Re: [Freesurfer] Creation of the aseg.stats table fails when only running -autorecon1 or -autorecon2

Hi Roberto, I had the same problem, you need to re run the recon process using recon-all -s -cortribbon. Hope it helps Pradeep. On Fri, Feb 6, 2015 at 6:37 PM, Roberto Medeiros de Souza < roberto.medeiros.so...@gmail.com> wrote: > Hi, > I'm knew to FreeSurfer. I am using the stable v5.3 and

Re: [Freesurfer] Converting dicom images to nifti

Please tell how to use dcmunpack. Any help converting dicom to nii. On Jan 27, 2015 9:03 PM, "Douglas Greve" wrote: > > Hi Pradeep, I don't think that we can convert that either. Sorry. > doug > > On 1/27/15 7:18 AM, pradeep mahato wrote: > > Hi expert

[Freesurfer] Converting dicom images to nifti

Hi experts, I am trying to convert dicom images namely 00A0,00A1,00A2 [ No file extension ] etc. These are generated by Philips machine. I used dcm2nii, it does not give correct result. It gives warning : this software will only convert the first slice of this multislice lossless compr

[Freesurfer] Creating a .gca file

Hello experts, I am using rebuild_gca_atlas.csh,v 1.22 2011/03/02 20:16:39. I am trying to create a atlas using previous registered subjects. It does not complete the mri_ca_normalize phase and stops there. It shows pbsubmit: Command not found as error. Please correct me. Also attaching the rebuil

[Freesurfer] 3D image for any region of interest

Hello experts, How to view 3D image of hippocampus or any region of interest. Thanking you Pradeep Kumar Mahato ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

[Freesurfer] Running separate recon-all for each hemisphere

Hello experts, I ran recon-all -all -hemi lh -s, it failed due to some rh.white file missing . Can someone tell me how i can run autorecon1 , autorecon2 and autorecon3 separately for each hemisphere. And also can I run the reconstruction process for left and right hemisphere parallely. How much ti

Re: [Freesurfer] Performance of Broadwell and Haswell processors

N. > > > On Mon, 2014-12-15 at 13:43 +0530, pradeep mahato wrote: > > Hello everyone, > > > > > > Have anyone used Broadwell or Haswell process for Brain MRI image > > processing. > > > > If used can you please mention the system configuration yo

[Freesurfer] Difference results due to difference in brain size

Hello Experts, There is a significant differences between a African, Asian or a Caucasian brain size. How does FreeSurfer recon-all performs for these different types of brain. I am doing brain MRI analysis for Asian brain, will the default brain atlas will be ok? If not how do I load another brai

[Freesurfer] Performance of Broadwell and Haswell processors

Hello everyone, Have anyone used Broadwell or Haswell process for Brain MRI image processing. If used can you please mention the system configuration you are using. How long does it take to run recon-all process for one brain MRI image. Thanking you Pradeep Kumar Mahato

Re: [Freesurfer] Getting voxel values from aseg.mgz

of > the segmentation if that is what you mean. The values for left and right > hippocampus (17 and 53) can be found in > $FREESURFER_HOME/FreeSurferColorLUT.txt > > cheers > Bruce > On > Wed, 10 Dec 2014, pradeep mahato wrote: > > > After the recon-all process I

Re: [Freesurfer] Extracting hippocampus

. Pls help On Thu, Dec 11, 2014 at 8:54 AM, Bruce Fischl wrote: > the ribbon.mgz isn't part of autorecon2 (or autorecon1) I don't think. > What are you trying to run? > > On Thu, 11 Dec 2014, pradeep mahato wrote: > > Hi Bruce, >> >> After running autoreco

[Freesurfer] Getting voxel values from aseg.mgz

After the recon-all process I want to access all the voxels in the left hippocampus ( any subcortical region ) . Please tell me is there any method to extract this voxel values from an segmented image. Thanking you Pradeep Kumar Mahato ___ Freesurfer ma

Re: [Freesurfer] Extracting hippocampus

e advantage of > it. If you want to use more than one core try using -openmmp 4 (to use 4 > cores). > > cheers > Bruce > > > On Mon, 8 Dec 2014, pradeep mahato wrote: > > > Hello, > > > > I need to extract Hippocampus from brain mri image. The recon-all

[Freesurfer] Best possible atlas to extract hippocampus

Hello, As the complete recon process takes huge time for a single image, is it possible to register the MRI image using a simple atlas. If yes, please explain how to do it. My primary goal is to extract hippocampus in a fastest possible way. Pradeep Kumar Mahato __

[Freesurfer] Extracting hippocampus

Hello, I need to extract Hippocampus from brain mri image. The recon-all process takes more than 30 hours to reconstruct from an single image. I am having an dataset of 200 subjects, it is not feasible to run the recon process for all individual brain mri images. Is there any method to possibly g