[Freesurfer] DICOM conversion

Dear All, I'm writing this here because I think some of you might be able to help. We're doing presurgical planning and surgical navigation based on fMRI. So far it was simple, but now, the program that we used for such evaluation was not able to evaluate the fmri, because of the poor SNR, so we

[Freesurfer] RAS to Vertex Index

Dear EXPERTS, I have a coordinate set (RAS) in a volume and would like to map those coordinates in a surface of same subjects. Is there a good way to convert Volume RAS to vertex index directly rather than searching with mouse? Thank you. Hiroyuki ___

Re: [Freesurfer] RAS to Vertex Index

in tksurfer tcl scripting you can use: select_talairach_point to find the vertex index associated with a tal coord. We never wrote one for volume RAS but we could (or you could apply the tal xform to convert volume ras to tal cheers Bruce On Tue, 12 Jan 2010, Oya, Hiroyuki wrote: > Dea

[Freesurfer] modification of tksurfer and tkmedit palette...

Hi: I want to modify the color palette that tksurfer uses to display overlay data... How can i modify it ?... the same question for tkmedit... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] ANN - SVM, Alzheimer's Disease and FreeSurfer

Hi, We have published another paper using FreeSurfer, maybe you can add it to the Article page in the Wiki http://iospress.metapress.com/content/r1533322r7481q35/?p=2cecbdd44e114a5fbff200e3feee3ad0&pi=12

[Freesurfer] modification of tksurfer and tkmedit palettes

Hi: I will write my question in another way: in which file could I find the palette that tksurfer and tkmedit uses to display overlay data ?... because I want to create other palettes... Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing li

[Freesurfer] Paired Analysis, Smoothing Step

Hi there, I've got a sample with T1s and T2s that I'm trying to compare. I did the entire longitudinal stream protocol, and am now doing the paired analysis protocol. I'm stuck on the Spatial Smoothing step: I've only gotten either a ">" or a message reading, "ERROR: Option -sval unknown" Is ther

Re: [Freesurfer] modification of tksurfer and tkmedit palettes

Hi Gonzalo, what kind of overlay data? The color lookup table is in $FREESURFER_HOME/FreeSurferColorLUT.txt for displaying segmentations. The heat scale and such for other overlays are not configurable unfortunately I don't think cheers Bruce On Tue, 12 Jan 2010, Gonzalo Rojas Costa wrote:

Re: [Freesurfer] Paired Analysis, Smoothing Step

What is your cmd. Also see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for more info on bug reporting. doug Stidd, Reva (NIH/NIMH) [F] wrote: > Hi there, > I've got a sample with T1s and T2s that I'm trying to compare. I did the > entire longitudinal stream protocol, and am now doing the pai

Re: [Freesurfer] DICOM conversion

We don't have anything that will convert to DICOM, sorry. doug Gergely Orsi wrote: > Dear All, > > > I'm writing this here because I think some of you might be able to help. > We're doing presurgical planning and surgical navigation based on fMRI. > So far it was simple, but now, the program that

Re: [Freesurfer] modification of tksurfer and tkmedit palettes

Hi Bruce: Yes... I asking about the color palette for other overlays... the heat scale... Because, I am trying to display as an overlay an image that have five discrete valuesa, and for that, I need another type of color palette... Sincerely, Gonzalo Rojas Costa Department of Radiology

Re: [Freesurfer] modification of tksurfer and tkmedit palettes

What you really have is a segmentation (if you set your discrete values to ints). For tkmedit, you can just create a LUT (like FreeSurferColorLUT.txt) and load as a -segmentation. For tksurfer, you can create an LUT as above, then run mris_seg2annot to create an annotation. doug Gonzalo Roj

[Freesurfer] thickness map from a label

Hello All, I have created some surface labels and want to create corresponding thickness maps (Not stats). Is there a way to do that ? Thanks Ri ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

Re: [Freesurfer] thickness map from a label

I'm not sure what you mean. Can you elaborate? doug Ritobrato Datta wrote: > Hello All, > > I have created some surface labels and want to create corresponding thickness > maps (Not stats). Is there a way to do that ? > > Thanks > > Ri > > ___ > Free

[Freesurfer] Freesurfer Ubuntu 9.04 installation

Dear all, This is a technical, linux-related question: I have just installed Freesurfer in a computer running Ubuntu 9.04. When testing the installation, I get an error message right in the first step. I try to do: tkmedit bert orig.mgz And the message I get is: tkmedit.bin: error while loadin

Re: [Freesurfer] Freesurfer Ubuntu 9.04 installation

is your system 32b or 64b? make sure the correct freesurfer distribution (32b or 64b) was installed. n. On Tue, 2010-01-12 at 20:39 +0100, Miguel Burgaleta wrote: > Dear all, > > This is a technical, linux-related question: I have just installed > Freesurfer in a computer running Ubuntu 9.04. W

[Freesurfer] unknown error

Hi experts, I run freesurfer to compute the thickness, but I find some subjects failed with error. Would you please tell me how to handle this error. Thank you very much! And the error is as follow:  talairach_af