Re: [Freesurfer] FSFAST ocn vs. cluster outputs

Ah never mind, I figured it out. tksurfer was automatically setting the range to go from 2-5 so cluster 1 was not getting displayed. So please convert this question to a user suggestion to automatically set the threshold setting to the full range when displaying ocn and cluster overlays (as th

Re: [Freesurfer] Installation Conflict

Hi Mark how did you install? There's no reason that the subjects dir should be executable, so the last command is correct. There's nothing we do that should mess with your paths to things like wc and grep. You should have just sourced our setup script in your .cshrc or the init file of whateve

[Freesurfer] Installation Conflict

Hello, I recently installed FreeSurfer on an OS x machine. After finishing the process, I received the following output: *Setting up environment for FreeSurfer/FS-FAST (and FSL)* *FREESURFER_HOME /Applications/freesurfer* *FSFAST_HOME /Applications/freesurfer/fsfast* *FSF_OUTPUT_FORMAT ni

Re: [Freesurfer] methods Q

Thank you Bruce. That makes a lot of sense. Josh On Fri, Jun 14, 2013 at 5:59 AM, Bruce Fischl wrote: > Hi Joshua > > we have such techniques (developed by Mert Sabuncu), but don't use them by > default because(a) they are very slow, and (b) they would require us to > distribute the manually la

[Freesurfer] Help with QDEC error

Hello Freesurfers,  I am trying to run regression analyses within patients and one variable of interest which adjusting for the nuisance variables age, IQ, thickness. When i select the group and the CD (variable of interest) and run analyses (DODS), I get the following error:  Qdec 1.4 (Qdec1.

Re: [Freesurfer] Overlapping perirhinal and entorhinal ex-vivo labels

Hi Sasa do the thresholded labels also overlap? I guess they might, but I would expect far less. They are probabilistic, so unless our estimates were perfect they pretty much have to overlap. It would be easy enough to combine them and prohibit overlap by picking the one with the higher probab

[Freesurfer] Errors during test of Freesurfer installation

I recently installed Freesurfer on a computer running Red Hat Enterprise 6 for which the updates are current. The first tests, involving freeview, tkmedit, and qdec all produce the error: libGL error: failed to load driver: nouveau. free view produces no other error messages, but tkmedit adds:

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Hi Tudor, Then the problem is certainly related to the fact that you don't have matlab (the folder /usr/local/freesurfer/matlab is not the matlab distribution, rather the matlab functions enclosed in the FreeSurfer distribution), and not the fact that you have several copies of make_outer_surf

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Many thanks for your reply Marie. "getmatlab" returns "ERROR: Cannot find matlab. Does not exist or is not in path." There is a matlab folder in my Virtualbox installation of FS, at the path /usr/local/freesurfer/matlab, however it only contains .m files rather than the software itself. Among tho

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Hi Tudor, Yes you will need matlab with the image processing toolbox installed. The issue may be that you are running FreeSurfer in a virtual machine, with matlab not installed there. But, as Doug mentioned, I would assume the algorithms to answer you that it didn't find matlab. So, a few id

Re: [Freesurfer] recon-all errors

Hi Linda napo4128: something is wrong with the 001.mgz. How did you create it? The direction cosines definitely shouldn't have a 0 determinant napo0195: this is new error for me. The topology fixing couldn't find a correct solution. If you upload the subject we'll see if we can replicate and

[Freesurfer] Converting fsaveraged EPI to volume

Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using

Re: [Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Hi Tudor, the lGI stream definitely uses matlab, so that will be a problem at some point if not now. I would have thought that it would have reported that it could not find matalb. Marie would know for sure. doug On 6/14/13 3:25 AM, Tudor Popescu wrote: Dear Freesurfer & localGI experts,

[Freesurfer] generate pathstats.overall.txt file from tract volume

Hello All, Is it possible to generate pathstats.overall.txt file from tract volume? I would like to do some tract statistics on the tract volumes generated by FSL. Best Jay ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.

Re: [Freesurfer] Reviewer not satisfied

true, although this is less of a problem for us as our main regularization is to assume that the surfaces are well-fit by quadratic patches, not planes, so more smoothness doesn't necessarily cause the surface to retract as in other more typical regularizations On Fri, 14 Jun 2013, Chen, Yashe

Re: [Freesurfer] Reviewer not satisfied

Hi Jürgen you could quantify this if you want. Use mris_curvature to compute the mean curvature maps independently (the first and second principal curvatures). These have the units of 1/mm and are exactly the radius of curvature. You could histogram them and look at the distribution. cheers

Re: [Freesurfer] methods Q

Hi Joshua we have such techniques (developed by Mert Sabuncu), but don't use them by default because(a) they are very slow, and (b) they would require us to distribute the manually labeled data which we don't have IRB approval for Bruce On Thu, 13 Jun 2013, Joshua Lee wrote: > Hi Experts, >

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

Hi, I corrected my proceeding and separated the echoes using the pipeline: recon-all -s subj_name -i /.../dicom_images.dcm recon-all -s subj_name -use-gpu -mprage -all mri_convert -odt float -f 0 ./... .dcm $SUBJECTS_DIR/subj_name/mri/000.mgz mri_convert -odt float -f 1 ./... .dcm $SUBJECTS_DI

[Freesurfer] Reviewer not satisfied

Dear FS experts In one of our paper, I tried to explain how FS is able to produce cortical thickness maps in a spatial resolution that go beyond the resolution of the original MRI acquisition. We wrote the following: The thickness maps produced are not limited to the voxel resolution of the imag

[Freesurfer] problem bbregister onto longitudinal pipeline

Dear Freesurfer Users, I'm having a problem to register my PET images into the longitudinal pipeline of freesurfer (version 5.1). I have use bbregister without any problem to put the PET image into the crossectional images but it fails to register to the long version of it. Someone can tell me if

[Freesurfer] recon-all -localGI results in "ERROR:: Too many arguments."

Dear Freesurfer & localGI experts, I want to compare local GI (gyrification index) between my two groups. Following the help , I ran this command for one of my subjects: recon-all -s M01 -localGI but it resulted in the error: make_outer_surface('/m