[Freesurfer] problem about file format

Hi All, Sorry to take up your time. My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: *tkregister2 --mgz --s linziyi --fstal --surf orig* The terminal then reports: *ERROR:

Re: [Freesurfer] hippocampal subfield segmentation

Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: Hi guys! I

[Freesurfer] processing flow

Hi everyone, I'm sorry, this is a probably very basic question, but I'm a little bit confused about the recon-all correct flowchart. I mean, the first step is recon-all -s subjid -all (comprising autorecon1, autorecon2 and autorecon3), correct? After this step if I want to add control points

Re: [Freesurfer] processing flow

hi claudia, do your all of your (cp, pial, wm) editing and once complete then you can combine all three steps you have below into one step: recon-all –s subject -autorecon2 –autorecon3 -robert From: Claudia Dacquino claudia.dacqu...@gmail.commailto:claudia.dacqu...@gmail.com Date:

Re: [Freesurfer] processing flow

Thanks. So the very first step I'll run recon-all -all, then I'll do all my corrections and rerun just recon-all -autorecon2-cp -autorecon3 ... Is that right? Cheers Claudia 2013/6/5 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia recon-all -autorecon2-cp -autorecon3 ... will run

Re: [Freesurfer] processing flow

yes On Wed, 5 Jun 2013, Claudia Dacquino wrote: Thanks.So the very first step I'll run recon-all -all, then I'll do all my corrections and rerun just recon-all -autorecon2-cp -autorecon3 ... Is that right? Cheers Claudia 2013/6/5 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia

Re: [Freesurfer] Tracula

Is the setenv SUBJECTS_DIR line really commented out? You must set SUBJECTS_DIR, see the example configuration file on the wiki and under $FREESURFER_HOME/bin/dmrirc.example. On Wed, 5 Jun 2013, std...@virgilio.it wrote: Hi list and Anastasia, I'm performing a set of data with tracula

Re: [Freesurfer] recon-all error

Dear Doug, I have re-sent the whole subject via the file drop, I think everything was fine this time. Please let me know when you have an ide of what's going on with it. Cheers, Rafa 2013/6/4 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Rafa this doesn't look like the whole subject dir, just

[Freesurfer] Monte Carlo simulation

Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p0.05. Is possible to obstain form each significant cluster the real value of p? Thanks, Stefano ___ Freesurfer mailing

Re: [Freesurfer] hippocampal subfield segmentation

Title Automated segmentation of hippocampal subfields from ultra‐high resolution in vivo MRI Authors Koen Van Leemput, Akram Bakkour, Thomas Benner, Graham Wiggins, Lawrence L Wald, Jean Augustinack, Bradford C Dickerson, Polina Golland, Bruce Fischl Year 2009 Hippocampus Volume 19 Issue 6 Pages

Re: [Freesurfer] Monte Carlo simulation

what do you mean by the real value of p? On 6/5/13 10:17 AM, std...@virgilio.it wrote: Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p0.05. Is possible to obstain form each significant cluster the real value of

Re: [Freesurfer] Monte Carlo simulation

On 06/05/2013 10:17 AM, std...@virgilio.it wrote: Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p0.05. Is possible to obstain form each significant cluster the real value of p? Thanks, Stefano

[Freesurfer] R: Re: Monte Carlo simulation

I'd like to know the effective p correlated with colour bar in a significant cluster. Thank you very much, Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 5-giu-2013 16.31 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Monte Carlo simulation

Re: [Freesurfer] R: Re: Monte Carlo simulation

Look in the summary file as JM suggested doug On 06/05/2013 10:56 AM, std...@virgilio.it wrote: I'd like to know the effective p correlated with colour bar in a significant cluster. Thank you very much, Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data:

Re: [Freesurfer] SPM ROI to Cortical Thickness

what space is your VBM map in? doug On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: Hi Doug, Thank you for your response! I am still a bit confused about the vol2surf command. I have a volumetric mask with voxels of interest based on a VBM analysis in SPM. I would like to extract the

Re: [Freesurfer] SPM ROI to Cortical Thickness

MNI space. On Jun 5, 2013, at 11:14 AM, Douglas N Greve wrote: what space is your VBM map in? doug On 06/05/2013 11:06 AM, Ozranov-Palchik, Ola wrote: Hi Doug, Thank you for your response! I am still a bit confused about the vol2surf command. I have a volumetric mask with voxels of interest

Re: [Freesurfer] Still confused by group analysis..

C) When running mri_surf2surf, I get an error saying that file /surf/lh.white cannot be opened. The 'average' folder produced after I ran make_average_subject does not contain a /surf/lh.white file, only a /surf/lh.white_avg file! I didn’t find a log

Re: [Freesurfer] mri_glmfit-sim error

Doug -- Sorry for asking your help again as I can't seem to resolve this on my own. I looked up the mri_glmfit-sim --help and added the path of csd file in the argument, but it still fails to find .csd file. Can you let me know once again what I did wrong? (see the command line below).

Re: [Freesurfer] SPM ROI to Cortical Thickness

Hi Doug, Thanks for the response. I'm still a bit confused. Let's just say that I have a vertex index that I determined on the surface of my FS average surface (created by 'make_average_subject'). Now I simply want to find the corresponding vertex index on all the source subjects. How can I

Re: [Freesurfer] SPM ROI to Cortical Thickness

Create a label with this vertex in it and use mri_label2label. See subject/label/lh.cortex.label for any subject as an example. doug On 06/05/2013 03:43 PM, Ozranov-Palchik, Ola wrote: Hi Doug, Thanks for the response. I'm still a bit confused. Let's just say that I have a vertex index

Re: [Freesurfer] Parameterization Optseq

Hi Laura, what is your command line? doug On 06/04/2013 09:02 AM, Laura Dekkers wrote: Dear Dr Greve, Together with Dr Hilde Huizenga I am implementing an fMRI study in which we would like to optimize the design by using Optseq2. We have a few questions. Could you please help us out?

Re: [Freesurfer] Surface area measurement method

Hi Andreas, it is not the same method but somewhat related. The method assures that total area (or volume) is preserved when mapping between subjects. How much detail do you need? doug On 06/04/2013 05:21 AM, Andreas Berger wrote: Hello FreeSurfers, after reading this [1] paper about

Re: [Freesurfer] first level glm analysis on surface space

Hi Subha, there are tools to do this in FS. You can use mri_vol2surf to map your time courses to the surface and save the output as a gifti (eg, mri_vol2surf --mov f.nii.gz --reg register.dof6.dat --hemi lh --o junk.gii --projfrac 0.5) Or you can use the FS functional analysis stream (FSFAST).

[Freesurfer] dimensions of sig.nii.gz

Hi, I am examining the difference in significance between different scan parameters in a retinotopy experiment and analysis. I have loaded the sig.nii.gz file in matlab using MRIread, and I am confused by the dimensions of the volume. I understand that this is a surface based file, but the

Re: [Freesurfer] dimensions of sig.nii.gz

Those are the sig maps for the real and imaginary components. If you want one sig that combines both, use the fsig (which is an F-test of the real and imag). dogu On 06/05/2013 05:46 PM, dgw wrote: Hi, I am examining the difference in significance between different scan parameters in a

[Freesurfer] R: Re: Tracula

Hi Anastasia, yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no.Do you note some line that might be wrong additionally to setenv SUBJECTS_DIR line. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data:

Re: [Freesurfer] R: Re: Tracula

What do you get when you run echo $SUBJECTS_DIR? On Thu, 6 Jun 2013, std...@virgilio.it wrote: Hi Anastasia, yes, I have check the SUBJECTS_DIR. I do not understand why all previous configuration file start normally and this no. Do you note some line that might be wrong additionally to

[Freesurfer] R: Re: R: Re: Tracula

/Applications/freesurfer/subjects/subject_prova Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: Tracula What do you get when you run echo $SUBJECTS_DIR? On Thu, 6 Jun 2013,

[Freesurfer] R: Re: R: Re: Tracula

I obtain /Applications/freesurfer/subjects/subject_prova my DWI file is in Diff01, Diff02 ... that are in subject_prova folder. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 6-giu-2013 0.42 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re:

[Freesurfer] converting tkmedit images

Hi Experts! I am trying to montage snapshots from tkmedit. the output of my tcl scripts are tiff. to save ink i am trying to change the background to white before concatenating them into larger images. the following works fine with tksurfer but does NOT work with tkmedit generated tiffs

Re: [Freesurfer] converting tkmedit images

Hi Polly I don't know why convert wouldn't work properly with tkmedit. I guess you could try freeview cheers Bruce On Wed, 5 Jun 2013, Polly Dhond wrote: Hi Experts! I am trying to montage snapshots from tkmedit. the output of my tcl scripts are tiff. to save ink i am trying to change