Re: [Freesurfer] frontal gray matter and frontal white matter volumes

fantastic! I didn't know of that feature :) thanks, roberto On Wed, Aug 19, 2009 at 4:07 PM, Bruce Fischl wrote: > actually, Doug's wm parcellation tool should be able to parcel out the > frontal white matter from a lobar segmentation. > > cheers > Bruce > On Wed, 19 Aug 2009, roberto toro wrote:

[Freesurfer] Error in calabel step.

Hi freesurfer, We need some technical support here. The dataset was processed successfully using earlier version. But it failed for the lastest 4.50 FS. Here's the message before the process ended. -- Fourth_Ventricle (15): line

Re: [Freesurfer] fsaverage Talairach Coordinates

Hi Doug, Thanks for the reply. I looked at Matthew Brett's transform, which I understand to be a non-linear transform between MNI and Talairach, but I was told that tksurfer's "Talairach" field is not accurate. Is this simply because Brett's transform is only one of many possible solutio

Re: [Freesurfer] thickness map

Yes, this is what our group analysis tools do. You can find tutorials on the wiki. You'll probably start with mris_preproc. doug On Thu, 20 Aug 2009, Feng-Xian Yan wrote: > Hi, > > Thank you for your responses before. > > > > I have another problem want to solve. I check the number of verte

Re: [Freesurfer] mris_fix_topology

you can view them on the inflated.nofix surface. I think the defect labels are written to curvature format files called ?h.defect_labels or something like that. You might also try using the new topology fixer (Nick can point you at it if you can't find it) cheeers Bruce On Wed, 19 Aug 2009,

Re: [Freesurfer] mris_fix_topology

are you out of disk space? On Thu, 20 Aug 2009, Falk Lüsebrink wrote: Hi Doug, I get the following error: rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face list Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@

Re: [Freesurfer] thickness map

Hi, Thank you for your responses before. I have another problem want to solve. I check the number of vertex for all subjects, but I found that the number of vertex for each subjects and each hemispheres is different. Because I want to compare cortical thickness using vertex-by-vertex, I wou

Re: [Freesurfer] fsaverage Talairach Coordinates

THere are two sets of coordinates that are reportable. First, the mni305. This is the coordinate system that we use internally (eg, surface coords of fsaverage are stored in mni305). We can convert these coords to "talairach" thru Matthew Brett's transform. This is what is reported in the "Tal

[Freesurfer] fsaverage Talairach Coordinates

Hi, I've been asked to report Talairach coordinates in a paper, but I've been told that the coordinates that are listed on the fsaverage brain (in the talairach.xfm file) are not accurate. Does anyone have a way to get the true Talairach coordinates on the fsaverage brain? Thanks, Matt

Re: [Freesurfer] mris_fix_topology

Hmmm, not sure what's going on, may have to wait for Bruce. Have you looked at the ?h.orig.nofix in tkmedit/tksurfer? Falk Lüsebrink wrote: > Hi Doug, > > I get the following error: > > rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face > list > > Falk > > -Original

Re: [Freesurfer] mris_fix_topology

Hi Doug, I get the following error: rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face list Falk -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, August

Re: [Freesurfer] mris_fix_topology

It was not mris_fix_topology that failed but mris_euler_number (but that might have failed because of something in the topology fix). What happens if you: cd /home/falk/freesurfer/subjects/yv98_05mm_div mris_euler_number ../surf/rh.orig doug Falk Lüsebrink wrote: > > Hi FreeSurfers, > > > >

Re: [Freesurfer] RAS Conversion

Try this: 1. Get vox2ras matrix for volume RAS (Call it T): mri_info --vox2ras-tkr volume.mgz 2. Get vox2ras matrix for scanner RAS (Call it S): mri_info --vox2ras volume.mgz 3. Compute M = S*inv(T) 4. Foreach xyz in label, NewXYZ = M*[X Y Z 1]' doug Joseph Barrington Keller wrote:

Re: [Freesurfer] tkregsiter2 problem

Use bbregister, something like: bbregister --s subjectname --mov 002.mgz --init-fsl --t1 --reg register.dat --o 002.anat.mgz Guang Zeng wrote: > Hi, there, > > I have the two scans (001.mgz and 002.mgz) of the same subject, > 001.mgz is used as the input of recon-all -autorecon1, > now I

[Freesurfer] tkregsiter2 problem

Hi, there, I have the two scans (001.mgz and 002.mgz) of the same subject, 001.mgz is used as the input of recon-all -autorecon1, now I have a brainmask.mgz using 001.mgz, I want to register 002.mgz using brainmask.mgz as reference volume, which command I can use? tkregister2? Thanks a l

[Freesurfer] RAS Conversion

Hello, I'm trying to convert labels in volume RAS to volume scanner RAS in order to use them in another program. How would I accomplish this? Any advice on this subject would be greatly appreciated. Thanks Joe ___ Freesurfer mailing list Freesur

Re: [Freesurfer] bbregister

Use mri_vol2vol, something like mri_vol2vol --mov fa.nii --reg register.dat --fstarg --o fa.anat.nii doug Victoria Williams wrote: > Hello, > > I used bbregister to create a register.dat file aligning a > subject's T2(lowb) dti image to their FreeSurfer orig volume. I am now > wondering with w

Re: [Freesurfer] (no subject)

Hi, Bruce, I have two quick question, 1. After auto-segmentation, we are using 3D slicer to edit hippocampus. Are there any other researchers who did the same way, auto + manual editing? 2. Since we have a lot of data for related studies that needs hippocampus volume, we still prefe

[Freesurfer] bbregister

Hello, I used bbregister to create a register.dat file aligning a subject's T2(lowb) dti image to their FreeSurfer orig volume. I am now wondering with what command can I apply this register.dat file to the other diffusion measures such as FA to bring them into alignment with the orig, as they

Re: [Freesurfer] Convert to original orientation

In this case, you should not need to do a registration because the two volumes share scanner space. doug Martin Reuter wrote: > Hi, > > also I would suggest to give mri_robust_register a try for the > registration. It is very accurate especially in cases with differences > in the images (jaw mo

[Freesurfer] [Fwd: Re: ROI reliability]

Hi Nick, It appears mri_compute_seg_overlap only works with .mgz files and not .label files, which is how I saved the ROIs. I tried renaming the labels as .mgz files, but that did not work. Any suggestions? Thanks. > the utility for comparing segs is 'mri_compute_seg_overlap', included > w

Re: [Freesurfer] a "redraw failed: no gl window open" problem

Guang, Ok, v4.5.0 is in use. So the tksurfer.bin fix mentioned in email is no longer necessary. Instead, in the /etc/X11/xorg.conf file, try changing this line: Depth 16 to this: Depth 24 and then logout and login again (or press Crtl-Alt-Backspace to reset X11). Nic

Re: [Freesurfer] a "redraw failed: no gl window open" problem

Guang, In the xorg.conf file, I noticed one of the Display depths is '16'. This should be set to '24' to ensure full color depth. Also, the email doesnt mention which freesurfer version is being used. In short, that tksurfer.bin link that was mentioned is no longer necessary with the new versions

Re: [Freesurfer] FreeSurfer Licence for Grid Computing?

Hi Henri, we don't have an established procedure for this, and you certainly could use a single license if you wanted to. However, much of our funding depends on our ability to track how many users we have, so if you have multiple researchers using FreeSurfer it would be a big help to us if eac

Re: [Freesurfer] frontal gray matter and frontal white matter volumes

actually, Doug's wm parcellation tool should be able to parcel out the frontal white matter from a lobar segmentation. cheers Bruce On Wed, 19 Aug 2009, roberto toro wrote: That will not be able to separate the only frontal WM from the rest of the WM, isn't it? I have used FSL (a mix of bet,

Re: [Freesurfer] Question about "Getting started with your own data"

Hi Kenta, they would be different runs of anatomicals on the same subject, typically within the same session (e.g. two different acquisitions of SPGR or mp-rage) cheers Bruce On Wed, 19 Aug 2009, [ISO-2022-JP] ±¬ÌÂÀ wrote: Hi freesurfer gurus, We are trying to do reconstruction in tksur

Re: [Freesurfer] a "redraw failed: no gl window open" problem

Hi, Nick, I forgot to attach the xorg.cong file, it is here. Thanks! # nvidia-xconfig: X configuration file generated by nvidia-xconfig # nvidia-xconfig: version 1.0 (buildmeis...@builder26) Wed Mar 29 15:31:59 PST 2006 # Xorg configuration created by system-config-display Section "ServerLa

Re: [Freesurfer] FreeSurfer Licence for Grid Computing?

Henri, FS will check the license in $FREESURFER_HOME I think It's easy to make it work on the grid. I have done this last year without problems. PPJ 2009/8/19, Henri Vrooman : > Hi there, > > I have a question about FreeSurfer Licensing. For our image processing > activities it would be ve

Re: [Freesurfer] Question about "Getting started with your own data

Hi Kenta, these are two different images usually from the same session. Freesurfer then does motion correction and averages the images to create a single input image for further processing. Best, Martin On Wed, 2009-08-19 at 16:26 +0900, 卯野賢太 wrote: > Hi freesurfer gurus, > > We are trying to d

[Freesurfer] FreeSurfer Licence for Grid Computing?

Hi there, I have a question about FreeSurfer Licensing. For our image processing activities it would be very nice and helpful to install FreeSurfer on one of our National Grid Facilities. The Grid (BIGGRID) is sponsored by the Dutch Government and the European Community. The grid is solely used b

[Freesurfer] Question about "Getting started with your own data

Hi freesurfer gurus, We are trying to do reconstruction in tksurfer section according to the text. We have a question in "Getting started with your own data" section. In the text, the following commands are written, recon-all -s \ -i /9-2-1.dcm -i /9-3-1.dcm In the above commands,