[Freesurfer] Dura Correction, Surface Based Stream and FS-Fast

Hello FSexperts, I used the mgh memprage and the dura correction scheme described in: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28479.html . Afterwards I applied recon-all -autorecon-pial -subjid subj_name to the subjects in order to include the changes in the subsequent

[Freesurfer] mri_nu_correct.mni options

Dear FS'ers. If I want to do bias correction of T1 and T2 images, without necessarily doing a recon-all - what are the different options/parameters I can add in the command line? Right now I have been testing : mri_nu_correct.mni --i input --o output and unfortunately the output looks worse

Re: [Freesurfer] Dura Correction, Surface Based Stream and FS-Fast

Hi Joerg you need to convert the individual echoes to be in conformed space without scaling the intensities, then run it with something like mris_make_surfaces -dura echo%d.mgz 4 subj_name lh otherwise it will just load 001.mgz 4 times and think it is the different echoes. That is, name the

Re: [Freesurfer] mri_nu_correct.mni options

Hi Cristian you can use mri_normalize directly on the T1, but it won't work for the T2 unless you specify control points and tell it to only use them. There are other (more esoteric) options in mri_normalize that you could use. Look at the recon-all code for the T2-based dura correction

[Freesurfer] Fwd: Conversion

Hi again freesurfers, I have some beginner's problems. I want to use some specific cortical and subcortical structures from Recon-all as ROI's in my SPM analyses. How do I extract and save these as binary masks ? Would this be a good idea: pick the structures I want from here

Re: [Freesurfer] Base Pial Surface Edits

Hi David, recon-all -base ID -autorecon-pial should be enough to pick up both edits (probably you already looked at the tutorial at http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial that describes most edits). Don't forget to re-run all longitudinals from scratch after

[Freesurfer] Fwd: mri_nu_correct.mni options

Dear Freesurfer List! Does anyone know what the purpose of the flag: mri_nu_correct.mni --i T1.nii --o nuT1.nii *--no-float* as opposed to: mri_nu_correct.mni --i T1.mgz --o nuT1.mgz *--n 2 *? Thank you! Cris -- Forwarded message -- From: Cristian Paz pazcristia...@gmail.com

Re: [Freesurfer] Hippocampal subfields intensity

Hi, Eugenio Hmmm, I guessed the values I got were different because they represented different stages of the processing. And you just confirmed that. Thank you. I would like to compare these intensities with the intensities I can read in aseg.stats. And I guess the comparison would be more

[Freesurfer] reg-feat2anat failure..

Hi, recon-all was successful. But when I try reg-feat2anat --feat '/home//func/2_reg' --subject xyz I get an error with MRISread(/home/sudhin/Data/freesurfer_subjects//xyz/surf/lh.white): could not open file Loading mov Projecting LH Surfs Loading lh.white surf No such file or directory

[Freesurfer] Group Analysis Error

Dear FreeSurfer Group I wanted to Group Analysis with qdec. I have MRIs of one patient in two different dates and I wanted to do group analysis on them to see the changes. I have gender, age, and diagnosis. In qdec deme, when I make the analysis based on thickness, I receive the attached error. I

Re: [Freesurfer] recon-all error: mri_watershed (picture include)

did you check the talairach transform? On Wed, 12 Jun 2013, Sudhin A. Shah wrote: Hi, This is the error I get: TEMPLATE DEFORMATION   second estimation of the COG coord: x=127,y=96, z=161, r=9988 iterations couldn't find WM with original limits -

[Freesurfer] fMRI ROI masks from Brain Voyager QX to FS

Hi list, I performed fMRI analysis by Brain Voyager QX. The masks that describe the fMRI regions of interest are in .vpm and .srf. 1-There is a solution to export these masks obtained by BrainVoyager QX in FS and visualize them on FS surface?2-I'd like to extract from each ROI individuate by

Re: [Freesurfer] fMRI ROI masks from Brain Voyager QX to FS

Hi Stefano, sorry, someone on the list may know how, but we haven't every used Brain Voyage (mostly because it's so expensive) Bruce On Thu, 13 Jun 2013, std...@virgilio.it wrote: Hi list, I performed fMRI analysis by Brain Voyager QX. The masks that describe the fMRI regions of interest

[Freesurfer] download error

Hi, I am currently trying to download the new 5.3 release for macbook lion osx. It downloads fine until about 1.9 GB, then it keeps stalling without giving me any error messages. I have let it continue to run over 20 hours and still no progress beyond 1.9 GB. This occurs with both safari and

Re: [Freesurfer] Editing masks

Hello Bruce, Yes, I am using the surfaces for this. I am trying to find cortical thickness differences between populations. I do not think that the mask covers the entire hippocampal area, just leaving out the corpus callosum. How would I include these areas into the mask? Thank you, Joshua On

Re: [Freesurfer] Editing masks

Hi Joshua The thickness isn't well defined in the hippocampus, so you don't want to use it there. Use volumes of the subfields instead Cheers Bruce On Jun 12, 2013, at 10:35 PM, Joshua deSouza desouzajoshu...@gmail.com wrote: Hello Bruce, Yes, I am using the surfaces for this. I am trying