Re: [Freesurfer] mysterious fsgd format error (not the end of line problem)

2016-03-02 Thread Bruce Fischl
No worries, it happens to all of us Bruce > On Mar 2, 2016, at 12:20 AM, Joseph Dien wrote: > > Oops, never mind. User error. I’m too embarrassed to even explain what I > did. :) > > Joe > >> On Feb 29, 2016, at 21:38, Joseph Dien wrote: >> >> Hi, >> I’m having an fsgd error that has t

Re: [Freesurfer] Unknown option DKTatlas40

2016-03-02 Thread Watson, Christopher
The option should be: --annot aparc.DKTatlas40 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of marmaduke woodman [marmaduke.wood...@univ-amu.fr] Sent: Wednesday, March 2, 2016 08:27 To: freesurfer@nmr.mgh.

[Freesurfer] Deflate surface

2016-03-02 Thread marmaduke woodman
Hi I would like to resample the cortical surface on the sphere at a lower resolution, and then deflate the surface to its folded form. Is this something which can be done using the inflated surface that FS generates? Thank you, Marmaduke ___ Freesurf

[Freesurfer] Problem with mriconvert

2016-03-02 Thread Óscar Soto Angona
Hello, We are medicine students who are using freesurfer for research. We had been using freesurfer in Ubuntu 12.02 without encountering any trouble; recently we updated to 14.04. Now, when we attempt to convert a mgz file to nii using mriconvert, we have an error regarding failure to write the f

Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Eugenio Iglesias
Hi Prabesh, I think this is due to a bug that I found recently and which I'm trying to track down. Has it happened to you with many scans? The failure rate is less than 1% in my data. Regarding your second question: I'm sure it's not too trivial ;-) but I don't understand exactly what you mean

Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Kanel, Prabesh
Hi Eugenio, Thank you, for your quick reply. It has happened to me in 4% of the cases, but my data sample is small like 100 data points. Addition to the second question: When I segment the hippocampus, I get the discrete segmentation volume at 0.333 mm resolution in the file [lr]h.hippoSfLa

Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Eugenio Iglesias
OK now I get it ;-) You can simply do: mri_convert T2.FSspace.mgz T2.FSspace.resampled.mgz -odt float -rl [lr]h.hippoSfLabels-T1-T2.v10.mgz The rl flag says: "reslice like the following volume" Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

2016-03-02 Thread Faeze Vedaei
Hi, Thank you for your response. sorry, I could not understand what you mean. How you found 23 230 60 values for paracentral region? I mean. Are these from Freesurfer LUT? Regards, Faezeh Vedaei On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei wrote: > Thank you for your response. It is better to

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

2016-03-02 Thread dgw
just change the values and re-run with different numbers and see what happens On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei wrote: > Hi, > > Thank you for your response. sorry, I could not understand what you mean. > How you found 23 230 60 values for paracentral region? I mean. Are these > from F

Re: [Freesurfer] Unknown option DKTatlas40

2016-03-02 Thread Z K
It appears to be an issue with the dev build and should be fixed in tomorrows build. -Zeke On 03/02/2016 08:31 AM, Watson, Christopher wrote: > The option should be: > --annot aparc.DKTatlas40 > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfe

[Freesurfer] Topological White Matter Correction

2016-03-02 Thread Kiersten Snyder
Hello FreeSurfer Experts, What image processing technique is behind the Topological White Matter Correction to correct topological defects? Is it true that FreeSurfer take into account your edits as a "suggestion" and incorporates into some type of algorithm? I would like to have a more thorough u

Re: [Freesurfer] hippocampus subfields

2016-03-02 Thread Kanel, Prabesh
Sweet, just what I wanted. Thank you, Prabesh From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Eugenio Iglesias Sent: Wednesday, March 2, 2016 2:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields OK now I get it ;-

Re: [Freesurfer] Topological White Matter Correction

2016-03-02 Thread Bruce Fischl
Hi Kiersten the topology correction algorithm is this one: http://www.ncbi.nlm.nih.gov/pubmed/11293693 cheers Bruce On Wed, 2 Mar 2016, Kiersten Snyder wrote: Hello FreeSurfer Experts,What image processing technique is behind the Topological White Matter Correction to correct topological de

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

2016-03-02 Thread Faeze Vedaei
Hi Thank you so much for your help. I just got your meaning. I created new LUT file by just changing randomly the RBG values for each 13 specific regions and opened the annot file in tksurfer. And the strange issue is that just for paracentral I used your values I had paracentral in tksurfer GUI n

[Freesurfer] conflicting Monte Carlo simulation results...

2016-03-02 Thread Karl Liu
Dear Freesurfer experts: I ran into a confusing problem when applying Monte Carlo simulation to control for multiple comparisons. I am using the buckner data from tutorial dataset. I first tried the simulation based on Freesurfer;s 2012 manual: (http://www.freesurfer.net/pub/docs/tarballs_for_