear Freesurfer experts, I analyzed functional data by spm and made a mask (analyze format). I have also run recon-all of structural data. My question is: how to extract mean volume (from structural data) of the mask(from spm)? I only extracted volume(or thickness) of ROI of a label edited by my

Re: [Freesurfer] How to extract subjects' volume based on mask from spm?

Try mri_binarize followed by mri_cor2label doug On 05/20/2013 03:57 AM, zhang mingxia wrote: > Dear Freesurfer experts, > > I analyzed functional data by spm and made a mask (analyze format). I > have also run recon-all of structural data. > > My question is: how to extract mean volume (from

Re: [Freesurfer] Tracula problem

Hi Matt - Yes, the dcmroot variable can be used if you have the same root directory for *all* input files. If not, don't define dcmroot and instead give the full path to each input file. Then you shouldn't have to modify any scrips. a.y On Fri, 17 May 2013, Hoptman, Matthew wrote: Hi Anas

Re: [Freesurfer] DTI metrics along the whole tract?

Hi Celine - The way this average is computed for pathstats.byvoxel.txt is by averaging the values for each one of the sample paths that are drawn by the MCM algorithm. This essentially "weighted" sinced voxels that more sample paths go through will be counted more than voxels that fewer sample

[Freesurfer] ERROR in long_mris_slope

Dear Freesurfer experts, I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack ?do-label ?time time --qcache fsaverage command for my longitudinal processing. However I keep getting the error message: mris_cal

Re: [Freesurfer] Tracula longitudinal "nan" values for highest probability path

Hi Vincent - Thanks for bringing this to my attention. I can see what might cause this glitch (only in the longitudinal case) and I'll fix it in the next version. In the meantime, if you delete one of the two identical lines from cpts.map.txt, and then rerun the dmri_pathstats command line tha

Re: [Freesurfer] Tracula problem

Gotcha, Thanks. -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Monday, May 20, 2013 10:06 AM To: Hoptman, Matthew Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Tracula problem Hi Matt - Yes, the dcmroot variable can be used if you ha

Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_

Hi Bruce, Sorry to get back late on this. The norm file was blank. Can you send me the updated binary??, My system specification is following: Red Hat Enterprise LINUX Workstation Release 6.0 (Santiago) Kernel Linux 2.6.37-71.el6.x86_64 GNOME 2.28.2 Also, just for information this is not going

Re: [Freesurfer] Freesurfer MAC installation

Flavia, You are going to have to be a little more specific in describing what you are trying to do and what exactly the problem is. You say you "cannot open the example Bert"... What does that mean? You can open it in tkmedit? What is the error? The procedure for getting the license is to go to t

Re: [Freesurfer] Tracula longitudinal "nan" values for highest probability path

Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look. a.y On Mon, 20 May 2013, Vincent Brunsch wrote: > Hi Anastasia, > Thanks for your help! I had this issue with 4 tracts in total. I just want to > add that before rerunning dmri_pathstats not only pat

Re: [Freesurfer] Tracula longitudinal "nan" values for highest probability path

Hi Anastasia, the files are here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/TC055FB.v2/dpathlong/lh.cst_AS_avg33_mni_bbr The base is here: /autofs/cluster/lazar/projects/Templeton/dng/dtionly/Tracula/tracall/longbaseTC055FB Freesurfer outputs: /autofs/cluster/lazar/proj

[Freesurfer] failures more frequent in one hemisphere

Hi All, I recently ran a number of 2-yr-old brains through Freesurfer, and overall Freesurfer did well considering the age group. However, a subset (~10%) had catastrophic failures in the left termporal lobe in which parahippocampal cortex bled over into the hippocampal region. I've since added c

[Freesurfer] shape difference in subcortical structures using FSL vertex Analysis

Hi All, I need to do a shape analysis between the freesurfer segmentation results with manual segmentation. Does anyone know how can I use FSL Vertex Analysis (first_utils) ? Fsl Vertex Analysis input file is .bvars . Is there a documentation or guide to create this file type? Mah

Re: [Freesurfer] mkbrainmask-sess

I imagine this issue has been solved by now but just for the record I ran into a similar issue. In my case the problem turned out to be that FSL installs by default in /usr/local/fsl/bin but FSFAST was looking for it in /bin This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesu