[Freesurfer] ask about demean in GLM model setup

Dear experts, I am confused by demean during GLM model setup and would like someone here can help me. Thanks! Suppose I have a continuous behavior data and I want to find out which brain region(s) correlated with it. The simple way is to calculate correltation between brain data and behavior d

[Freesurfer] FreeSurfer problem on VirtualBox Linux

Hi there, My operating system is Windows XP SP3 and it has been loaded with VirtualBox 4.2.6 for Windows hosts and we would like to run freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi. But when we attempt to launch FreeSurfer, the terminal seems to hang with the following message:

[Freesurfer] freesurfer question

Hi, I am currently editing some scans (ie adding control points etc), however I keep finding that after the editing often the brains look "worse" than they did before; especially the medial temporal lobe area. I have taken care not to put too many control points in/made sure not to place t

[Freesurfer] longitudinal processing

Hi, just to clarify, When beginning longitudinal analysis, the first step is the same as cross-sectional processing, eg just the "normal" recon-all command, for each subject, and each individual time point? Then the norm.mgz files are used? Thanks -- The University of Edinburgh is a chari

Re: [Freesurfer] QA Tools Snaps Scrambled

Hi Louis- No problem doing command line conversion of an rgb to either jpg or gif in terms of error messages. However, the converted files are scrambled. Might there be a dependency on which ImageMagick relies which still in place, but corrupted? I was under the impression ImageMagick was self-

Re: [Freesurfer] error: could not read 65536 bytes at slice 76 in skull stripping process

Hi Sandra can you check to make sure that you have enough disk space and that that partition isn't full? cheers Bruce On Wed, 9 Jan 2013, Sandra Preissler wrote: > Dear freesurfer users, > > I have an unexpected error using autorecon1. > The error occurred during the skull stripping process of

Re: [Freesurfer] freesurfer question

Hi Catherine what version are you running? We have a fix in 5.2 that helps this problem. It's not quite out yet, but you could download a beta if you want cheers Bruce On Wed, 9 Jan 2013, Catherine Bois wrote: > Hi, > > I am currently editing some scans (ie adding control points etc), > howeve

[Freesurfer] creating picture using 3D slicer

Dear FreeSurfer people, I have a problem creating a picture with my FreeSurfer volumetric data, for which I have been using 3D Slicer. First, let me explain what I am trying to do. We have a list with cortical and subcortical grey matter areas that were significantly different between our patie

Re: [Freesurfer] QA Tools Snaps Scrambled - Clairification

Hi Louis- I was speaking cryptically and/or imprecisely. Of course there are dependencies for IM-- in fact about 8 libraries which are uniquely required by IM. I was thinking about a higher (or lower) level of dependency. This would suggest a more system-level problem, but I'm not having proble

[Freesurfer] longitudinal processing

Sorry, another question about longitudinal processing; just realized that my institution has been using version 5.0, so all the cross sectional processing has been done with this version, is it ok to go ahead and do base and long with version 5.1 once I have managed to get this installed?

[Freesurfer] Problems in testing out newly installed Freesurfer with autorecon-1 option

Hi, I'm currently in the process of verifying that my install of Freesurfer works. I have an Ubuntu 12.04.1 LTS box. I encountered what appeared to be 4 errors after running *recon-all -s bert -autorecon1.* The last line I included here states that the command completed without error, so I'm not

Re: [Freesurfer] unable to download updated mri_segstats

Try now. I've also put a .mac version there. doug On 01/09/2013 01:04 AM, Salil Soman wrote: > Hi, > > The link > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux > from > the release notes for freesurfer 5.1 > (http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseN

Re: [Freesurfer] error: could not read 65536 bytes at slice 76 in skull stripping process

Hi Bruce, Thanks for your fast reply. I checked it again and there is 131 GB disk space free on the device. Best regards Sandra Zitat von Bruce Fischl : > Hi Sandra > > can you check to make sure that you have enough disk space and that > that partition isn't full? > > cheers > Bruce > On Wed

Re: [Freesurfer] freesurfer question

Hi Catherine, If it's the mtl pial surface around the hippocampus then the pial surface is not expected to be accurate in that region. See FAQ question at link below. http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfacesnearthemedialwall.2Chippocampus.2Candamygdalaaren.27

[Freesurfer] Postdoctoral Position at Harvard Medical School/Boston Children's Hospital

The Gaab Labhttp://www.childrenshospital.org/research/gaablab and (www.babymri.org)) at the Laboratories of Cognitive Neuroscience at Children's Hospital Boston (Developmental Medicine Center) invites applications for a NIH funded post-doctoral associate in the area of d

Re: [Freesurfer] longitudinal processing

Hi Catherine, yes, the first step is independent (cross sectional) processing of all time points (normal recon-all). We usually do not recommend to mix versions. But the 5.1 longitudinal stream has been designed in a way that it can take the cross sectional data from 5.0. So it is possible. Just

Re: [Freesurfer] Tracula preprocessing step error

Hi Anastasia, Thanks so much for your help. I was able to correct this problem in my configuration file. I have now run into another error- "bvecs and bvals don't have the same number of entries." I have read other postings about this error and can see that my bvec file is not formatted correctly

Re: [Freesurfer] Problems in testing out newly installed Freesurfer with autorecon-1 option

Susan, there appear to be two problems here. the first and main problem is the one: nu_correct: Command not found. nu_correct is a script which has as its first line: #!/usr/bin/perl -w so can you check that you have perl installed at /usr/bin/perl? better yet, run this script: fixup_mni_pa

Re: [Freesurfer] Tracula preprocessing step error

Hi Allison - Instead of using excel, I would use a unix-based text editor, whichever is available on the system where you are running the analyses. This way you can ensure that unix commands read your text files properly. The 3 values for each diffusion gradient vector are its x, y, z componen

Re: [Freesurfer] FreeSurfer problem on VirtualBox Linux

Carissa, Unfortunately I dont think we can help with this problem, as we currently do not have the resources to support the Windows VM instance. However, an alternative that has worked for others is to do the following: install the FSL Windows VM, described here: http://fsl.fmrib.ox.ac.uk/fsl/fsl

Re: [Freesurfer] problem with preprocessing

Hi Maryam, can you verify that the rh surfaces for that subject are ok? Load rh.white with rh.thickness as an overlay doug On 01/09/2013 05:31 PM, Maryam Vaziri Pashkam wrote: > Hi Doug, > > I am running preprocessing on freesurfer 5.1 using this line: > > preproc-sess -s 121210_xu_Object4catmod

Re: [Freesurfer] longitudinal processing

Hi Catherine, with edits I think it is best to re-use the 5.0 cross data for the longitudinal processing. Also conceptually there is a difference between longitudinal processing and longitudinal statistical analysis. The image processing will reduce variability of your measures and even if you a