RE: [Freesurfer] (no subject)

e old parcellation...Can I? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 16, 2007 2:30 PM To: Bagnato, Francesca (NIH/NINDS) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) if you rerun them do they get better? On Wed, 16 May

RE: [Freesurfer] (no subject)

/NINDS) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) if you rerun them do they get better? On Wed, 16 May 2007, Bagnato, Francesca (NIH/NINDS) [E] wrote: > No I am having some bad parcellations on images done with the previous > software and I am just try

RE: [Freesurfer] (no subject)

- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 16, 2007 2:26 PM To: Bagnato, Francesca (NIH/NINDS) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) I don't think so. They would not look okay if the surfaces were regenerated, but I think the new

RE: [Freesurfer] (no subject)

, Francesca (NIH/NINDS) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subject) I don't think so. They would not look okay if the surfaces were regenerated, but I think the new tools should be able to display the old parcellations. Are you having problems with this? On Wed, 16 May

RE: [Freesurfer] (no subject)

round - i.e. they do not look okay because of the mismatch between softwares? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 16, 2007 2:22 PM To: Bagnato, Francesca (NIH/NINDS) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] (no subjec

RE: [Freesurfer] (no subject)

Subject: RE: [Freesurfer] (no subject) I don't think so, but maybe I don't understand. The parcellations are defined on the surfaces, so if they look okay you should be all set (they can't be misregistered) On Wed, 16 May 2007, Bagnato, Francesca (NIH/NINDS) [E] wrote: >

RE: [Freesurfer] (no subject)

tch between the two interfaces (old and new version) render the output wrong? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Wednesday, May 16, 2007 2:17 PM To: Bagnato, Francesca (NIH/NINDS) [E] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subje

RE: [Freesurfer] (no subject)

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) you should be able to On Wed, 16 May 2007, Bagnato, Francesca (NIH/NINDS) [E] wrote: > Can I open images parcellated with an old version of freesurfer (the > one parcellating 80 regions) with the new one (based upon the Desikan > atals)?

Re: [Freesurfer] (no subject)

you should be able to On Wed, 16 May 2007, Bagnato, Francesca (NIH/NINDS) [E] wrote: Can I open images parcellated with an old version of freesurfer (the one parcellating 80 regions) with the new one (based upon the Desikan atals)? Thanks, Francesca Francesca Bagnato, MD-PhD Staff Scientist,

[Freesurfer] (no subject)

Can I open images parcellated with an old version of freesurfer (the one parcellating 80 regions) with the new one (based upon the Desikan atals)? Thanks, Francesca Francesca Bagnato, MD-PhD Staff Scientist, NIB-NINDS-NIH Building 10, Room 5S205 9000 Rockville Pike Bethesda, MD, 20892-1400 MSC Ph

[Freesurfer] (no subject)

hi, I don't know the procedure of the FreeSurfer? Although the recon-all illustration contains lots of the steps, I don't know the meaning. So I want to know the brief step about the FreeSurfer how to deal with 3D data? Thank you very much [EMAIL PROTECTED] 2007-05-05

[Freesurfer] (no subject)

hi,I have some question to ask, First,now I want to add four parts of the occipital lobe's gray matter volume(Lateral Occipital,Lingual,Cuneus,Pericalcarine) to evaluate occipital lobe development,can I do like this? second, I also want to use the occipital lobe's cortical thickness to eva

Re: [Freesurfer] (no subject)

this is just our standard gzipped (hence the z at the end) volume format On Sun, 13 May 2007, hankee wrote: Hi, In freesurfer software,some file's name is *.mgz,what does the mgz abbreviate? Thanks. [EMAIL PROTECTED] 2007-05-05 ___ Freesurfer mailing

[Freesurfer] (no subject)

Hi, In freesurfer software,some file's name is *.mgz,what does the mgz abbreviate? Thanks. [EMAIL PROTECTED] 2007-05-05 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] (no subject)

You can run aparcstats2table on all of your subjects to create a spreadsheet, then import the spreadsheet into your stats program doug hankee wrote: > Hi, > In the ?h.aparc.stats file,I want to use the average thickness > directly to do the statistics analysis? Can I do like that? > Thank you. >

[Freesurfer] (no subject)

Hi, In the ?h.aparc.stats file,I want to use the average thickness directly to do the statistics analysis? Can I do like that? Thank you. [EMAIL PROTECTED] 2007-05-05 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

[Freesurfer] (no subject)

hi, Do FreeSurfer have Gray matter volume map,just like thickness map? Because I want to overlay the gray matter volume to inflate map,like thickness map? [EMAIL PROTECTED] 2007-05-05 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m

Re: [Freesurfer] (no subject)

That's a typo, it should be mm^3 hankee wrote: > Hi, > In the ?h.aparc.stats file,the Gray Matter Volume's units is mm,not > mm^3. Is itright? Can you tell me the reason,because I want to use > this option.Thank you very much! > [EMAIL PROTECTED] > > 2007-05-05 > >-

[Freesurfer] (no subject)

Hi, In the ?h.aparc.stats file,the Gray Matter Volume's units is mm,not mm^3. Is it right? Can you tell me the reason,because I want to use this option.Thank you very much! [EMAIL PROTECTED] 2007-05-05 ___ Freesurfer mailing list Freesurfer@nmr.mgh.ha

Re: [Freesurfer] (no subject)

Hankee, The parcellation unit mapping to the lobes is found at the bottom of this page: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation The occipital lobe consists of: Lateral Occipital Lingual Cuneus Pericalcarine Nick On Sat, 2007-05-05 at 17:22 +0800, hankee wrote:

[Freesurfer] (no subject)

Hi, How many parts consisted of the occipital lobe in freesurfer's ?h.aparc.stats file and what the name of this parts in this file? Thank you! [EMAIL PROTECTED] 2007-05-05 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m

Re: (ÈðÐÇÌáʾ-´ËÓʼþ¿ÉÄÜ ÊÇÀ¬»øÓʼþ)Re: [Freesurfer] (no subject)

best, > hankee > > [EMAIL PROTECTED] > 2007-04-26 > - Original Message - > From: rahul > To: duhanjian > Sent: 2007-04-26, 23:18:32 > Subject: (ÈðÐÇÌáʾ-´ËÓʼþ¿ÉÄÜÊÇÀ¬»øÓʼþ)Re: [Freesurfer] (no subject) > > > Hi Hankee, > > You certainly can use the s

Re: [Freesurfer] (no subject)

Hi Hankee, You certainly can use the statistical information in the stats dir regarding the volume, thickness, and surface area of individual regions, such as the parahippocampal gyrus (as derived from the ?h.aparc.annot file), to compare between various groups of subjects. The only recommendation

[Freesurfer] (no subject)

hi,I have question about the ?h.aparc file in stats directory. Can I use the parahippocample's gray matter volume or other brain structure's gray matter volume to do statistics analysis? For example,select 15 normal people and 15 AD disease patient,using FreeSurfer software to deal with them,whe

Re: [Freesurfer] (no subject)

Hi Hankee, sorry, no, we don't label LGN explicitly. Bruce On Thu, 26 Apr 2007, hankee wrote: hi,ereryone I have a question.Can FreeSurfer measure the lateral geniculate nucleus's size? If can, how to implement such function? [EMAIL PROTECTED] 2007-04-26 _

[Freesurfer] (no subject)

hi,ereryone I have a question.Can FreeSurfer measure the lateral geniculate nucleus's size? If can, how to implement such function? [EMAIL PROTECTED] 2007-04-26 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

Re: [Freesurfer] (no subject)

Giri and Binyam, This problem was encountered once before (by Binyam), and I was not able to recreate the segmentation fault locally, so can one or both of you do the following to help me debug this problem? I have posted a version of mri_ca_register which contains the debugging symbols here: ft

Re: [Freesurfer] (no subject)

Hi Nurunisa, If you are using tksurfer to view the annotation files or an individual label, you can first select the label you want to color code by clicking on it. Then, you can bring the 'color spectrum' bar in tksurfer and choose whichever color you would like. Best, Rahul > Hi, I am trying

[Freesurfer] (no subject)

Hi, I am trying to color code my labels according to the stats associated with each label. I was playing with the colortable but that did not work. I will appreciate any guidance/ help on that. How can I give to a given label the color I want to? thanks, Nurunisa __

Re: [Freesurfer] (no subject)

On Tue, 2006-12-05 at 13:31 -0500, Bruce Fischl wrote: > Hi Li-Chen, > > there is some intentional randomness in the algorithms. Try overlaying the > surfaces and you'll see that they are visually identical I would think. > Nick: is there a switch to recon-all to specify what the seed should be

Re: [Freesurfer] (no subject)

Hi Li-Chen, there is some intentional randomness in the algorithms. Try overlaying the surfaces and you'll see that they are visually identical I would think. Nick: is there a switch to recon-all to specify what the seed should be for the random # generators? thanks, Bruce On Tue, 5 Dec 20

Re: [Freesurfer] (no subject)

Li-Chen, Some of the utilities make use of random number generation in their algorithms, specifically: mris_smooth, mris_sphere, mris_topo_fixer and mris_ca_label. While the number of vertices can change because of this, the resulting stats (cortical thickness) should not differ by more than 0.5%

[Freesurfer] (no subject)

Dear All, I tried to extract a surface from a MRI scan (T1, 1.5T) using Freesurfer 3.0.3 on a Linux computer. I just run "recon-all" script for the same scan 6 times (same computer, no human interaction). To my supprise, I got 6 different results ( different #triangles, #vertices). Go back to che

Re: [Freesurfer] (no subject)

Are you sure the volume is conformed? On Thu, May 18, 2006 at 12:14:30PM -0400, Mark Pinsk wrote: > I just installed the latest release on my mac ox 10.4 > > Trying to set control points on a monkey volume, and something wierd > keeps happening... I will middle-click to set the control point, a

Re: [Freesurfer] (no subject)

is your volume "conformed"? That is, did you run mri_convert --conform on it? tkmedit doesn't like other types of volumes, so it needs to be isotropic and 256^3. On Thu, 18 May 2006, Mark Pinsk wrote: I just installed the latest release on my mac ox 10.4 Trying to set control points on a

[Freesurfer] (no subject)

I just installed the latest release on my mac ox 10.4 Trying to set control points on a monkey volume, and something wierd keeps happening... I will middle-click to set the control point, and the green cross will appear, but when I move to another location to set another control point, the

[Freesurfer] (no subject)

Hi Eric, Message: 1 Date: Wed, 10 May 2006 09:37:43 -0400 From: "Faden, Eric (NIH/NIMH) [F]" <[EMAIL PROTECTED]> Subject: [Freesurfer] Skull Stripping a Macaque To: Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" Hey all, Is anyone using freesurfer

Re: [Freesurfer] (no subject)

 Valentina -Original Message- From: Nick Schmansky [mailto:[EMAIL PROTECTED]] Sent: Saturday, April 08, 2006 7:23 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Julia Hamstra; Freesurfer Mailing List Subject: Re: [Freesurfer] (no subject) Use: recon-all -s -skullstrip A

RE: [Freesurfer] (no subject)

PROTECTED] Sent: Saturday, April 08, 2006 7:23 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Julia Hamstra; Freesurfer Mailing List Subject: Re: [Freesurfer] (no subject) Use: recon-all -s -skullstrip Also, recon-all -help will list-out most of the steps which can be run individually

RE: [Freesurfer] (no subject)

ee if it works better for you. From: Nick Schmansky [mailto:[EMAIL PROTECTED] Sent: Sat 4/8/2006 8:22 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Julia Hamstra; Freesurfer Mailing List Subject: Re: [Freesurfer] (no subject) Use: recon-all -

Re: [Freesurfer] (no subject)

Use: recon-all -s -skullstrip Also, recon-all -help will list-out most of the steps which can be run individually (see section titled STEP-WISE DIRECTIVES). On Sat, 2006-04-08 at 19:47 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Hi, > I'm using Freesurfer and I'd like to run the

[Freesurfer] (no subject)

Hi, I'm using Freesurfer and I'd like to run the autorecon1 just for the skull stripping (without intensity and spatial normalization). Is there a command just to do that? Thanks valentina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

RE: [Freesurfer] (no subject)

ubject: Re: [Freesurfer] (no subject) And your command-line is ...? Bagnato, Francesca (NIH/NINDS) [F] wrote: I am sorry: Mris_anatomical_stats.. Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-30

RE: [Freesurfer] (no subject)

-402.6391 fax #: 001-301-402.0373 -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thursday, January 19, 2006 10:33 AM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)   And your command-line is

Re: [Freesurfer] (no subject)

: Doug Greve [mailto:[EMAIL PROTECTED]] Sent: Wednesday, January 18, 2006 6:25 PM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) we don't have an mris_stats. What do you mean? Bagnato, Francesca (NIH/NINDS) [F] wrote:

RE: [Freesurfer] (no subject)

To: Bagnato, Francesca (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) we don't have an mris_stats. What do you mean? Bagnato, Francesca (NIH/NINDS) [F] wrote: >Dear Users: >I would like to know which is the name of the file (and its location)

Re: [Freesurfer] (no subject)

we don't have an mris_stats. What do you mean? Bagnato, Francesca (NIH/NINDS) [F] wrote: Dear Users: I would like to know which is the name of the file (and its location) where all he results end up after the mris_stats... Thanks, francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive

[Freesurfer] (no subject)

Dear Users: I would like to know which is the name of the file (and its location) where all he results end up after the mris_stats... Thanks, francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373

Re: [Freesurfer] (no subject)

Hi Aaron, First, is it something simple and annoying like that your script doesn't look for an orig.mgz volume (vs. the 'orig' which was standard until fairly recently)? I have needed to edit my scripts to accommodate for this. okay! On Wed, 2 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote:

[Freesurfer] (no subject)

Hi, I have a script that basically opens up tksurfer and tkmedit for manual editing, and then runs recon-all stage2 once you’re done editing. We recently tried to run the script on a different computer with the same freesurfer distribution, and got an error I’m not used to seeing.   It sa

Re: [Freesurfer] (no subject)

Jeff, Can you tell me the error it is saying about MINC? Also, do you have a prior installation of the MINC tools? I am guessing you do, and that there is some prior setting of the MINC_BIN_DIR and MINC_LIB_DIR variables that is conflicting with the new installation. The MINC toolkit is inclu

[Freesurfer] (no subject)

Hi, I am trying to install and set-up freesurfer on a SuSE Linux system, I downloaded and installed the Redhat version, I'm not sure if this was the correct version to use, but when I try to fix the perl path with the command given on the wiki, it says that the command is not found, nor is nu_corre

Re: [Freesurfer] (no subject)

just download and install the whole MNI package. Much easier than trying to install various pieces On Thu, 9 Jun 2005, Arvind Gururajan wrote: Hello, I am very new to Freesurfer. Could anybody please tell me which specific MNI tool, I need to install? I tried the following command. .

[Freesurfer] (no subject)

Hello, I am very new to Freesurfer. Could anybody please tell me which specific MNI tool, I need to install? > > I tried the following command. > > ./recon-all -smooth1 ZM > > program versions used > $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp

[Freesurfer] (no subject)

Hi Bruce: Thanks! I tried on a previous .tri file, and got the same answer. But when I tried a surface file from "save surface" in TkSurfer, it looks weird, and the total vertex number is not 163842, which is the standart in ic7.tri. Furthermore, it seems that we can only generate half brain surfa

Re: [Freesurfer] (no subject)

the decimation code only finds equally spaced points, I don't think it generates a tesselation. One way to downsample is to map onto on of the ico surfaces, then pick the first n points, where n is one of the downsampled icosahedra. Otherwise, I think there are other people who have written sur

[Freesurfer] (no subject)

Hi: I am trying to generate a down sampled tessellation file from inflated pial in TkSurfer. I used write decimation in tool->surface menu, and can find vertices. How can I fill the boundary of those points, and save the vertices and faces, so that I can get a new .tri file? Thanks a lot! ___

Re: [Freesurfer] (no subject)

Have you checked the talairach.xfm file? If not, visually inspect it using file->transforms->load transform for main volume to make sure it's right. You can always manually set it with mri_fill -cc . See the FAQ. cheers, Bruce On Thu, 3 Mar 2005, Harshad Shanbhag wrote: Hi all, My earlier er

[Freesurfer] (no subject)

Hi all, My earlier error was due to perl not properly configured. Thank you all for the help. However, on running recon-all -stage1 -subjid TEST, I am now getting the error message mri_fill: could not find corpus callosum No such file or directory INFO: Modifying dst c_(r,a,s), using the transfor

[Freesurfer] (no subject)

Hi, My name is Ruth Smans and I am new phd student learning how to work with FS (2003). I have come across a problem in coregistration when overlaying my functional images on my flattened anatomical, (both converted from SPM). My functional images include only 40 slices from the posterior par

Re: [Freesurfer] (no subject)

Hi, nu_correct is N3 package from MNI. We use two tools from MNI: mni_autoreg and N3. Unfortunately in order to use them, you must have the following list of MNI tools installed. 1. netcdf 2. mni_perllib 3. GetOpt-Tabular Perlmodule 4. Text::Format Perl module (get this from CPAN) 5. minc 6

Re: [Freesurfer] (no subject)

Hi Nam, I'm not sure what to tell you. nu_correct is their script for running John Sled's N3 intensity nonuniformity correction. We have it in our mni_tools directory locally, you must be able to get it from them. cheers, Bruce On Tue, 19 Oct 2004, Joongnam Yang wrote: Hi Bruce, I've checked t

Re: [Freesurfer] (no subject)

Hi Bruce, I've checked the system and found the MNI package is installed. (Someone installed it a while ago) When I did "locate nu_correct" for the error message, there was nothing on "nu_correct". There was a huge directory that includes MNI stuff. So, it is installed but there is NO such thing

Re: [Freesurfer] (no subject)

it looks like you don't have the MNI software installed (nu_correct comes from there) Bruce On Tue, 19 Oct 2004, Joongnam Yang wrote: Hi, I used the following command recon-all -stage1 -subjid blobby and I got the following error message (Please let me know what is wrong with Freesurfer). ---

[Freesurfer] (no subject)

Hi, I used the following command recon-all -stage1 -subjid blobby and I got the following error message (Please let me know what is wrong with Freesurfer). -- copy of the exact error messages --- program versions used $Id: rec

Re: [Freesurfer] (no subject)

Hi Keyma, that usually means that the inflated surface doesn't match the ?h.white/?h.pial surface in terms of # of vertices/faces. Use mris_euler_number to see what they are. The euler # should be 2 for all the surfaces after topology correction. cheers, Bruce On Thu, 8 Jul 2004, Chekema N

[Freesurfer] (no subject)

I am trying to load the thickness overlay on the inflated brain but when I select the h.thickness surface it doesn't overlay anything. The inflated brain just refreshes but no overlay appear. Is there another way to get the overlay loaded? -Keyma ___ Fr

[Freesurfer] (no subject)

I've tried to run "csurf" on both the Ichiban and Bonaire public computers but it will not work, moving the cursor to the next line after I press enter but providing no further response. On the other hand, tkmedit and tksurfer do seem to work. Only recently (two weeks or so) the program had worked

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