Freesurfer November 2004

freesurfer@nmr.mgh.harvard.edu

22 participants
53 discussions

Re: [Freesurfer] load overlay in TkSurfer
by Joongnam Yang 17 Nov '04

17 Nov '04

Hi Bruce, I found the error messages in SUBJECTID/scripts/csurf.log The error was that there is no talairach.xfm in /mri/transorms directory. I though that using tkregister2 for co-registration would be enough. Would you let me know how to generate talairach.xfm? Nam.

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Re: [Freesurfer] load overlay in TkSurfer
by Joongnam Yang 17 Nov '04

17 Nov '04

The following is in .xdebug_tksurfer. Segfault xDebug stack (length: 1) 00: 00: Segfault Does it ring a bell, Bruce? Nam.

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load overlay in TkSurfer
by Joongnam Yang 17 Nov '04

17 Nov '04

The "Load Overlay" window in TkSurfer is not working for me. The window has two fileds to fill in, "Load Overlay" and "User Registration". What's strange is that whatever I type in those two fields, TkSurfer doesn't complain. For example, if I type in "hello" and "abc.dat" literally for those two fields, TkSurfer doesn't complain. No error message. (This is why my functinoal overlay is not working, I guess.) Could someone give me a clue? Nam.

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functional data not showing up
by Joongnam Yang 16 Nov '04

16 Nov '04

Hi All, I hope someone can locate the problem for me. Here is what I did. 1. clicked for "flattened" surface on csurf, which opens tksurfer (I see a flattened surface window) 2. clicked "load overlay" on tksurfer, which asks two inputs. For "Load overlay", I typed in XXX for XXX_000.bfloat Use registration, I used register.dat, which seems OK. 3. Then click OK 4. No functional overlay is made. I mean no functional data show up on the flattened surface. I looked at the XXX_000.bfloat, which is around 3 Megabytes. Question: 1. Is there a way that I can verify that *.bfloat is valid? (I used mri_convert XXX.img *.bfloat to create those files) 2. What is a way of creating *.w files from functional data? Any lead would be welcome. Thanks Nam.

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csurf version?
by Joongnam Yang 16 Nov '04

16 Nov '04

Hi all, SessionTools menu in my csurf has only one submenu "View Functional Data". In some web sources that I read, there are many other submenus under it, such as "Setup Align/Funct Scans", "Calculate 3D Fourier Stats", etc. Is this version of csurf OLD? This freesurfer was installed last August. Thanks. Nam.

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Error: Overlay layer 1 (empty)
by Joongnam Yang 16 Nov '04

16 Nov '04

Hi All, I've got "Overlay Layer 1(empty)" when I opened TkSurfer to do funcitonal overlay. Is something wrong? Here is what I did. open csurf set functional directory. open tksurfer using "flattened" surface. open load-->overlay. The last line gives me a window at the bottom of which there is "Field". in the "Field", all options are shown "empty". So, clicking OK on that window doesn't do anything for me on overlay. Thanks in advance. Nam.

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Tksurfer Overlay not working
by Joongnam Yang 15 Nov '04

15 Nov '04

Hi Bruce, I used Tksurfer to overlay fuctional onto anatomical. On the Load->Overlay window, I did indicate the functional *.bfloat and register.dat, but in the "Field" at the bottom, "Overlay layer 1 (empty)" is shown (inside "Field", all layers are empty). I guess that something is wrong. (Should I do something for it?) (Even with that, I clicked the OK button. the Tksurfer image window flashes, but nothing is changed.). Please help me. Nam.

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Re: functional overlay looks right or wrong?
by Joongnam Yang 15 Nov '04

15 Nov '04

Hi Bruce, We used stimuli of concentric rings whose radii expanded from trial to trial. We wanted to get retinotopic map using fMRI. So, we got structural data and functional scans. (We did the FSL Feat analysis and got stats results) We want to see the retinotopic map corresponding to the stimuli. Using Freesurfer (csurf), I did the overlay between the functinoal and structural and wanted to see some activated regions depending on the conditions of the stimuli. I saw only outlines.... When you said "color look up tables", you mean some options to wiggle around in the tkmedit GUI window? Thanks in advance Nam.

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functional overlay looks right or wrong?
by Joongnam Yang 15 Nov '04

15 Nov '04

Thanks, Bruce. When I did successfully using csurf and tkmedit (I will try tksurfer later, though), I saw functional data overlaid onto structural data. Question: I was expecting some activated regions for my retinotopy data, but all I see is a large green or red contours. Is this what freesurfer provides? Or something is wrong? Nam.

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convert functional into bfloat
by Joongnam Yang 15 Nov '04

15 Nov '04

Hi everyone, Is there a Freesurfer command to convert ANALYZE format functional data into *.bfloat? (I am trying to do functional overlay) Something like, xxxxxxx functionaldata.img *.bfloat Or do I have to use FSL Feat to get all the thresh_zstat*.img files using mri_convert command? Thanks in advance. Nam.

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Freesurfer November 2004