Re: [Freesurfer] Are the average subjects generated by different version of Freesurfer differ greatly?

the average subject is mostly for visualization, so I wouldn't think it would matter that much. cheers, Bruce On Fri, 12 Sep 2008, Zhangyuanchao wrote: Are the average subjects generated by different version of Freesurfer differ greatly? I obtained the cortical thickness,lGI using Freesurfe

[Freesurfer] freesurfer

Hi All, I was looking for methods to create a superior temporal sulcus mask (upper and lower boundary). >From my understanding, Freesurfer does a pretty good job in labeling the sulcus, hence I was wondering if there are possible ways to write the particular ROI as a mask image for each individua

[Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

I've just read Fisch et al 2007 (Cerebral Cortex) where Figure 1 (I think made in tkmedit) shows canonical slices with small green crosses - is there a way to do a similar thing (preferably not by placing the crosses manually) on the inflated brain? Thanks again, Keith ___

Re: [Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

Hi Keith, I guess you could write your cross locations into an annotation file then they would be displayed as small colored patches. I'm not sure which figure you are referring to, or exactly what you're trying to do though. Bruce On Fri, 12 Sep 2008, Keith Duncan wrote: I've just read Fi

Re: [Freesurfer] How to display a large set of peaks on inflated brain?

Hi Keith, this is inevitable when sampling from the volume onto the surface, particularly if the volume maps are blurry. Then a single volume blob will intersect e.g. two banks of a sulcus and show up as two distinct blobs. cheers, Bruce On Thu, 11 Sep 2008, Keith Duncan wrote: Hi FS ex

Re: [Freesurfer] freesurfer

Hi HweeLing, I think the aparc.a2005s has the STS labeled in it, so you should already have what you need in individual space. You could use mri_annot2label, mri_label2vol and mri_vol2vol to transform this into MNI if you need to. cheers, Bruce On Fri, 12 Sep 2008, Hwee Ling Lee wrote:

Re: [Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

Hi Bruce, Basically I have data from 45 subjects, and I would like to show the variability in the location of the individuals peak activation. They are all on the ventral surface, and are in occipitotemporal sulcus and fusiform gyrus - so ideally I'd like to use the inflated brain as it would

Re: [Freesurfer] How to display a large set of peaks on inflated brain? Pt. 2

No problem. What I would do is create a surface-based label file with the peak in each subject, then use mris_spherical_average to generate an average label (this will be in spherical coords). A typical command line would be: set average_subject=fsaverage mris_spherical_average -osurf sphere -

[Freesurfer] MNI152

Hi, I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152 volume. Any ideas on how to do it? Usually I'd mri_label2label and then mri_label2vol, but I don't think there is a surface version of MNI152, is there? Thanks! Cherif ---

[Freesurfer] Methodology Papers.

Dear everyone, Hopefully someone can help me. If I do "recon-all --help" i can see a list of 31 steps for the main cortical thickness pipeline. Does anyone have a list that links each of the 31 steps to the most current methodology paper? I've been reading most of the methodology papers re

Re: [Freesurfer] MNI152

You can use mri_label2vol and spec $FREESURFER_HOME/average/mni152.register.dat as the registration file. Cherif Sahyoun wrote: Hi, I'd like to morph ROIs drawn on the fsaverage surface onto the MNI152 volume. Any ideas on how to do it? Usually I'd mri_label2label and then mri_label2vol, but

Re: [Freesurfer] Methodology Papers.

Hi Matt, the methodologies are described in those papers. Sorry, I don't think there's any one or two paper summary - it's just too much stuff over the years (topology correction, segmentation, surface analysis, morphing, etc). Bruce On Fri, 12 Sep 2008, Matt Clarkson wrote: Dear ever

Re: [Freesurfer] freesurfer

You can also skip the 1st two steps and just convert aparc+aseg.mgz to MNI with mri_vol2vol (make sure to use the --interp nearest flag). Then look for voxels with values 1030 (left STG) or 2030 (right STG). doug Bruce Fischl wrote: Hi HweeLing, I think the aparc.a2005s has the STS labeled

Re: [Freesurfer] ces and percent signal change

It corresponds to the signal change, which is more-or-less A-fixation, but not exactly. The percent signal change is in cespct. doug Reza Rajimehr wrote: Hi, For a stimulus condition 'A' and a fixation condition, does the ces file for the contrast 'A - fix' correspond to the % signal change

[Freesurfer] segmentation fault (core dumped)

Dear Mr or Ms, My computer was installed with Freesurfer v4.0.3,centos4, To make an average surface,I launch "make_average_subject" command, I come across an error : Processing subject 25/52 sh45 ... Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg Segmentation fault (core dumped)

Re: [Freesurfer] Methodology Papers.

Hi Bruce, for sure, I didnt expect it to all be in one place! For example, what I believe are the original papers (Neuroimage 9 1999, and the 1993 Cognitive Neuroscience paper), describe the first method, then we have all the other subsequent papers. So for example, does the current methodolo

Re: [Freesurfer] Methodology Papers.

Hi Matt, the Segonne paper is the current skull stripping (the hybrid one), although it's evolved somewhat since then (unpublished). The segmentation is both those papers (the first one is the segmentation methodology, the 2nd is the addition of a nonlinear warp), plus the more recent one with

[Freesurfer] segmentation fault (core dumped), when making average subject

Dear Mr or Ms, My computer was installed with Freesurfer v4.0.3,centos4, To make an average surface,I launch "make_average_subject" command, I come across an error : Processing subject 25/52 sh45 ... Reading /media/sda5/yczhang/sh45/surf/lh.sphere.reg Segmentation fault (core dumped)

[Freesurfer] mris_volmask error

Hi, I ran recon-all, and it exited with an error at this command: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance subj10 The error message reads: mris_volmask.bin: error while loading shared librar

Re: [Freesurfer] tksurfer woes

Hi all, FYI, this same problem has been bugging me for several months. Most ATI chipsets have a nice driver installer bundle that, once installed, will let you run tksurfer without a problem. However, this particular chipset, the ES1000, which is the chipset on Dell PowerEdge servers, is

Re: [Freesurfer] mris_volmask error

Dahlia, Try again now, I just fixed it. Nick On Fri, 2008-09-12 at 12:21 -0700, Dahlia Sharon wrote: > Hi, > > > > I ran recon-all, and it exited with an error at this command: > > > > mris_volmask --label_left_white 2 --label_left_ribbon 3 -- > label_right_white 41 --label_right_ribbon

[Freesurfer] (no subject)

Hello, Group, I have a hard time to register the functional ROIs to the exact location (x,y,z) on thickness map. I can't find articles that register the fsl result onto freesurfer thickness map and then do the ROI analysis. Could someone kindly list some references for me? I appreciate if anyo