Re: [Freesurfer] long_mris_slopes command: temporal average calculation

Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2

Re: [Freesurfer] long_mris_slopes command: temporal average calculation

Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi wrote: >Hi, >I had a question about how the temporal average is calculated for >subjects >w

[Freesurfer] long_mris_slopes command: temporal average calculation

Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after

Re: [Freesurfer] CT Method Comparison

Sorry, I'm still a little lost. Let me see if I have it right: For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if it is out. You have a registration between roi.nii and orig.mgz You run mri_vol2su

Re: [Freesurfer] coordinate transform

Hi Octavian, these types of things are generally not difficult to program, but they can be difficult to get set up correctly. If you do a search for "coordinates" on our wiki, it will take you to a page that explains the process. doug On 09/26/2012 02:57 PM, octavian lie wrote: > Dear all, > I

Re: [Freesurfer] Should control points be removed?

Usually you don't need to remove them Bruce On Sep 26, 2012, at 1:52 PM, Jonathan Holt wrote: > Quick small question, > > I'm editing a few brains at the moment that have needed multiple script runs. > I've added control points as necessary before each run and afterward the > resulting brain

Re: [Freesurfer] coordinate transform

Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie. *To follow up and simplify for a

Re: [Freesurfer] questions about recon-all pipelines

thank you very much! 2012/9/26 Bruce Fischl > or you could do it all in one command with: > > > recon-all -i first_dicom_image_name.dcm -s subjID -all > > cheers > Bruce > > > On Wed, 26 Sep 2012, Darren Gitelman wrote: > > Pietro >> You should first import your *.dcm files with the command >>

[Freesurfer] Should control points be removed?

Quick small question, I'm editing a few brains at the moment that have needed multiple script runs. I've added control points as necessary before each run and afterward the resulting brain will typically need either more control points added, white matter aux volume edits, or both. I'm wonderin

[Freesurfer] coordinate transform

Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file (see attached) in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie. trodes.mat Des

Re: [Freesurfer] question about fsaverage vs. my subjects average

On 09/26/2012 12:36 AM, Darren Gitelman wrote: > Hi > > I have 3 questions: > > 1) Does it affect the stats (or does it just affect the display) if I > use the fsaverage brain vs. the average of my subjects brains when > running mris_preproc or when simulating the cluster statistics using > mr

Re: [Freesurfer] questions about recon-all pipelines

or you could do it all in one command with: recon-all -i first_dicom_image_name.dcm -s subjID -all cheers Bruce On Wed, 26 Sep 2012, Darren Gitelman wrote: Pietro You should first import your *.dcm files with the command recon-all -i first_dicom_image_name.dcm -s subjID  Then when you p

Re: [Freesurfer] questions about recon-all pipelines

Hi Pietro 1. No, you would need 002.mgz etc.. if you had more than 1 scan that you wanted to motion correct and average for that subject/session. 2. The easier way to run recon-all is to use the -i flag, where should be one slice in the proper dicom series (e.g. an mprage). Then you don't

Re: [Freesurfer] questions about recon-all pipelines

Pietro You should first import your *.dcm files with the command recon-all -i first_dicom_image_name.dcm -s subjID Then when you process your data you would type recon-all -s subjID -autorecon1 -autorecon2 or whatever steps you are using. Darren On Wed, Sep 26, 2012 at 9:33 AM, pietro de ros

[Freesurfer] questions about recon-all pipelines

Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all –autorecon1 –autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the c

Re: [Freesurfer] how to make avgsubject for hippocampal subfields

Hi Jeong, Koen or Eugenio would know. cheers Bruce On Wed, 26 Sep 2012, BumSeok Jeong wrote: Dear Freesurfer expert, I'm interested in hippocampal subfields and performed it at each subject. If I'd rather get average hippocampal subfields (volume or surface), what I have to do? The make_avera

Re: [Freesurfer] Longitudinal processing 3 time point error

Hi Martin, Thanks for the suggestion! I'm afraid that I'm limited to the Mac - how can I get the new binary? Thanks, Jamie -- Jamie Kawadler PhD student Imaging & Biophysics Unit UCL Institute of Child Health 30 Guilford Street London WC1N 1EH 02079052192 jamie.kawadler...@ucl.ac.uk

Re: [Freesurfer] Longitudinal processing 3 time point error

Hi Jamie, Three time points should not be a memory problem. You can try to run this on linux. Or you can get a new binary for the mac from our development version with several improvements and fixes including a memory leak that might have caused this. Let me know (you may want to rerun all your

[Freesurfer] Longitudinal processing 3 time point error

Hello, I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors. Please see the output below: Resolution: 0 S( 256 256 256 ) T( 256 256 256 )

[Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries

Dear FreeSurfers, I am trying to run trac-all -prep on a single subject, and get the following error: dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/dif

[Freesurfer] how to make avgsubject for hippocampal subfields

Dear Freesurfer expert, I'm interested in hippocampal subfields and performed it at each subject. If I'd rather get average hippocampal subfields (volume or surface), what I have to do? The make_average_subject command did not produce it. Does Freesurfer have average hippocampal subfield volume?