[Freesurfer] VBM in SPM and FreeSurfer

Hi, FreeSurfer and VBM experts I'm a newer in the field, and not sure if this question is relevant to the list - any help will be appreciated. I am wondering about the difference between the data of FS and that of VBM in SPM. After searching in Google, I find a topic following, url: https://mail.

Re: [Freesurfer] VBM in SPM and FreeSurfer

Hi Lijie while SPM (and others) call it "density", it's really just a smoothing of the labeled voxels over space. We tools that would allow you to do the same thing with FS segmentations, but haven't ever put them together into a pipeline as the neurobiological interpretation of such a map is v

[Freesurfer] Announcement: The 2011 FSL & FreeSurfer Course

We are pleased to announce the 2011 FSL & FreeSurfer Course, to be held in Montreal, Canada. It will run immediately before the Human Brain Mapping conference, which will be in Quebec City, a short plane/train/road journey from Montreal. The intensive course covers both the theory and practi

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

which version are you using? The seq.info file has not been used in a long time. doug Pablo Polosecki wrote: > Hi all, > > I am trying to define an analysis for a block-based functional scan > using mkanalysis-sess. > When I run it, I get the following output with an error message: > > Setting T

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Hi, I forgot to put the version, my bad. The version is 4.5. Thanks, Pablo On Fri, Feb 18, 2011 at 11:21 AM, Douglas N Greve wrote: > which version are you using? The seq.info file has not been used in a long > time. > doug > > Pablo Polosecki wrote: > >> Hi all, >> >> I am trying to define an

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

What is your command-line? Pablo Polosecki wrote: > Hi, > > I forgot to put the version, my bad. The version is 4.5. > Thanks, > Pablo > > On Fri, Feb 18, 2011 at 11:21 AM, Douglas N Greve > mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > which version are you using? The seq.info

[Freesurfer] very high/low values in the mri_glmfit results

Hi FreeSurfers, I'm running a group-level analysis of the fMRI data (beta-maps of individual subjects normalized onto fsaverage). One example would be like: mri_glmfit --y grouprfx/lh.con_0001.norm.mgh --surf fsaverage lh \ --glmdir grouprfx/lh.con_0001.osgm --osgm I understand that this

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Hi, The command line it's within the attached script, so it might not look as informative whn looked at on its own. However it is: mkanalysis-sess \ -fsd bold \ -funcstem $funcstem \ -analysis $analysis \ -paradigm $paradigm \ -dt blocked \ -sf sf \ -df df \ -forc

Re: [Freesurfer] very high/low values in the mri_glmfit results

Matlab's software probably resolves the precision issues better than ours does. With 250 degrees of freedom, you can get extremely significant values. You can look at the f.mgh file. If you load that and the gamma.mgh into matlab and compute t = sqrt(f).*sign(gamma) you should get the same t tha

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Can you send the actual command without any variables? thanks doug Pablo Polosecki wrote: > Hi, > > The command line it's within the attached script, so it might not look > as informative whn looked at on its own. However it is: > > mkanalysis-sess \ > -fsd bold \ > -funcstem $funcstem \

[Freesurfer] Neuroimaging Data Processing Workshop 23-24 March 2011, Edinburgh, UK

Dear all, I am delighted to invite you to a Neuroimaging Data Processing Workshop which will be held on 23-24th of March 2011 at University of Edinburgh, UK. During the workshop we will cover neuroimaging data analysis and management with reusable, scalable and reproducible processing workflows th

[Freesurfer] glmfit-sim question

Hello FreeSurfers I'm running some permutation tests and this induce me to a question, I'm using mri_glmfit-sim as recommended with the mc-z method, running 1000 permutations and seeding randomly, I have ran this with the same data two different times, and the results are bit different, co

Re: [Freesurfer] glmfit-sim question

What do you mean that they are different? We usually recommend 10,000 iterations. doug Gabriel Go.Es. wrote: > > > > Hello FreeSurfers > > I'm running some permutation tests and this induce me to a question, > > I'm using mri_glmfit-sim as recommended with the mc-z method, running > 1000 perm

Re: [Freesurfer] error in test run

Hello, I got errors below when testing my installation, I need help please. I had to donwload the centos4 version for my 32 bit desktop and there is no version for Fedora 14. [Pom@pom-PC freesurfer]$ recon-all -s bert -autorecon1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurf

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Hi Doug, Sure, here is the command line with all the variables replaced by their actual values. mkanalysis-sess \ -fsd bold \ -funcstem fmcus2 \ -analysis a1u \ -paradigm face_localizer_monkey.para \ -dt blocked \ -sf sf \ -df df \ -force \ -inorm \ -timew

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Please ignore the extra line btween the line starting with -paradigm and the one with -dt. It somehow sneaked in there, but it's not there when I call the command. On Fri, Feb 18, 2011 at 2:32 PM, Pablo Polosecki < ppolose...@mail.rockefeller.edu> wrote: > Hi Doug, > > Sure, here is the command l

[Freesurfer] Modify volume origin in nifti format?

Hi, I'm trying to normalize ADC maps into a template image of my choice using SPM8. In this purpose, I converted my DICOM files into nifti files using "mri_convert" and now I would like to modify the origin of the volumes. Is that possible? Thanks, Vincent

Re: [Freesurfer] Recon-all Error: _FindFacePath

what does "old topo fixer" mean? thanks ilana On 15 February 2011 09:55, Bruce Fischl wrote: > Hi Nasim, > > can you tar and gzip the entire subject dir and send it to us? I'll try > to track it down. In the mean time if you just rerun with the old topo > fixer it should work. Nick can post the

Re: [Freesurfer] Recon-all Error: _FindFacePath

it means mris_fix_topology, which was the original topology correction algorithm. Florent Segonne wrote a newer (better) one based on non-separating loops but it seems to have a rare and hard-to-track-down bug in it where it can't find a path that should exist cheers Bruce On Fri, 18 Feb 2011,

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hi Ilana, Nick kindly helped me addressing this issue in one of my subjects. In my case the brainmask had some cortex stripped from the top and the failure had stemmed from there. I would suggest that you also check your brainmask.mgz and see if the skull stripping was successful there. If that

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

When I run this in version 4, it runs fine. Can you send me the full terminal output? Pablo Polosecki wrote: > Hi Doug, > > Sure, here is the command line with all the variables replaced by > their actual values. > > mkanalysis-sess \ > -fsd bold \ > -funcstem fmcus2 \ > -analysis a1

Re: [Freesurfer] Modify volume origin in nifti format?

You can try setting the location of the center with the -ic (same as --in_center) option. doug Vincent Roch wrote: > Hi, > > I'm trying to normalize ADC maps into a template image of my choice > using SPM8. In this purpose, I converted my DICOM files into nifti files > using "mri_convert" and

Re: [Freesurfer] mkanalysis-sess says ERROR: bad format for seq.info file

Hi, The full terminal output is pretty much what I sent previously: Processing analysis: a1u INFO: analysis a1u exists, but overwrite forced by user. Setting TER to .1000 /home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy ERROR: bad format for seq.info file, /home/pp

[Freesurfer] installation problem in ubuntu

Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below

Re: [Freesurfer] installation problem in ubuntu

Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and