[Freesurfer] Assign p value for every voxel and plot it in freeview

Hello: I have a very simple question, after recon-all, I did some statistical analysis with some other softwares, so for example I got the p value for every voxel(volume_based),or p value for every vertex(surface-based), so I know how to map theses p values for surface-based pipeline, but for v

Re: [Freesurfer] Use CA and other subfields as seed for FS-FAST

Ciao, Stefano, Several things: 1. In 5.3, each subfield has a probability map in an independent file, so you don’t need the codes. 2. Having said that: you should probably use the new subfields in 6.0beta. Then, you can use the codes in the range 200-226. Kind regards, /Eugenio Juan Eugenio Igle

Re: [Freesurfer] Tracula Set: No Match

Hi Katherine - You need to have an appropriate field mapping MRI scan. Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [katherine.da...@gmail.com] Sent: Sunday, January 01, 2017 5:16 PM

Re: [Freesurfer] flirt: command not found

Hi Michal - Are you running the freesurfer setup script? https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration Also, in your config file: - You're missing a "\" at the end of the line with the first nifti file - bvalfile is for defining a single b-value table,

Re: [Freesurfer] Problem with trac-all correction step for DTI image processing

Hi Mahtab - If your dicom file is anonymized, can you upload it here for us to take a look? https://gate.nmr.mgh.harvard.edu/filedrop2/ Please address the upload to ayendiki and greve. Thanks, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun..

Re: [Freesurfer] preproc-sess brain masks in masks subdirectory

There should be, but if everything is running properly, then it is not a problem. If the masks are needed and are not there, then the processing will die. On 01/02/2017 01:47 PM, Ladan Shahshahani wrote: > Dear experts, > Hi, > > I ran the preproc-sess command. I was following the tutorial page

Re: [Freesurfer] Assign p value for every voxel and plot it in freeview

You haven't told us what you saved it as, but assuming whatever software you used can save in .nii.gz or .mgz simply save as that. Load the volume and change the colormap and opacity to your liking. hth d On Tue, Jan 3, 2017 at 11:48 AM, Hao wen wrote: > Hello: > > I have a very simple question,

Re: [Freesurfer] View sig map on anatomical volume from volume-based group anaysis

If you have a value for a given ROI, you can do something like this in matlab seg = MRIread('aparc+aseg.mgz'); overlay = seg; overlay.vol = zeros(size(overlay.vol)); HippocampusIndex = find(seg.vol == 17); % 17 from $FREESURFER_HOME/FreeSurferColorLUT.txt overlay.vol(HippocampusIndex) = You

Re: [Freesurfer] Error from trac-all prep: data and bvals/bvecs do not contain the same number of entries

Hi Hao - Every single image in your DWI series should have a corresponding column (or row) in the b-value and gradient table. So if the first image in your DWI series is a b=0 image, and it doesn't have a corresponding column (or row), you should add 0 to the b-value table and "0 0 0" to the gra

Re: [Freesurfer] Tracula Set: No Match

Is it possible to run tracula with out a phase mapping MRI scan? All I have in this data is a MPRAGE and DWI images weighted at either 0 or 1000. Thank you. On Tue, Jan 3, 2017 at 1:07 PM, Yendiki, Anastasia wrote: > Hi Katherine - You need to have an appropriate field mapping MRI scan. > > Bes

Re: [Freesurfer] Tracula Set: No Match

It absolutely is. The field map is completely optional, as shown in the tutorial and in the sample configuration file. From: Katherine Damme [katherine.da...@gmail.com] Sent: Tuesday, January 03, 2017 7:47 PM To: Freesurfer support list; Anastasia Yendiki Subject: