Re: [Freesurfer] Matrix is singluar to working precision

That subject only has 5 conditions (#6 is not represented in the par file). The easiest thing to do is to randomly assign one of the other conditions to #6. doug Maximilien Chaumon wrote: > Hi Freesurfers, > > I'm trying to selxavg3 my data. > > My design includes 6 conditions including a 0 re

Re: [Freesurfer] [martinos-tech] surfcluster & simulations

It depends on which program you ran and how you ran it. Frida Polli wrote: > > > hey bruce, nick, doug > > when we use qdec to generate simulations to find CWP, the cluster > sizes that we get are smaller area than if we make a label from the > cluster and use label_area to determine the size

Re: [Freesurfer] freesurfer in a cluster computer

Sharif, what Pedro Paulo suggests is how we use our cluster here at the NMR Center: we simply treat each node as a separate machine, running an instance of recon-all. so with 200 nodes, 200 subjects can be processed. recon-all does not yet support multi-threading, so multi-core machines are not

Re: [Freesurfer] freesurfer in a cluster computer

Depends on your cluster configuration. But if you are using a PBS cluster you can just spawn one recon-all per subject and the queue will take care of them. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telec

Re: [Freesurfer] map .xls or .txt file to fsaverage

We don't have anything that will read xls format into a surface. From matlab you can save it as a curv or mgh file as I describe below. I think you can run these under windows since they are simply matlab files. You'd need to have access to them on your windows machine, but you can do this by copyi

[Freesurfer] freesurfer in a cluster computer

Hi all there, Could you please tell me how I can run freesurfer in a cluster computer so that I can use the full power of the cluster. Thank you very much for your kind attention. Regards, Sharif___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] Tksurfer overlay custom color look up table

Sorry, not something that can be done in tksurfer. doug Julien Dubois wrote: > Hello everyone > > is there a way to display an overlay in tksurfer with a clut other > than the three available from the gui? > > Thanks a lot in advance. > - Julien >

Re: [Freesurfer] SUBJECTS_DIR problem when trying to goregister functional and structural data

When you set up the directory, you should have created a filed called "subjectname" in the CA directory. This should be a simple ascii text file with the name of the FreeSurfer subject (as found in $SUBJECTS_DIR). Is that file there and does it have the right name in it? doug Natalia Zaretskay

Re: [Freesurfer] skull stripped image with the original resolution

is rawavg.mgz the image on the left? if not, and you want the image on the left to be the skull-stripped image, then use that instead of rawavg.mgz. you can use tkregister2 to create a transform aligning your image to a colin27 image, then use mri_vol2vol to reslice the image. nick On Tue, 200

Re: [Freesurfer] surf2surf for annots

Hi Alex, it uses the surface-based spherical registration if you specify --surfreg. cheers, Bruce On Tue, 13 Oct 2009, Alex Fornito wrote: > > Hi all, > I have a custom annot in fsaverage space that I would like to map to the > surface of each of my subjects. I have 2 questions about how mri_su

Re: [Freesurfer] CentOS5.3 and freesurfer

yes, you can use centos 5.3. we use it here at the center. the centos4 distribution of freesurfer will work on centos 5. nick On Tue, 2009-10-13 at 18:11 +0800, tulu wrote: > Dear FS Experts, > > Is it compatible to use CentOS 5.3 for install freesurfer ? both > tksurfer and tkmedit, freeview

[Freesurfer] SUBJECTS_DIR problem when trying to goregister functional and structural data

Hi all, I am doing retinotopy with freesurfer and fsfast on Mac OSX. Made the data directory structure as required. When I try to coregister anatomical and structural data with tkregister-sess -sf sessid -regheader I get the following message:

[Freesurfer] surf2surf for annots

Hi all, I have a custom annot in fsaverage space that I would like to map to the surface of each of my subjects. I have 2 questions about how mri_surf2surf does this: 1 - Does it use the surface-based registration performed in autorecon2, or is it a volume-based registration? 2 - If it is a volume

Re: [Freesurfer] Poor grey and white matter segmentation

hmmm, no idea. Can you send me the recon-all.log file for that subject? On Tue, 13 Oct 2009, Angel Wong wrote: > Hi Bruce > > I have downloaded the latest version (v4.5.0) and tried again. But > unfortunately, I cannot reproduce the results same as yours. The new > generated results are similar t

Re: [Freesurfer] Poor grey and white matter segmentation

Hi Bruce I have downloaded the latest version (v4.5.0) and tried again. But unfortunately, I cannot reproduce the results same as yours. The new generated results are similar to the results generated by the older version. The command I used is recon-all -i -s -sd -all and I viewed the images

[Freesurfer] CentOS5.3 and freesurfer

Dear FS Experts, Is it compatible to use CentOS 5.3 for install freesurfer ? both tksurfer and tkmedit, freeview can run successfully ? Any suggestion is helpful Thanks in advance Jung lung hsu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.