Re: [Freesurfer] Coordinate transformation between raw space and freesurfer confirm space

Hi Liang can you clarify what you mean by freesurfer space? What are you trying to do with the coords? We have several coordinate systems, all of which are documented on our wiki. cheers Brce On Sun, 9 Sep 2012, liang wang wrote: Hi, I need to convert a vast amount of  coordinates

Re: [Freesurfer] Coordinate transformation between raw space and freesurfer confirm space

Thanks, Bruce. I had solved this question. Liang 2012/9/11 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Liang can you clarify what you mean by freesurfer space? What are you trying to do with the coords? We have several coordinate systems, all of which are documented on our wiki. cheers

Re: [Freesurfer] Coordinate transformation between raw space and freesurfer confirm space

glad to hear it Bruce On Tue, 11 Sep 2012, liang wang wrote: Thanks, Bruce. I had solved this question. Liang 2012/9/11 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Liang can you clarify what you mean by freesurfer space? What are you trying to do with the coords? We have

Re: [Freesurfer] problem with tksurfer

Hi Maryam, I finally figured out what is going on. The bottom line is that it is just a weird coincidence. The volume size is 70*70*33=161700 which happens to be exactly how many vertices are in the left hemisphere of this subject. When tksurfer sees this, it thinks that each voxel must be a

[Freesurfer] [TRACULA] trac-preproc error while reruning with an 'init=1' option

Hi Anastasia, After an intial tracula pipeline procedure, I found some tracts were not successfully reconstructed. Their aparc+aseg looked fine to me. So I reran the trac-preproc -prior and trac-path with an option, 'init=1' in a dmrirc file. Now, the analysis's running well on some, but not

[Freesurfer] surface does match - how to verify subjects

Hi I was trying to create an average subject using the make_average_subject command. When it got to one of the subjects there was the following error: #@# processing subject 4/85 3106... Reading /home/drg/3106/surf/lh.sphere.reg mrisReadTriangleFile(/home/drg/3106/surf/lh.orig): surface

Re: [Freesurfer] surface does match - how to verify subjects

You can run recon-all -s subject -vno-check or just vno_match_check $subjid $hemi doug On 09/11/2012 11:24 AM, Darren Gitelman wrote: Hi I was trying to create an average subject using the make_average_subject command. When it got to one of the subjects there was the following

Re: [Freesurfer] Differences between BrainSuite and FreeSurfer

Sorry about that, mailing list cc’d. Reply vs reply all… Stuff attached, but also uploaded. (message bounced) The colorscale.tiff is an example of the strange color scale abnormality, and the colorscaleabnormality.png shows the settings to get a similar one. The PPTX shows the results – better.

Re: [Freesurfer] Repost: Converting BV ROIs to FS

Another question. If I have a list of talairach coordinates, is there someway to load those without having to do it individually? Or someway to save the points after scripting to run through select_talairach_point individually (as just redoing the command will lose the previous point each time)?

Re: [Freesurfer] Repost: Converting BV ROIs to FS

Hi Katie what do you want to do with them? Bruce On Tue, 11 Sep 2012, Katie Bettencourt wrote: Another question.  If I have a list of talairach coordinates, is there someway to load those without having to do it individually?  Or someway to save the points after scripting to run through

Re: [Freesurfer] terrible movement; salvagable?

Hi Anthony yes, you can using the expert options to change the parameters of mri_normalize. Motion could mess it up, as it assumes a sharp enough gradient at the gray/white boundary to prevent the white matter region growing from crossing into the gray matter. Make sure that it's not just the

Re: [Freesurfer] Differences between BrainSuite and FreeSurfer

Hi James the recon looks pretty accurate to me. One thing you might try is acquiring a 1mm isotropic T2-space FLAIR in addition to the structural (if there is the equivalent sequence on GE). It allows us to distinguish between dura and gray matter, which can look identical on a T1. cheers

[Freesurfer] Color scale?

OK, thanks. I am making this a new thread...what about that color scale problem? I'm not sure what to do - I can only use the one color scale for some reason. --- James C. Patterson II, MD, PhD Professor of Psychiatry LSU Health - Shreveport --- The colorscale.tiff is an example of the strange

[Freesurfer] error with the cut plane in tksurfer

Hello, I am trying to cut the occipital plane, but I get the crashes and the error message, tksufer.bin:tnl/t_vertex.c:407: update_input_ptrs: Assertion 'a[j].inputstride == vptr- stride' failed. Abort(core dumped) Anybody did figure it out and fix? Any advice would be most appreciated.

Re: [Freesurfer] error with the cut plane in tksurfer

Can you tell us what kind of machine, what operating system and what fs version you are running? On Sep 11, 2012, at 5:21 PM, Hye Young Heo hyeyoung...@gmail.com wrote: Hello, I am trying to cut the occipital plane, but I get the crashes and the error message,

[Freesurfer] multicenter morphometric analysis

Hi all, I was wondering if there was a consensus view on the optimal way to approach morphometric analysis (cortical thickness, volumetry associated analyses) of MRI data acquired on multiple scanners. From VBM literature our own experience it appears that comparing MRI scans of patients from