Re: [Freesurfer] How to get an individual gray matter volume?

the values we provide include partial volume correction, so they won't be the same as just counting the number of voxels in a label. cheers Bruec On Sat, 23 Mar 2013, Ran Xu wrote: > Dear Freesurfer experts, > I used the Index from aseg.txt to get the left thalamus (Index 10), but the > real v

[Freesurfer] How to get an individual gray matter volume?

Dear Freesurfer experts, I used the Index from aseg.txt to get the left thalamus (Index 10), but the real volume I got is different from the size in aseg.txt. Its volume is 5007 in aseg.txt and I programmed a matlab code to find all values equaling to 10 in aparc+aseg.nii. However, the volume I go

Re: [Freesurfer] R: Re: hippo subfield

It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22,

Re: [Freesurfer] Merging PArcellation labels

First save each parcellation that you want as its own separate label by selecting it in tksurfer (simply click on it with your mouse and its boarder will be highlighted in yellow) and then file -> label -> save selected label... Then you can merge these separate labels into one label at the comma

Re: [Freesurfer] Brodmann area thickness, surface area and volume

Ok, that was my guess... I am running against a deadline, any news on automatically computing the correct threshold script? Will I be able to use it in 5.0? Thanks you! Andreia Quoting Bruce Fischl : > yes. Surface area will be the affected much more than thickness (and > volume of cours

Re: [Freesurfer] cortical recontruction error

Hi Claudia hmmm, someone else mentioned that mri_cc hangs for them but we've never seen it. If you upload your dataset I'll see if we can replicate the problem Bruce On Fri, 22 Mar 2013, Claudia Dacquino wrote: Dear Freesurfers, I'm new and I'm starting using Freesurfer. I'm having a proble

Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology

p.s. I don't know why that option doesn't work - I didn't even realize it existed On Sat, 23 Mar 2013, falk.lu...@gmx.net wrote: Hi Bruce,   well, there is an option called -correct_defect within mris_fix_topology, which is meant to correct just one defect at a time. However, after the defect i

Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology

Hi Falk have you tracked down the source of the defect in the wm.mgz? Sometimes very minor edits can correct even major defects. If you are having trouble with this feel free to upload the dataset and one of us will take a look Bruce On Sat, 23 Mar 2013, falk.lu...@gmx.net wrote: Hi Bruce,

[Freesurfer] Merging PArcellation labels

Dear All, Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https:/

[Freesurfer] contrast matrix

Dear Prof Donald McLaren I am sorry to disturb you! I have four discrete variables {factor 1(A,B), factor 2(C,D), factor 3(E,F), and gender(M,F)} and a continuous variable (age), I want to use the GLM to analysis the result of the interaction among factor 1(A,B), factor 2(C,D) and factor 3(E,

[Freesurfer] RE: Two questions regarding mri_fill and mris_fix_topology

Hi Bruce, well, there is an option called -correct_defect within mris_fix_topology, which is meant to correct just one defect at a time. However, after the defect is corrected one is getting a message like: “TERMINATING AFTER CORRECTED DEFECT no such file or directory” I haven’t