[Freesurfer] wrong values for volume

Dear Freesurfer Users I did the whole group analysis process, but unfortunately the measure for volume didn't work correctly. I think the problem is, that i couldn't create the "source-files" (the ?h.volume files in the /subject/surf folders) like for the other measures. I did that with a command

Re: [Freesurfer] Directed contrast in FS group analysis

Yes, the regressor order is in the order of the classes and varialbles as listed in the FSGD. For DODS (the default), there will be a regressor for each variable for each class. If you have any doubts, you can look at the Xg.dat file created by mri_glmfit. This is the design matrix which should m

[Freesurfer] Doubt in thickness computation

Hello all In Neuroimage Han. et all ( 2006) it is said about Freesurfer automatic thickness computation : For each point on the gray/white surface, the shortest distance to the pial surface is first computed. Next, for each point on the pial surface, the shortest distance to the gray/white surf

[Freesurfer] dev environment

Hi, Since the change to the new version of Freesurfer, I have had some problems with some of our lab's older scripts that make use of the Freesurfer matlab toolbox. I haven't delved deep enough into the specifics to ask a question about that (and I don't think the matlab toolbox is supported

Re: [Freesurfer] mri_convert - segmentation fault (again)

I think I fixed it last night, can you try again? doug On Fri, 7 Sep 2007, Jenn Segawa wrote: Hi, Sorry if this is redundant, I think I'm having the same segmentation problem as others last week, with the mri_convert command I've previously used (with Unix) with no problem. I've tried sete

Re: [Freesurfer] Doubt in thickness computation

Hi Jorge, I'll take a stab at this since it sounds like many of the FS developers are out of town currently, but I'm just an FS user, so hopefully an FS developer can confirm whether my response is accurate. Each vertex on the pial surface has a one-to-one correspondence with another vertex on th

Re: [Freesurfer] mri_convert - segmentation fault (again)

Hi Doug, I just ran it again, and it gave me the same error. Do I perhaps have separate issue? Thanks, Jenn On 9/7/07, Doug Greve <[EMAIL PROTECTED]> wrote: > > > I think I fixed it last night, can you try again? > > doug > > > On Fri, 7 Sep 2007, Jenn Segawa wrote: > > > Hi, > > > > Sorry if t

[Freesurfer] Directed contrast in FS group analysis

Dear Freesurfer users In order to be absolutely sure about the direction of a contrast I have the following question: gamma = 1*beta1 + -1*beta2 + 0*beta3 + Does beta1 always correspond to the class that is entered most superior in the fsgd file and beta2 to the class that is entered as the

Re: [Freesurfer] Switch hemispheres

I can do that, but that only chages their names. I still have the right hemisphere where the left should be. The only real difference is that now the rigth is called left and the left is called right. But the orientation of the image is still the same 2007/9/6, Pedro Paulo Oliveira Jr <[EMAIL P

[Freesurfer] Convert values in label

Hi again, Is there any way to have access to the numerical values of cortical thickness in an ROI? Thanks, Ines ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_convert - segmentation fault (again)

Hi, Sorry if this is redundant, I think I'm having the same segmentation problem as others last week, with the mri_convert command I've previously used (with Unix) with no problem. I've tried setenv trick that was previously suggested, but it didn't make any difference. Has anyone had any luck w

RE: [Freesurfer] Switch hemispheres

I think think that will quite work. You can use mri_convert to left/right swap all the volumes then rerun the surface generation I guess (autorecon2-wm and autorecon3 I think would do it) On Thu, 6 Sep 2007, Pedro Paulo Oliveira Jr wrote: I think you can: rename the lh.* files to xx.* renam

Re: [Freesurfer] about inflate the surface

is this a macaque brain? What resolution is it? The inflation is dependent on the vertex spacing, and I suspect your data is higher res. Try inflating it more: mris_inflate -n 15 lh.smoothwm lh.inflated or try a bigger n (the default is 10) cheers, Bruce On Thu, 6 Sep 2007, Ning Liu wrote:

Re: [Freesurfer] Doubt in thickness computation

"that location" means for that vertex index. On Fri, 7 Sep 2007, jorge luis wrote: Hello all In Neuroimage Han. et all ( 2006) it is said about Freesurfer automatic thickness computation : For each point on the gray/white surface, the shortest distance to the pial surface is first computed.

Re: [Freesurfer] Convert values in label

I think if you load the label and load the thickness as an overlay, then save the label it will put the thickness values into the last column of the label file. cheers, Bruce On Fri, 7 Sep 2007, Inês Souta wrote: Hi again, Is there any way to have access to the numerical values of cortical t

Re: [Freesurfer] variability

Hi Leila, Xiao Han's NeuroImage paper discusses thickness variability, and we've looked at parcellation variability in-house, but I don't think we've published on it. The V4 parcellation is should be a bit more accurate at the midline, but not substantially different. cheers, Bruce On Wed, 5

Re: [Freesurfer] Volume calculation

Hi Derin, for each face, it's the product of the average thickness at that face (over the 3 vertices attached to it), times the average white and pial surface areas of that face. cheers, Bruce On Wed, 5 Sep 2007, Derin Cobia wrote: How is the volume of each cortical structure (and hemisph