[Freesurfer] Brain segmentation (gray, white, csf) using freesurfer

Hi folks, I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and

Re: [Freesurfer] CT Method Comparison

Hi Doug, many thanks for your answer, I try to detail it more: 1.- bbregister is registering two Colin27 brains. First one is a 2mm found in spm/canonical/single_subject_T1.nii, and second one is the FS_spm_Canonical found in SurfRend distribution. It was in .COR format and I run recon-all to

[Freesurfer] Pooled Structure

Hi, I would like to find out how to pool parcellation statistics (i.e. ?.aparc.stats table entries) from several areas into a bigger one. For example: how to get the pooled statistics for the area parietal which would be made up of superiorparietal and inferiorparietal cortical structures?

[Freesurfer] intracranial volume and dicom

Hi, I have calculated relative volume by dividing each volume by the intracranial volume and multiply it with 100. When I add the relative volume of total gray matter, cortical white matter, lateral ventricle, 3rd centricle, 4th ventricle and ventral DC, I get 82-86 %. Can this be caused by

Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer

Hi Fabian What are you trying to achieve? The easiest thing to do is to run recon-all with the -all flag so we generate an aseg, then that can be collapsed into different measures. cheers Bruce On Tue, 25 Sep 2012, Fabian Schrumpf wrote: Hi folks, I successfully managed to do a brain

Re: [Freesurfer] intracranial volume and dicom

Hi Knut can you check the accuracy of the talairach xform? And what version are you using? Bruce On Tue, 25 Sep 2012, Knut J Bjuland wrote: Hi, I have calculated relative volume by dividing each volume by the intracranial volume and multiply it with 100. When I add the relative volume of

Re: [Freesurfer] bad tissue segmentation, WM/GM boundary

Hi EK make sure that you don't have any control points in any voxels that contain any GM. It looks like maybe you do in the region where you drew a red arrow, although it's impossible to tell for sure from those images. cheers Bruce On Tue, 25 Sep 2012, EK Kim wrote: Dear all expert,

Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer

Hi bruce, At first I want to build a voxel-based FEM-Model based on the surfaces freesurfer creates. For finally creating the models I want to use the MATLAB toolbox iso2mesh. But I would also be interested in building BEM models as a second approach. best regards Fabian -

Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer

try using mris_fill then to create a volume that is the filled interior of any of the surfaces. cheers Bruce On Tue, 25 Sep 2012, Fabian Schrumpf wrote: Hi bruce, At first I want to build a voxel-based FEM-Model based on the surfaces freesurfer creates. For finally creating the models I

Re: [Freesurfer] intracranial volume and dicom

On 09/25/2012 03:09 PM, Bruce Fischl wrote: check the accuracy of the talairach xform Hi I am using Freesurfer version 5.1 with all bug fixes. I have snapshots off all talairach xforms made through qa_tools. I have seen on a few subjects that the talirach transformation went okay. The pial

[Freesurfer] recon-all error while data's FOV256

Dear all, I met a problem while running the recon-all. I have a data with FOV= 300256, so I add the flag -cw256 with reon-all. Then when I check the converted data raw.mgz, I find the brain image is imperfect while some region at the top of head is cut off. My question is, could I choose to cut

[Freesurfer] manual parcellation

Hi experts, I want to make a new, custom-made parcellation, based on the aparc but with much higher resolution. (I've tried mris_divide_parcellation, which yields strip-shaped instead of isometric labels, and mris_make_face_parcellation, which loses spatial specificity. The wiki describes a way

Re: [Freesurfer] Pooled Structure

Hi Zsolt, you can use mri_annotation2label to separate the annotation into labels, then mri_mergelabels to recombine several of them together, then run mris_anatomical_stats on the merged label. doug On 09/25/2012 08:34 AM, Zsolt Cselényi wrote: Hi, I would like to find out how to pool

Re: [Freesurfer] CT Method Comparison

So you have ROIs in Colin27 space and you want to map them into your CT space and compute average CT intensities over them? Are the ROIs volume-based or surface-based? doug On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, many thanks for your answer, I try to detail it more:

Re: [Freesurfer] Brain Volume

Depends on how you define brain volume. If you're using BET, then I assume that you are just counting the number of voxels in the mask? If so, you can use mri_binarize and use the --count countfile to give you a count of the voxels. doug On 09/22/2012 08:22 PM, Ana Arruda wrote: I've just

[Freesurfer] reference of adult normal volume from cortical parcellation

Dear FS experts, Is there any reference about the volume of cortical gyrus after FS cortical parcellation in normal adult people ? I need the reference value of regional volume base on the cortical parcellation made by FS. Please instruct me the reference paper. Thanks help JLH

[Freesurfer] Reconstructed skull malformations

Hi group, I recently reconstructed a high-resolution 3D T1-weighted structural MRI using Freesurfer. The subject had non-metallic extensions that were tied to her head through a series of braids. Looking at the MRI in TkMedit, I can noticeably see pieces of the extensions above her scalp. My

Re: [Freesurfer] CT Method Comparison

I have both. In origin, the ROI-s are 2mm volume based .nii that I convert to FS .mgh with register.dat I obtained with bbregister. -- In the case of label2label method I create the surface version with mri_vol2surf (and the correspondence is perfect), and then use mri_label2label in order to get

[Freesurfer] question about fsaverage vs. my subjects average

Hi I have 3 questions: 1) Does it affect the stats (or does it just affect the display) if I use the fsaverage brain vs. the average of my subjects brains when running mris_preproc or when simulating the cluster statistics using mri_glmfit-sim? 2) I downloaded the simulations for multiple