Re: [Freesurfer] tesselating

Chacko, I'm not sure why it ran. Can you send a snapshot of the image not being displayed correctly? When I have seen partial displays in tksurfer in the past, the problem was solved by updating the NVidia graphics driver (assuming the machine had such a card), but if subject bert is displaying c

[Freesurfer] mris_fix_topology

I think my fix topology sequence froze...I typed "top" in another terminal and this is what came up... ID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND 899 surf 25 0 2169m 1.6g 1984 R 99.1 43.1 1042:33 mris_fix_topolo 18609 root 15 0 457m 196m 8616 S 0.7 5.3

Re: [Freesurfer] mris_fix_topology

You must have a number of *huge* defects: 163949 ambiguous faces found in tessellation segmenting defects... 93 defects found, arbitrating ambiguous regions... usually the # of defective vertices is less than 1/10 of this. Try loading the ?h.defect_labels (with tksurfer->file->load curv) onto

Re: [Freesurfer] mris_fix_topology

Well, I figured out what my problem is. The skull strip only took off about a quarter of the skull on the top. Any suggestions on how to correct this? Quoting Bruce Fischl <[EMAIL PROTECTED]>: > You must have a number of *huge* defects: > > > 163949 ambiguous faces found in tessellation > > se

Re: [Freesurfer] mris_fix_topology

look at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fSkullStripFix?action=highlight&value=skull+stripping On Fri, 23 Jun 2006 [EMAIL PROTECTED] wrote: Well, I figured out what my problem is. The skull strip only took off about a quarter of the skull on the top. Any suggestions o

[Freesurfer] volumes

Dear All, Is the total white matter volume computed by mris_anatomical_stats the total volume inside the gray/white surface? Or does it exclude subcortical structures? i.e. is total brain volume = total gray matter volume + total white matter volume ? Thanks, Sasha Sasha Wolosin Research Ass

Re: [Freesurfer] volumes

it's the volume of the wm.mgz, and it's deprecated. Use the various wm volumes in the aseg files (or aseg.stats) instead. cheers, Bruce On Fri, 23 Jun 2006, Sasha Wolosin wrote: Dear All, Is the total white matter volume computed by mris_anatomical_stats the total volume inside the gray/wh

[Freesurfer] recon-all error

Hello All, So I tried using recon-all to get a few parcellations stats from a minc file it but I'm getting the following error. Please could someone say how this can be rectified. Thanks. - Anil Roy. This is the command I'm giving: # recon-all -force -i /root/Desktop/F100.mnc -subjid F100 -sd /u

Re: [Freesurfer] volumes

is there a way to compute the volumes contained within the ?h.pial and ?h.white surfaces? >>> Bruce Fischl <[EMAIL PROTECTED]> 6/23/2006 4:41 pm >>> it's the volume of the wm.mgz, and it's deprecated. Use the various wm volumes in the aseg files (or aseg.stats) instead. cheers, Bruce On Fri, 23

Re: [Freesurfer] volumes

mris_anatomical_stats will give you the volume of the ribbon. There's also a program Xiao Han wrote called mris_volume that will compute the interior volume of any closed surface. Not sure if it's in your distribution, but it's in dev (and stable3 I think) Bruce On Fri, 23 Jun 2006, Sasha Wo

Re: [Freesurfer] recon-all error

what steps have you run previously? You don't need to specify -i on later stages, just the subjid and sd. On Fri, 23 Jun 2006, Anil Roy wrote: Hello All, So I tried using recon-all to get a few parcellations stats from a minc file it but I'm getting the following error. Please could someone s

[Freesurfer] NIfTI-1 convert

Title: Message Hi folks, I want to use mri_convert to convert 30 direction diffusion data to NIfTI-1 format. I ran it and it seemed to work good. I just wanted to clarify one thing. The docs seem to say that unless I use --conform it will not interpolate my data to 1mm res, or change it in

Re: [Freesurfer] NIfTI-1 convert

Hi Greg, yes, you definitely don't want to interpolate the diffusion data to 1mm Bruce On Fri, 23 Jun 2006, Kirk, Gregory wrote: Hi folks, I want to use mri_convert to convert 30 direction diffusion data to NIfTI-1 format. I ran it and it seemed to work good. I just wanted to clarify one thi

Re: [Freesurfer] recon-all error

This is the first step. I assumed that recon-all should do all the processing by itself without the need to run anything previously. Please mention if any extra steps have to be taken before the parcellation stats (or the entire recon-all process) can be obtained from the minc file. Thanks - Anil.O

Re: [Freesurfer] recon-all error

well, you specified -autorecon3, which assumes some stuff has been run before. If you want to do everything from beginning to end run -all instead Bruce On Fri, 23 Jun 2006, Anil Roy wrote: This is the first step. I assumed that recon-all should do all the processing by itself without the nee

[Freesurfer] The "5 mm limit" on cortical thickness?

Probably Nick or Bruce: Could you confirm what I think I remember: that in the algorithm to move the surface out from the white position to the pial, FS is constrained by a 5 mm limit? -- Is this documented somewhere, with other details like what unwanted behavior this prevented, in what reg

Re: [Freesurfer] The "5 mm limit" on cortical thickness?

Hi Graham, actually the limit is in the thickness measurement, not the deformation. You can recreate the thickness files with mris_thickness -max $maxthick ... if you want a larger value. What's going wrong? Bruce On Fri, 23 Jun 2006, Graham Wideman wrote: Probably Nick or Bruce: Could yo

Re: [Freesurfer] The "5 mm limit" on cortical thickness?

Bruce: Thanks for your reply -- actually the limit is in the thickness measurement, not the deformation. You can recreate the thickness files with mris_thickness -max $maxthick ... if you want a larger value. What's going wrong? Well we're trying to guess why the pial surface is somewhat co

Re: [Freesurfer] The "5 mm limit" on cortical thickness?

probably not. Check the intensity of the white matter underlying the gray and see if it's significantly less than 110. If so, try putting a few control points there (make sure they aren't in partial-volumed wm) Bruce On Fri, 23 Jun 2006, Graham Wideman wrote: Bruce: Thanks for your reply -

Re: [Freesurfer] The "5 mm limit" on cortical thickness?

At 6/23/2006 06:57 PM, you wrote: probably not. Check the intensity of the white matter underlying the gray and see if it's significantly less than 110. If so, try putting a few control points there (make sure they aren't in partial-volumed wm) Bruce: You would recommend this, even though the

Re: [Freesurfer] The "5 mm limit" on cortical thickness?

if you put them in the body of the wm (where the intensity in the T1.mgz vol is < 110), it shouldn't effect the placement of the boundary substantially On Fri, 23 Jun 2006, Graham Wideman wrote: At 6/23/2006 06:57 PM, you wrote: probably not. Check the intensity of the white matter underlying