Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

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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Re: [Freesurfer] functional combo box
by Joongnam Yang 15 Nov '04

15 Nov '04

When I clicked "Volume-Stats" button on the top right corner of the window that shows up after I clicked "View Functional Data" button of csurf, I got the tksurfer window, but with the following error Error: Parsing command line options Option -invphaseflag not recognized This option was not recognized and ignored. Could someone let me know how to fix it? Nam.

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functional combo box
by Joongnam Yang 15 Nov '04

15 Nov '04

Hi everyone, For functional overlay, In csurf GUI window, on the right-most side, there is a "functional" combo box, where you are to set two items "session" and "scandir". Would someone tell what I am supposed to type in for those two? Thanks Joongnam Yang

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Flattening section of the Cortex
by Ajay Pillai 15 Nov '04

15 Nov '04

Hello Everyone, I have the following problem. I have a section/patch of the Cortical Surface (Auditory area.) which I would like to unfold/flatten. The data is in matlab and I have it as vertex and faces of the cortical surface. I know how to write it to a ?h.pial.asc file format from matlab. I also have activation maps from SPM2. My questions are : 1. Can I read this surface in freesurfer and an unfold/flatten it ? If yes how ? 2. Can I overlay the activation maps in freesurfer on to the cortial patch I described above? If so could some one list the possible steps please? 3. Finally if I can indeed ufold the above mentioned cortical surface will I be able to export it back to .asc file format? Thank you Ajay

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vertex "area"
by Doug Greve 14 Nov '04

14 Nov '04

I have just fixed a bug in FreeSurfer that involves computing the area of some surface structures. For those of you who care, this was a bug that emerged after converting our surface meshes from quadralaterals to triangles. This change was made a few years ago. This change should have little effect on the reconstruction. It will have an effect on programs that report the area of subsections of cortex (but not total cortical area). At least three such programs that are affected are: mris_compute_overlap, mris_label_area, and mri_surfcluster. The bug causes the reported area to appear to be 1.5 times what it really is. For example, in mri_surfcluster, a cluster threshold of 300 mm^2 would actually be a threshold of 200 mm^2. For those in the NMR center, these three programs have been updated. For those outside, you can get these programs from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve New versions of freesurfer will, of course, have the update. Sorry for any inconvenience. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Re: [Freesurfer] functional overlay
by Joongnam Yang 12 Nov '04

12 Nov '04

Thanks Doug, So, "structural data registration" "functional data registration" "co-registration" have to be done separately? How do I do the first two? The manual is pretty murky on that. Please enlighten me... I am trying to do functional overlay using csurf and there are so many hidden things when I use the manual. I appreciate your help, Doug. Nam.

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Re: [Freesurfer] functional overlay
by Joongnam Yang 12 Nov '04

12 Nov '04

Thanks Doug, When I run tkregister2 --targ structuralimage --mov functionalimage --reg register.dat I got the following error. ====================== target volume XXXXX.img movable volume XXXXXX.img reg file register.dat LoadVol 1 $Id: tkregister2.c,v 1.22 2003/11/05 21:30:50 greve Exp $ Diagnostic Level -1 regio_read_register(): No such file or directory Could not open register.dat Segmentation fault (core dumped) ========================== What could have been wrong? Thanks. Nam.

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