Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Hi Vincent - Problems 1-4 all look like head motion. Because the acquisition of the slices is interleaved (all the odd slices are acquired and then all the even slices are acquired), if the subject moves somewhere in between, you'll see that the even slices are shifted with respect to the odd

Re: [Freesurfer] medial wall crossing the surface

Does the aseg cross as well? On Oct 17, 2013, at 10:07 PM, "silve...@gmx.com" wrote: > Dear All, > > I too am seeing the medial pial surfaces crossing hemispheres in some > subjects. > > The approach that appears to be working for me involves making copies of > brainmask.mgz and aseg.mgz

Re: [Freesurfer] How do you create labels from binary masks?

Is *binLeftHippoBody.mgz a volume label or a surface label? If a volume label, map it onto the surface with mri_vol2surf, the run mri_cor2label *specifying --surf doug On 10/17/13 5:00 PM, Marcos Martins da Silva wrote: Hi, Doug Thank you for your answer. I am trying cor2label as you su

Re: [Freesurfer] aparcstats2table error

Hi Corinna, is it just that subject or does it happen on more? Can you send me the stats file? doug On 10/17/13 3:55 PM, Corinna Bauer wrote: Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --he

[Freesurfer] medial wall crossing the surface

Dear All, I too am seeing the medial pial surfaces crossing hemispheres in some subjects. The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the

Re: [Freesurfer] Comparison between fsaverage and a template created from scratch

Hi Sophie I think fsaverage was made from 40 subjects so your 80 subject average will naturally be smoother Cheers Bruce On Oct 11, 2013, at 11:35 AM, Sophie Maingault wrote: > Hello Experts, > > I did the procedure to create a template from scratch by following the steps > explaining in t

[Freesurfer] mri_fill failure in macaque

Dear FreeSurfer experts, I'm attempting to make cortical surfaces for a macaque brain, and am having trouble getting mri_fill to work. The command has worked without any errors for a different macaque dataset in the past, and I can't seem to figure out why it isn't working this time. I am using v

Re: [Freesurfer] inferior horn of lateral ventricle

Hi Bruce As far as I can tell this is not causing any problems downstream. Happy to accept the result as long as it is reproducible across different cases (which it appears to be) Regards Nawaf > On 17 Oct 2013, at 11:29 pm, Bruce Fischl wrote: > > Hi Nawaf > > is it causing you any problem

Re: [Freesurfer] Tracula configuration error

Hi Mike - Good to know. This would make perfect sense b/c in 5.1 trac-all required a variable to be defined that isn't used any more in 5.3. a.y On Tue, 15 Oct 2013, Michael Datko wrote: Hi Anastasia,I updated freesurfer from 5.1 to 5.3 and that fixed the problem!  Thanks for taking a look

Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control

Hi Gari - The command is: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.5 a.y On Tue, 15 Oct 2013, Garikoitz Lerma-Usabiaga wrote: Hi Anastasia, could explain a little bit more what do you check exactly here?  "What I usually look at is dlabel/diff/a

[Freesurfer] aparcstats2table error

Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas thickness --tablefile symm_aparc_stats_rh.txt error: ERROR: The stats file /media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.s

[Freesurfer] Extract Cortical Thickness from my data based on ROIs from Qdec

DEar FS experts, I need to extract the CTh from my whole data (90 subjects) based on generated ROI from Qdec(mc-z.neg.th13.sig.ocn.mgh). Would you please advise if I can do it in the same way you have mentioned in this post : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22973.html

Re: [Freesurfer] Freeview Volume & Surface alignment

Hi Kambiz, It would still be very helpful if you could send us the volume and the surface files so that we can investigate. Thanks, Ruopeng On Oct 16, 2013, at 4:10 PM, Kambiz Tavabi wrote: > Hi Ruopeng, > Sorry for the confusion in my initial post. The screen capture is actually a > grab fr

Re: [Freesurfer] inferior horn of lateral ventricle

Hi Nawaf is it causing you any problems? That is the current correct outcome, although we are considering whether to change the surface behavior in the medial temporal lobe. You shouldn't have to edit the wm.mgz as we detect those regions as non-cortical, and exclude them from the downstream a

Re: [Freesurfer] tkmedit error message

Hi Elissa has tkmedit ever worked? This looks like an internal mac problem. For example, a google search turns up: https://discussions.apple.com/message/12614494#12614494 does freeview work? As far as the invalid messages go, you'll need to send us the details for us to comment. And yes, upda

Re: [Freesurfer] DOSS FS 5.3

Thanks for the reply. Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values, are they generated by q-dec? Thanks in advance, On Wed, Oct 16, 2013 at 5:51 PM, Douglas N Greve wrote: > > From the

[Freesurfer] Postdoc position available - Alzheimer's Disease

Postdoctoral Position in Neuroimaging - Pasqual Maragall Foundation, Barcelonabeta Brain Research Center, Barcelona, Spain. Job Summary: Pasqual Maragall Foundation invites applications for a full-time postdoctoral position to conduct post-processing and analyzing of MRI neuroimaging data (