[Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage

Hi, I am attaching this message again and I wI'll appreciate if somebody could kindly comment on the approach. Thanks Regards -VM -- Forwarded message -- From: "neuroimage analyst" Date: Dec 18, 2016 2:22 PM Subject: Registering ASL-CBF maps to fsaverage To: "Freesurfer suppor

Re: [Freesurfer] Missing values in fsgd file

no, sorry, you'll have to remove those data sets or run an analysis that does not rely on that parameter On 12/20/16 11:05 PM, Jennifer Szeto wrote: > Hi freesurfer experts, > > I am trying to run some mri_glmfit analyses on freesurfer5.3. However there > are some missing values in some of m

[Freesurfer] Missing values in fsgd file

Hi freesurfer experts, I am trying to run some mri_glmfit analyses on freesurfer5.3. However there are some missing values in some of my fsgd files due to missing data in my dataset. Is there anyway we can run mri_glmfit analyses with missing values in fsgd files? Thank you very much, Jen

[Freesurfer] Ynt: Ynt: Neighborhood of a vertex

Hi Bruce, I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ? sincerely yours, Onur Gönder

Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex

nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

Thank you for your reply Dr. Reuter. I have about 3 scans in which the acquisition parameters are slightly different between time 1 and time 2 which probably contributes to these differences. Do you recommend that I do not use these scans? For my other scans, sometimes the differences in intensit

Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

Hi Hao - This will also be fixed in the new version. For now, if you do not have them as dicoms, please do your testing without a field map. Thanks, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen [

Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

Hello: More information to give, I think the problem is from the format of the magnitude and phase image for the registration-based B0-inhomogeneity compensation, I tried to comment the registration-based B0-inhomogeneity compensation, and it seems to work, So: In TRACULA, we can not define t

[Freesurfer] trac-all error with .nii.gz images, mri_probedicom

Hello, FreeSurfer experts: I know that we are going to have a new version of FS 6.0.0, but with the curent newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) for FS5.3.0, I am working on UBUNTU14.0. To run tracula in parallel on my machine, here is my config file( for

Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

Sorry, the command is not trac-all -path -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txtt, it is : trac-all -prep -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt

[Freesurfer] Structural analysis

Dear FreeSurfer team, I'm currently doing a structural FS analysis with 50 Multiple Sclerosis (MS) patients and 25 Healthy Controls (HC). FLAIR-lesions were drawn onto the aseg.mgz as White Matter Hypointensities (=77). I've finished the analysis, but have some questions regarding my results.