[Freesurfer] Freesurfer-Error message

Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp

[Freesurfer] freesurfer tutorial data

Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the "bruckner_data_tutorial_subjs.tar.gz" I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any a

Re: [Freesurfer] creating a skull

Also, is there a way to create a skull from a CT scan? From: Borzello, Mia Sent: Friday, August 31, 2012 12:17 PM To: freesurfer Subject: RE: [Freesurfer] creating a skull I've been referred to the following link on the freesurfer site to handle this, but

Re: [Freesurfer] creating a skull

Hi Mia you would need to mess around with watershed and such, it might work or might not. cheers Bruce On Mon, 3 Sep 2012, Borzello, Mia wrote: > Also, is there a way to create a skull from a CT scan? > > From: Borzello, Mia > Sent: Friday, August 31,

Re: [Freesurfer] freesurfer tutorial data

Hi Dix, not sure what's going on. Have you tried multiple times? Bruce On Mon, 3 Sep 2012, dix.meibe...@ukb.uni-bonn.de wrote: Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the "bruckner_data_tutorial

Re: [Freesurfer] Freesurfer-Error message

Hi Chikku you need to give it the path to an image file (any one will do) and it will figure out the other slices that makeup the same series. What is the resolution of your data? 50 slices isn't usually enough to cover the brain at high enough resolution to get good thickness results. cheer

Re: [Freesurfer] question about painting SPM results onto Freesurfer

Hi Karry painting is done by mri_vol2surf and you can use it to specify how you want the sampling to be done. We typically sample the volume halfway our from the gray/white boundary, or sometimes a bit lower to avoid vascular artifacts at the pial surface. That said, it is quite flexible and y

Re: [Freesurfer] question about painting SPM results onto Freesurfer

Hi Bruce, Thanks for your detailed explaination! I have one more question about it! Is it possible to get cluster size for being painted SPM results on freesure surface (like getting the cluster size of cortical thickness in QDEC )? Is there any command getting it? Any idea will be appreciated!

Re: [Freesurfer] question about painting SPM results onto Freesurfer

you mean the size of the cluster on the surface? Yes, you can do that, but you'll need to wait for Doug's return for the details cheers Bruce On Mon, 3 Sep 2012, keepmoon wrote: Hi Bruce,   Thanks for your detailed explaination! I have one more question about it! Is it possible to get cluste

Re: [Freesurfer] FDR Correction of NHP Surface Data

Hi Clark sorry, the end of the summer has been a period when things slip through the cracks. I think what you want is possible without a talairach or aseg, but it will need to wait for Doug to get back. Can you repost at the end of next week? Bruce On Thu, 30 Aug 2012, Clark Fisher wrote:

Re: [Freesurfer] cortical volume and ortical jacobian_whitematter

Hi Knut these are hard questions to answer. Volume is thickness x surface area, so the question is how reliable is surface area and what does a change in it mean? Where does the "jacobian_whitematter" measure come from? cheers Bruce On Thu, 30 Aug 2012, Knut J Bjuland wrote: > Hi, > > I have

Re: [Freesurfer] how i can compute volume of a VOI

Hi Eustratios the label file is a simple text format that contains the number of voxels in the first line or two. Since our voxels are 1mm isotropic that will also correspond to the volume. You could create a volume and use mri_segstats, but this would be much easier. cheers Bruce On Fri,

Re: [Freesurfer] creating a skull

did you try using freeview? For example: freeview -v brain.mgz On Fri, 31 Aug 2012, Borzello, Mia wrote: > Hi, > > I make it an mgz. When trying to load (tried using a load and read command) > to make sure it looks okay, but it's not working. How can I view this mgz > file or ascertain that i

Re: [Freesurfer] creating a skull

Hi Mia what platform are you running on? Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote: > I've been referred to the following link on the freesurfer site to handle > this, but is this still current (i.e. is linux still needed to do this?): > http://mailman.science.ru.nl/pipermail/fieldtrip/20

Re: [Freesurfer] FDR Correction of NHP Surface Data

Hi Bruce, Will do. Thanks again. -Clark On Sep 3, 2012, at 2:33 PM, Bruce Fischl wrote: > Hi Clark > > sorry, the end of the summer has been a period when things slip through the > cracks. I think what you want is possible without a talairach or aseg, but it > will need to wait for Doug to

Re: [Freesurfer] question about painting SPM results onto Freesurfer

Hi Bruce, Thanks for your answer! Yes. I would like to know the size of the cluster after painting on the surface. Expecting Doug's reply! Thanks in advance! Karry On Mon, Sep 3, 2012 at 7:51 PM, Bruce Fischl wrote: > you mean the size of the cluster on the surface? Yes, you can do that,