[Freesurfer] MRI intensity normalize

Dear FS experts, I am wondering the process of MRI intensity normalization. Before I am running recon -all, can I run following process to normalize our MRI images. mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm or any other preprocessing methods to avoid bias. thanks Lawrence Emory University

Re: [Freesurfer] Error viewing corrected results

Dear Sahil, -approx tail and -twotail are completely different things: -approx tail switch on the tail approximation which speeds up the permutations. -twotail switch on two-sided hypothesis, without -twotail the hypothesis is only one-sided. It is reassuring that you see some clusters in

[Freesurfer] Repost: tracula stats including NAs?

Hi FreeSurfer, I have analyzed my diffusion data using Tracula and combined the voxelwise diffusion measures across all subjects in one file (following the guidelines on the wiki). In this text file, I saw that for some of these voxels some people have NAs, so their tract is most likely

Re: [Freesurfer] subject directory

The error is ERROR: cannot find /home/username/freesurfer/subjects/surf/lh.thickness.fwhm10.fsaverage.mgh However, the file should run on /servername/username/FATCAT/subjects/… I don’t know why it tries to find the files in the default home/… folders. Thanks, Gaurang From: Douglas Greve

[Freesurfer] wm.mgz Edits Ignored With Current Dataset in FS 5.3/6 Cross and Long Streams

Hello, I have worked quite a bit in the past with fs 5.3 on datasets which required a fair number of manual edits to the white matter volume in order to correct defects in the white matter surface. Typically, these edits take the form of removing voxels in the wm.mgz volume that have been

Re: [Freesurfer] Kind Request - Unexpected Crashing of the Program

I believe this occurs when opening the the freeview application by clicking the icon within the /Applications/freesurfer folder. Unfortunately this method has issues and should be avoided until we can come up with a proper fix. For now you should open freeview by typing the 'freeview' command

[Freesurfer] Kind Request - Unexpected Crashing of the Program

I am attempting to Load a Volume into free surfer to perform WM/GM segmentation. Every time I attempt to upload a volume (even including the bert sample volumes provided with the installation), Freesurfer quickly crashes and exits. I have attached a screenshot of the crashing prompt. Do you

[Freesurfer] Faulty alignment to standard surface

Dear experts, I've run the standard recon-all pipeline on a subject, for whom the log does not report any errors and the white and pial surface follow the structural nicely. However, the coregistration to the standard surface has gone wrong: it seems like the central sulcus (e.g. labels BA1,

Re: [Freesurfer] WM edits

Hi Manuel I think the area you are talking about is in the hippocampus, no? In which case it is not neocortex and you don't have to worry about it. cheers Bruce On Fri, 10 Mar 2017, Manuel Delgado wrote: > Dear Freesurfer list, > I am using Freesurfer 6.0 in Ubuntu 16.04. In the

Re: [Freesurfer] WM/pial edits

Hi Octavian if you want to regenerate the pial surface you have to run autorecon3 also. And I don't think you want to edit the wm.mgz for wm edits. Probably you should edit brain.finalsurfs.mgz for both wm and pial. Can someone who has done more recent recons than I have confirm this?

Re: [Freesurfer] FS v6.0 recon-all freezes

a feature in the new freeview that helps with this is to load the ?h.orig.nofix then load the ?h.defect_labels as an overlay on it, and check the "use surface overlay" box when selecting the color of the surface. This will color regions of the surface that are in a defect differently than the

Re: [Freesurfer] Inflation of RH only

Hi XJ your approach sounds reasonable. cheers Bruce On Thu, 9 Mar 2017, XJ Kang wrote: Hi Experts, I am trying to inflate the brains with lesions in the LHs. The inflation failed because of those lesions. I need the RH data from the files "mri/wmparc.mgz" and "stats/rh.aparc.stats". Here

Re: [Freesurfer] subject directory

Hi Gaurang you need to send us the full screen output of what you ran. And what do you mean by "customize"? Did you change the subject dir after running recon-all? cheers Bruce On Fri, 10 Mar 2017, Limachia, Gaurang (NIH/NINDS) [F] wrote: Dear Freesurfer Experts,   I want to customize

Re: [Freesurfer] Adjust bbregister affine to target raw T1

That min cost (.86) is too high for sure. My guess is that it is the fsl init. In general, bbregister is pretty insensitive to the initialization method (as long as the init does not fail), so I would not worry about some being done with coreg and some with flirt On 3/9/17 3:40 PM,

Re: [Freesurfer] FS v6.0 recon-all freezes

Dear Andrius, You can load the ?h.inflated.nofix in freeview and the overlay ?h.defect_labels to see what's going on. It may be that a chunk of skull or the cerebellum is still attached, in which case you'll want to correct the brainmask.mgz or wm.mgz, respectively, to remove the non-brain

[Freesurfer] FS v6.0 recon-all freezes

Hi, Maybe some could give advice regarding my problem with FS v6.0. Now I am running recon-all for my patients cohort on Linux Centos 6, FS v6.0. It is PC with i5 intel, 4 Core, 8 Gb RAM. 80% of my subjects finished recon-all process without errors pretty fast (it takes about 11-14 hours per

Re: [Freesurfer] Error viewing corrected results

Dear Sahil, thinking of that, the comparisons I suggested in previous mail are probably valid only for the case of orthogonal design.  And even with the orthogonal design as Anderson said, the values can a bit differ: