Re: [Freesurfer] Maximum number of subjects in make_average_subject?

2007-02-21 Thread martijn van den heuvel
Hi bruce, Thanks for looking into my 'maximumnumber?' problem. Good to hear that you have run in on 300+, at least I know it should be possible and there is no fixed maximum number. Hope to hear from you, thanks, Martijn On 2/21/07, Bruce Fischl <[EMAIL PROTECTED]> wrote: Hi Martijn, it

Re: [Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

2007-02-21 Thread Bruce Fischl
I see. I'll defer to Doug on this. On Wed, 21 Feb 2007, Martin Kavec wrote: Hi Bruce, On Wednesday 21 February 2007 20:25, Bruce Fischl wrote: Hi Martin, what is IOD? We use multiframe images (multiecho) all the time using: IOD stands for Information Object Definition, but is it not that i

Re: [Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

2007-02-21 Thread Martin Kavec
Hi Bruce, On Wednesday 21 February 2007 20:25, Bruce Fischl wrote: > Hi Martin, > > what is IOD? We use multiframe images (multiecho) all the time using: IOD stands for Information Object Definition, but is it not that important. What is important is that my 3D volume is not stored in a director

Re: [Freesurfer] strange overlay of averages

2007-02-21 Thread Bruce Fischl
what space did you average the functional data in? On Wed, 21 Feb 2007, Joongnam Yang wrote: Hi all, I have a functional average (using FSL group analysis) and an anatomical average (using Freesurfer make_average_subject) across 6 subjects. (The functional average shows strong activation pat

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-21 Thread Anil Roy
I think my last email didn't get through. Bruce, I've uploaded the 001.mgz. It should arrive in your mailbox. I can upload it again if there was any problem. Thanks, Anil. On 2/20/07, Anil Roy <[EMAIL PROTECTED]> wrote: > > Its uploaded > > On 2/20/07, Bruce Fischl < [EMAIL PROTECTED]> wrote:

Re: [Freesurfer] Re: Files uploaded for you on Martinos Center FileDrop site

2007-02-21 Thread Anil Roy
I think my last email didn't get through. Bruce, I've uploaded the 001.mgz. It should arrive in your mailbox. I can upload it again if there was any problem. Thanks, Anil. On 2/20/07, Anil Roy <[EMAIL PROTECTED]> wrote: Its uploaded On 2/20/07, Bruce Fischl <[EMAIL PROTECTED]> wrote: > > I n

Re: [Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

2007-02-21 Thread Doug Greve
I've never seen this flavor of DICOM before. What kind of scanner do you have? Can you upload them to: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html doug Martin Kavec wrote: Hi, our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image file. When I try to

[Freesurfer] strange overlay of averages

2007-02-21 Thread Joongnam Yang
Hi all, I have a functional average (using FSL group analysis) and an anatomical average (using Freesurfer make_average_subject) across 6 subjects. (The functional average shows strong activation patterns in FSL ouput, report.html) However, when I overlay the averages, the expected functional ac

Re: [Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

2007-02-21 Thread Bruce Fischl
Hi Martin, what is IOD? We use multiframe images (multiecho) all the time using: mri_convert -nth $echono output_echo${echono}.mgz what error do you get? Bruce On Wed, 21 Feb 2007, Martin Kavec wrote: Hi, our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image file. W

[Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

2007-02-21 Thread Martin Kavec
Hi, our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image file. When I try to use this format with FreeSurfer mri_convert fails. I assume it is not designed for this type of images, isn't it? Anybody knows a workaround? Thanks in advance for help (and great software), Ma

Re: [Freesurfer] Maximum number of subjects in make_average_subject?

2007-02-21 Thread Bruce Fischl
Hi Martijn, it looks like we have a memory leak. We'll look into it and get back to you. I'm surprised you don't get past 253 with 16G of ram though. I've run it on 300 or so. Bruce On Wed, 21 Feb 2007, martijn van den heuvel wrote: Dear Freesurfer-list, I'm trying to construct an average

Re: [Freesurfer] Reprocessing the data with new FS release

2007-02-21 Thread Nick Schmansky
Antonio, Prior to downloading a new release, to determine its impact, consult the Release Notes page: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes This page describes the bug fixes and any new features, and will mention any large impact on elements of processing. In general, though, f

Re: [Freesurfer] Reprocessing the data with new FS release

2007-02-21 Thread Jenni Pacheco
Hi Antonio, Your edits will be preserved whenever you run recon-all (any part of it) unless you specifically indicate that they shouldn't by using one of the "-clean..." flags. I would recommend re-running the entire thing "recon-all -all" to be sure that all of your subjects are processed wi

[Freesurfer] Reprocessing the data with new FS release

2007-02-21 Thread Gallo, Antonio (NIH/NINDS) [F]
Hi all, Since we have updated Freesurfer with the last (3.0.5) release, we were wondering at which point we should reprocess (i.e autorecon1, autorecon2, etc) our data in order to retain the edits we have made using the previous version. Thank you, Antonio Antonio Gallo, MD NIB-NIN

[Freesurfer] Maximum number of subjects in make_average_subject?

2007-02-21 Thread martijn van den heuvel
Dear Freesurfer-list, I'm trying to construct an average group surface map using 'make_average_subject'. My group consists of a rather large number of subjects, around 400 subjects. Unfortunately, running 'make_average_subject' gives an error when processing subject 253, saying it has an 'mgh re