[Freesurfer] Looking for correct coordinates

rfaces? Thanks -- Daniel Goldenholz - ___ Freesurfer mailing list [EMAIL PROTECTED] http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] inside or outside the brain

point is INSIDE or OUTSIDE the 3D volume called "brain" bounded by the surface I read in? Thanks, -- Daniel Goldenholz - ___ Freesurfer mailing list [EMAIL PROTECTED] http://mail.nmr.mgh

[Freesurfer] ROI labels from clusters on surface .w

s .w files, and then figure out automatically where clusters (blobs) appear, and then create a label file for each one) Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ ___ Fre

[Freesurfer] Remote tksurfer

, and then view it remotely. For reasons that are not clear to me, this didn't work either. So. What I want to do is given a particular view that I set up in a tcl script, I would like to get an RGB file of that, without drawing it locally. Any ideas or creative workarounds? Thanks -

[Freesurfer] labels to annot files?

Is there a command out there that converts a set of labels into an annot file automatically? It would be very useful... -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg

Re: [Freesurfer] labels to annot files?

7;t think so. I guess you'd need a color file as well. It would be pretty easy Bruce On Wed, 21 Jul 2004, Daniel Goldenholz wrote: Is there a command out there that converts a set of labels into an annot file automatically? It would be very useful... __

Re: [Freesurfer] labels to annot files?

On Thu, 22 Jul 2004, Daniel Goldenholz wrote: Ok. Well I wouldn't mind whipping this up in matlab, but I need to know the format. Daniel On Thu, 22 Jul 2004, Doug Greve wrote: You'd also have to make sure that the labels did not overlap as there is no way to represent this in the annot fil

[Freesurfer] Making a patch of area A

walk from the centroid in any direction for a certain distance, and still be within my "patch." Knowing that distance (radius), I could just use pi*r^2 and call that the area of the patch. But how do I find this idealized patch in real life? Thanks Daniel

Re: [Freesurfer] Making a patch of area A

of course, has some metric distortion, but if the patch is small, it might not be to bad. Once you've identified the vertices in the patch (or maybe a slightly bigger patch), then you can refine it in the folded space. doug Daniel Goldenholz wrote: Hi. I have a graph theory question: I would

Re: [Freesurfer] Making a patch of area A

the patch) ? Thanks Daniel On Tue, 8 Mar 2005, Bruce Fischl wrote: Hi Daniel, don't use Euclidean distance. Use the length of the great circle connecting each point to the central vertex on the ?h.sphere surface. Bruce On Tue, 8 Mar 2005, Daniel Goldenholz wrote: Doug I was thinking of trying

[Freesurfer] Decimation?

does, because for surface spacings of 6, I expect euclidean distances to be less than 6, and for surface spacings of 10, I expect euclidean distances to be less than 10. Thoughts from freesurfing fellows? -- Daniel Goldenholz - Cell: 617

[Freesurfer] CSURF bugs and hint

Hi. I would like to report two bugs in CSURF, and also ask for a hint about using it. BUGS: 1. If you save an image to TIFF or RGB, the screen does not redraw itself before saving. Therefore, any menus or windows that might have drawn over the image will get saved into the file. This bug can be

[Freesurfer] Re: remote VNC solution

I was just asked this same question twice in a short time, so I guess that is a sign that others might want to know the answer too. The short version of the question is: "How can I get freesurfer to work from a remote VNC setup?" The answer is, thanks to a hint from Paul Raines, very simple. When

Re: [Freesurfer] MEG data and ASCII format

eimer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ begin:vcard fn:D

Re: [Freesurfer] freesurfer for MEG/EEG source imaging

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ "Mavet v'chaim b'yad halashon" "Life and death are in the hands of language"

[Freesurfer] Getting the resolution out

Hi. I was handed some data analyzed with freesurfer, and I would like to know what is the exact resolution of the T1 mri, i.e. 1.25mm x 3mm x 2mm for example. Where can I look in the freesurfer folder to find out? Thanks -- Daniel Goldenholz

Re: [Freesurfer] Getting the resolution out

-10.110786 29.012054 -11.469879 Bruce Fischl wrote: Hi Daniel, you need to look at your original data (e.g. dicom files). You can mri_info to tell you. Bruce On Tue, 20 Sep 2005, Daniel Goldenholz wrote: Hi. I was handed some data analyzed with freesurfer, and I would like to know what is

Re: [Freesurfer] Group analysis

ion is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Other parcellations

Hi. I was wondering if anybody out there has made other parcellations of the entire brain besides the standard freesurfer one with 81 named regions? For instance, did anybody go to the painful trouble of making a 4 lobe parcellation? Thanks Daniel Goldenholz

[Freesurfer] Multiple warnings and errors in autorecon1

t implemented yet in cache_volume_range_has_changed() Mode: atlas analysis VALIDATION*** THE SEGMENTATION IS PROBABLY NOT CORRECT -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ "Mavet v'chaim b'yad halashon&q

Re: [Freesurfer] tcl script - rotate and save graphics

option for vector graphics or high resolution tiff or png images? Best, Darren ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Daniel Goldenholz -

Re: [Freesurfer] Translate label file from average subject to all subjects

Freesurfers I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.

[Freesurfer] Faster and Parallel recon-all

Ooops. I sent the below with the wrong subject tag. Here it is again: Daniel Goldenholz wrote: Freesurfers I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now,

Re: [Freesurfer] Faster and Parallel recon-all

aniel Goldenholz wrote: Ooops. I sent the below with the wrong subject tag. Here it is again: Daniel Goldenholz wrote: Freesurfers I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct

Re: [Freesurfer] Faster and Parallel recon-all

The script looks good. The one thing it needs though is for the right and left hemi steps to log to separate files, otherwise output to recon- all.log will be interleaved, making debugging impossible. On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote: Ooops. I sent the below wit

Re: [Freesurfer] Faster and Parallel recon-all

. I am still probing into this. If you can think of something that might be of help then let me know. -Dhruman -Original Message- From: Daniel Goldenholz [mailto:[EMAIL PROTECTED] Sent: Tuesday 21 March 2006 11:25 To: Goradia, Dhruman D Subject: Re: [Freesurfer] Faster and Parallel r

Re: [Freesurfer] Faster and Parallel recon-all

kes about 30 hrs to process 1 scan currently. -Dhruman -Original Message- From: Daniel Goldenholz [mailto:[EMAIL PROTECTED] Sent: Tuesday 21 March 2006 17:09 To: Goradia, Dhruman D Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Faster and Parallel recon-all Dhruman Thanks for c

Re: [Freesurfer] Faster and Parallel recon-all

e file...alas i just changed the recon-all script to call mri_mask when it gets the -norm2 flag...this seems to have worked. sarah Original message Date: Wed, 22 Mar 2006 18:09:11 -0500 From: Daniel Goldenholz <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] Faster and Parallel

[Freesurfer] still trouble with this motioncor problem

_average: MRIread(/autofs/space/megraid_043/seder/freesurfer/nmr00069/mri/tmp-mri_motion_correct.fsl-11962/cor-2.img) failed Linux rerun 2.6.9-22.0.2.106.unsupportedsmp #1 SMP Fri Jan 20 04:48:30 CST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Mar 23 11:43:38 EST 2006 -

Re: [Freesurfer] Re: tcl command to raise tksurfer window

Sorry, there's no way to do that. There's also no way to set the backgroud color in the window. -- Daniel Goldenholz - Cell: 617-935-9421 http://people.bu.edu/danielg/ "Mavet v'chaim b'yad halashon"