[Freesurfer] incomplete forceps

Dear Freesurfer experts, we have a problem with the forceps. After the first trac-all we had a forcpes minor with a really unusually structure so we tried to fix it with an rerun of the trac-all. The result was a forceps minor with a third thigh in the sagittal axis. We did a second rerun and

Re: [Freesurfer] Probably activation due to vessels

Thanks for your help. It works fine if one uses preproc-sess -per-run -fwhm 5 -fsd bold -s sess01 ... . On Fri, 19 Oct 2012 12:49:00 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to run preproc like: preproc-sess -per-session -fwhm 5 -fsd bold -s sess01 In this

Re: [Freesurfer] Probably activation due to vessels

Sorry, I have to cancel my last contribution. Another Problem crossed my way. If I have more than one run, only the first one is preprocessed if i use -per-session. What can I do about it? If I use -per-run all runs are preprocessed, but selxavg3-sess tells me that it can not determine the file

Re: [Freesurfer] Loading V5.2 on Virtualbox

Hello Will, Clicking the Terminal icon on the desktop will load Freesurfer. From that point on its just a matter of typing the appropriate commands. -Zeke On 05/04/2013 09:27 AM, will brown wrote: I am endeavouring to install FreeSurfer on a windows 8 PC. Virtualbox is installed along with

[Freesurfer] Gradient unwarp software / Siemens Verio scanner

Hi, I'm currently exploring gradient unwarping of data on a Siemens Trio scanner (sonata coils) and a Siemens Verio scanner. I have got lists with coil coefficients for both scanners. According to the FS mail archives, you provide a binary for gradient unwarping, but not any scanner tables (due

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

Gonzalo, Freeview will have a few small usability features to make it behave more like tkmedit and tksurfer, but that update doesnt affect recon-all. Nick Hi Nick: Ok... Tomorrow Sunday I will download and begin to test it... And which other new features has version 5.3.0 over 5.2.0

Re: [Freesurfer] The Asymmetry of surface area or thickness

Follow the steps here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 05/06/2013 01:41 AM, xiangbo_2010 wrote: Dear experts I want to analysis the asymmetry of surface area or thickness, what I do next? thanks! Bo Xiang

Re: [Freesurfer] Probably activation due to vessels

If you use -per-session, all of them should be processed. Why do you think they are not? Also, just saying something is not working is not very informative. Send command lines and terminal output of the error. thanks! doug On 05/06/2013 05:46 AM, Jörg Pfannmöller wrote: Sorry, I have to

Re: [Freesurfer] question about glm setup

Hello Dr. Greve, Thank you for your reply. I have set up the qdec. I have gender as the discrete factor and age and clinical score as continuous factors. In order to look at the relationship between clinical score and whole brain cortical thickness while accounting for age and gender

[Freesurfer] R: Re: version 5.3 coming out soon

Hi Bruce, thank for new 5.3. I'm finishing tracula analyis with 5.2 (I only have a subject that give me some problem). Do you advice me to cancel my analysis and re-run it by new version 5.3? Is the results obtained with version 5.2 reliable? Thank you very much, Stefano Messaggio

[Freesurfer] Open Brain Mapping at the 1st HBM Hackathon

Sent on behalf of Thomas Grabowski, OHBM 2013, LOC Chair: Open Brain Mapping at the 1st HBM Hackathon: Open Brain Mapping in the Cloud ** OHBM 2013 is only six weeks away, bringing the brain mapping community to Seattle, a city at the forefront of open neuroscience and information technology.

Re: [Freesurfer] Pial surface errors

Hi Valeria what version are you running? It's hard to tell from a single slice, but what is the white-matter appearing stuff that is outside the white matter surface? I think that is what's messing stuff up. If you want to upload the data subject one of us will take a look (that is, upload the

[Freesurfer] DTI metrics along the whole tract?

Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt

[Freesurfer] BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)

Hi, all. I'm trying to refine my pial surfaces with a T2 (or, in this case, t2*) image and I'm running into an error inside bbregister/fslregister. I'm running the command: recon-all -s gf04 -3T -autorecon3 -T2pial -T2

Re: [Freesurfer] BBregister issue during autorecon3 with T2pial option (5.2.0 with updated beta binaries)

Newer version of linux changed the way cshell behaves which causes bbregister to crash in some instances. Get a new version from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister doug On 5/6/13 8:10 PM, Todd Thompson wrote: Hi, all. I'm trying to refine my pial