[Freesurfer] convert volume-based mni152 space into fsaverage surface space(MNI305)

2014-04-21 Thread charujing123
Hi FS experts and users, I created a mask volume, whose space is in MNI152 space. And I want to convert this volume into surface-based in fsaverage. How can I realize this? Thanks All the best. Rujing Zha 2014-04-22 charujing123___ Freesurfer mailing

Re: [Freesurfer] resetting wm-mean [CA Normalize]

2014-04-21 Thread Bruce Fischl
Hi Mark have you looked at the atlas? You can view it directly with freeview to see what the actual means are. What command line did you use to build it? Bruce On Mon, 21 Apr 2014, Mark Plantz wrote: Hi freesurfers,   I am running into an error where the white matter and gray matter means of

[Freesurfer] resetting wm-mean [CA Normalize]

2014-04-21 Thread Mark Plantz
Hi freesurfers, I am running into an error where the white matter and gray matter means of my atlas are automatically setting to 0 during the #@# CA Normalize pathway. I copied a code segment below to help explain better. Has anyone else run into this problem? Is there a way to manually change t

[Freesurfer] FS QA Tools: Output, html and .gif Files

2014-04-21 Thread Jessica Bernard
Hi All, I've been running the Freesurfer QA Tools on some new data, and have been having some difficulties with the outputs. I am running this using the -snaps-detailed flag. In the past, we have had .html links, but also detailed .gif files for each person. We've consistently had trouble with the

Re: [Freesurfer] NHP surface reconstruction in FS5.3

2014-04-21 Thread Bruce Fischl
Hi Stephen no, sorry. There are others on the list that have extensive experience in using FS for NHP. Hopefully one of them can answer? Bruce On Mon, 21 Apr 2014, S.V.Shepherd [work] wrote: Hi, Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd sti

Re: [Freesurfer] An overwrite issue with selxavg3-sess

2014-04-21 Thread Douglas Greve
I just looked at the code, and I don't think -c will work. Sorry, I don't think there is an easy way around it. You might be able to make the files read-only, but that might cause selxavg3-sess to crash doug On 4/20/14 4:50 PM, Sebastian Moeller wrote: > Hi Reza, > > > On Apr 20, 2014, at 14

Re: [Freesurfer] NHP surface reconstruction in FS5.3

2014-04-21 Thread S.V.Shepherd [work]
Hi, Did you have a chance to take a look at this? The basics shouldn't be NHP-specific, so I'd still value your input even though I know you work only with humans. stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620 On