Re: [Freesurfer] Intensity information of Hippocampal Subfields

27, 2017, at 12:53 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > > There is usually a T2.norm.mgz file in the mri folder. If that is there, > then you should use that rather than the raw data that is not bias field > corrected > > >> On 02/27/201

Re: [Freesurfer] Intensity information of Hippocampal Subfields

mgz --default-ctab --sum sum.dat --i input.mgz > > where seg is the hippo sub field seg and input is the input where you > want to get the intensities from (probably norm.mgz). Note that you need > to use the hipp sub field output that is 1mm (not the high res one) > > >>

Re: [Freesurfer] Intensity information of Hippocampal Subfields

--sum sum.dat --i input.mgz where seg is the hippo sub field seg and input is the input where you want to get the intensities from (probably norm.mgz). Note that you need to use the hipp sub field output that is 1mm (not the high res one) On 02/24/2017 09:53 AM, ali reza mohammadi nejad wrote:

[Freesurfer] Intensity information of Hippocampal Subfields

Dear FreeSurfer Experts, I want to compute some intensity information (e.g., mean and std) of each Hippocampal subfields (similar to aseg.stats file). I think one option could be mri_segstats command, but I am not sure. If it works, what are the inputs of this command? Thank you in advance for

[Freesurfer] [Repost] question about mris_anatomical_stat

Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference

[Freesurfer] question about mris_anatomical_stats

Dear Freesurfer experts Based on the FS wiki, I calculated the cortical thickness difference between the LH and RH of a subject in subject's native surface.Now, I want to use FS commands to extract the information such as "?h.aparc.stats" for this difference map (LH - RH).Now this difference

[Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

native surface. > Unfortunately, I did not find the appropriate options of this command to do > this work. > Thanks for any help. > > Best regards, > Ali-Reza > > Ali-Reza Mohammadi-Nejad > Pre-doctoral research fellow > Radiology and Neurology Research > He

[Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

not find the appropriate options of this command to do this work.Thanks for any help. Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoral research fellow Radiology and Neurology Research Henry Ford Health System  Detroit, MI 48202, USA___ Freesurfer

[Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

not find the appropriate options of this command to do this. Thanks for any help.   Best regards,Ali-Reza Ali-Reza Mohammadi-Nejad Pre-doctoralresearch fellow Radiology and NeurologyResearch HenryFord Health System  Detroit,MI 48202, USA ___ Freesurfer

Re: [Freesurfer] Brain extraction problem

...@nmr.mgh.harvard.edu wrote: Hi Ali-Reza I'm not sure I understand the problem. In the images you sent it looks to me like all the zero voxels are not part of brain tissue, but are rather either ventricular or sulcal csf cheers Bruce On Fri, 2 Jan 2015, Ali-Reza Mohammadi-Nejad wrote: Hi

[Freesurfer] Out of memory error on mri_cvs_register

Hi I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0 on a 64-bit CentOS linux vmware on a 64 bit windows 7 with 16GB memory. I am running a signle mri_cvs_register and after certain time the process terminates with out of memory error. I have done this work a lot of