[Freesurfer] annot 2 label file conversion

Hi there, I've some troubles with parcellisation schemes. I've used mri_annotation2label to extract labels within annot file. When I read the annot file within matlab (read_annotation.m), I found 869 entries, everything looks good so far. However, when I look at the output directory of labels, I o

[Freesurfer] annot 2 surf

Dear all, There is a way to convert annot file into surface? -- Arnaud Messé, PhD Laboratoire d'imagerie fonctionnelle (LIF) UMRS 678 Inserm/UPMC CHU Pitié-Salpêtrière 91 boulevard de l'Hôpital F-75634 Paris Cedex 13 +33(0)1538284 03 (fax: 48) arnaud.me...@imed.jussieu.fr http://www.imed.jussieu

[Freesurfer] Clusterwise correction for multiple comparisons

Hi, I'm performing a clusterwise correction for multiple comparisons with the command mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \ --sim-sign abs For version v4.5.0 this took about 40 hours to complete. However, for v5.1.0 it is now running for more than 6 days and from the c

[Freesurfer] fsgd file

Dear FreeSurfers, I hope you can help me out with a problem in coding my fsgd file. I want to examine the difference between two cognitive measures on cortical thickness in one group. Furthermore, I will correct for age (centered covariate). So, I have 4 variables: group (class), 2 cognitive scor

Re: [Freesurfer] Fwd: pars triangular and BA44 segmentation bug?

Hi Gabor, I actually don't know, but I think Anastasia has a fix for the thresholding issue. cheers Bruce On Wed, 11 Jul 2012, Gabor Perlaki wrote: Dear Bruce, Did you also identified a strong rightward asymmetry (with pars triangular and BA44) in your data analyzed by freesurfer 5.1? Just

Re: [Freesurfer] annot 2 label file conversion

Hi Arnaud this question may need to wait for Doug to return. If you don't get an answer in a couple of days try reposting, and please include your exact command line and screen output and FS version. cheers Bruce On Wed, 11 Jul 2012, Arnaud Messé wrote: Hi there, I've some troubles with

Re: [Freesurfer] annot 2 surf

Hi Arnaud no, although I'm not even sure what you mean. Annot files contain a label value for every vertex location but no information on where in space it should be or what it's neighbors are. cheers Bruce On Wed, 11 Jul 2012, Arnaud Messé wrote: Dear all, There is a way to convert annot

[Freesurfer] cortical thickness and ICA of resting state fMRI

Hi all, I was wondering if anyone knows about any articles that compare/relate cortical thickness analysis with resting state ICA results? More specifically, I'm looking for articles that study cortical thickness changes in different regions of brain and its possible relation to group clusters

[Freesurfer] ROI functional & anatomical cross

Hello, I'm trying to do an ROI analysis that crosses the group-level functional activation with specific anatomical structures. Currently the clusters found for our group-level functional activation are too large and need to be separated into many structures. Is there a command I could use that w

[Freesurfer] error message for recon-all

Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FRE

Re: [Freesurfer] error message for recon-all

Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i . And one acquisition is usually suffi

Re: [Freesurfer] slanted

Hi Mia, you'll probably have to wait until Doug is back to get an answer. In the meantime, feel free to upload your data so we can take a look cheers Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: > Hi, > > I'm not exactly sure what the problem is, but for some reason, this brain is > kind o

Re: [Freesurfer] slanted

Will he be back today? Upload it in an e-mail? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 12:21 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted Hi Mia, you'll probabl

Re: [Freesurfer] slanted

You can either upload it to our ftp server or use the email file drop system. See link below for details. https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange On Wed, 11 Jul 2012, Borzello, Mia wrote: > Will he be back today? Upload it in an e-mail? > > Thanks, > m > _

Re: [Freesurfer] slanted

Hi Mia, no, there are instructions on the wiki for uploading your data using either ftp or the filedrop. And no, I think it will be another couple of days Bruce On Wed, 11 Jul 2012, Borzello, Mia wrote: > Will he be back today? Upload it in an e-mail? > > Thanks, > m > _

Re: [Freesurfer] slanted

i saw the instructions, but it doesn't give an e-mail specifically for that and ftp surfer.nmr.mgh.harvard.edu doesn't work. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.ha

Re: [Freesurfer] slanted

when you say ftp doesn't work, what do you mean? It works for me: ftp surfer.nmr.mgh.harvard.edu Connected to surfer.nmr.mgh.harvard.edu (132.183.202.158). 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 22

Re: [Freesurfer] slanted

oh i'm trying to do the e-mail file drop though, that's fine too right? i'm just not sure what e-mail to use for the recipient e-mail. From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nm

Re: [Freesurfer] slanted

can i just send it to freesurfer@nmr.mgh.harvard.edu? thanks From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 11, 2012 1:58 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] slanted when you say ftp does

Re: [Freesurfer] slanted

No! Do you have a dropbox account? Copy there and send the link to them. - Pedro Paulo de Magalhães Oliveira Junior Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/i

Re: [Freesurfer] slanted

oh, you can give mine if you want On Wed, 11 Jul 2012, Borzello, Mia wrote: > oh i'm trying to do the e-mail file drop though, that's fine too right? i'm > just not sure what e-mail to use for the recipient e-mail. > > From: Bruce Fischl [fis...@nmr.mgh.h

Re: [Freesurfer] slanted

no! Don't do that - just use mine On Wed, 11 Jul 2012, Borzello, Mia wrote: > can i just send it to freesurfer@nmr.mgh.harvard.edu? > > thanks > > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, July 11, 2012 1:58 PM > To: Borzello, Mia >

[Freesurfer] the make_average_subject without aparc.annot

Hi, Doug I found from the archive that you made a version of make_average_surface without the need for aparc.annot. I tried to download it but the link is not valid anymore. Could you please send me a copy of the file? I need to generate an averaged surface for a group of non-human primates and

Re: [Freesurfer] the make_average_subject without aparc.annot

Doug is away so it may be a couple of days until he answers... On Wed, 11 Jul 2012, Leon wrote: > Hi, Doug > > I found from the archive that you made a version of make_average_surface > without the need for aparc.annot. I tried to download it but the link is not > valid anymore. Could you please

Re: [Freesurfer] error message for recon-all

It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: > Hi Bruce, > > Thank you very much for your fast response. > > Unfortunately though, I still get an error response when typing in "recon-all > -i /Applications/freesurfer/subjects/MRI_04_2012

Re: [Freesurfer] error message for recon-all

sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > > It worked! > > Thank you so so much! > > Best, > Muriel > > On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: > >> Hi Bruce, >> >> Thank you very much for your fast response. >> >> Unfortunately though, I still get

Re: [Freesurfer] Combining linear transformations

Hi Martin, Thanks for the suggestion. I resolved the issue by using the --regheader flag in tkmregister, and --reg as the default output by mri_vol2vol (even though I did supply a reg-final flag). It seems like I mixed up the difference between reg-final and the default registration matrix. would y

Re: [Freesurfer] error message for recon-all

Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folde

Re: [Freesurfer] error message for recon-all

oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > Hei, > > Thanks you very much again for your help! > > Neve

Re: [Freesurfer] Combining linear transformations

Hi Usman, I'm an not very familiar with mri_vol2vol , maybe Doug knows the difference between --reg and --reg-final. I would also expect it to give the same result in your case (as you don't apply any manual --rot or --trans). Anyway, happy you got it working. Best, Martin On Wed, 2012-07-11 at

Re: [Freesurfer] error message for recon-all

On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: > I added the -all at the end and skipped the -i flag, but I still get an error > message: > > Checking for (invalid) multi-frame inputs... > ERROR: input(s) cannot have multiple frames! > /Applications/freesurfer/subjects/MRI_04_2012/GID02/

Re: [Freesurfer] the make_average_subject without aparc.annot

Hi, Bruce Thanks for the information. I can wait for his information after he comes back. Best Leon From: Bruce Fischl To: Leon Cc: "freesurfer@nmr.mgh.harvard.edu" ; Douglas N Greve Sent: Wednesday, July 11, 2012 4:23 PM Subject: Re: [Freesurfer] the m

Re: [Freesurfer] error message for recon-all

Hi Muriel what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > > On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: > >> I added the -all at the end and skipped the -i flag, but I still get an >>

Re: [Freesurfer] error message for recon-all

Hi Bruce, To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there. Best, Muriel On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: > Hi Muriel > > what was the scan that you are trying t

Re: [Freesurfer] error message for recon-all

you can run freeview on the 001.mgz and see what is in it. If it has more than one frame freeview will include a slider that lets you change from one to the other. Or you can email it to me and I'll take a look. On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > Hi Bruce, > > To be quite honest, I

[Freesurfer] Using bet with Freesurfer

Hello, We're working with a pediatric data set and have found that Freesurfer's skullstripping process is inadequate for our purposes. We're interested in using FSL's bet, which we have found to do a better job of skullstripping, in combination with the other steps of Freesurfer. In a previous

Re: [Freesurfer] Using bet with Freesurfer

Hi Heather I guess you could run autorecon1, then run BET if the results are not satisfactors to replace the brainmask.mgz, then run autorecon2 and 3. cheers Bruce On Wed, 11 Jul 2012, Lugar, Heather wrote: Hello,   We?re working with a pediatric data set and have found that Freesurfer?