[Freesurfer] Scientific programmer position in neuroimage analysis and machine learning (University of Texas Southwestern, Dallas, USA)

External Email - Use Caution Scientific programmer position in neuroimage analysis and machine learning (University of Texas Southwestern, Dallas, USA) The laboratory of Albert Montillo ( http://www.utsouthwestern.edu/labs/montillo ) in the Bioinformatics Department of UT S

[Freesurfer] ASEG Extraction Inquiry

External Email - Use Caution Hi FreeSurfer Experts, I have extracted ASEG volumes using "asegstats2table" and have a few questions about the output. 1. I get values of "0" for Left and Right "WM-hypointensities" as well as "non-WM-hypointensities". Does the ASEG segmentation for

[Freesurfer] volume to surface registration

Hi Team, I have a functional image which located in the FSL volume-based template(MNI152), and now I wanna to register this image to FS-based surface template (MNI305). How can I do this? Please let me know how to do this! PS: I'm not sure that the MNI152 is same as the FS's MNI152. Dataset

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

External Email - Use Caution Thanks a lot Bruce for sharing this information. - Original Message - From: "Bruce Fischl" To: "freesurfer" Sent: Thursday, May 10, 2018 9:50:44 PM Subject: Re: [Freesurfer] run recon all with forced orientation, spacing and dimension becau

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

because internally we expect things to be a certain way (which is why we convert the data to that format). There are also some requirements on the data that you have to meet. For example 2mm is not high enough resolution to get accurate cortical models. The acquired data has to be no bigger than

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

External Email - Use Caution Hi Bruce, Thanks Bruce i understand that. But can't i run free-surfer with all these parameters (size, spacing and orientation) ? Thanks, Ritesh Mahajan - Original Message - From: "Bruce Fischl" To: "freesurfer" Sent: Thursday, May 10, 20

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote: >External Email - Use Caution > > Thank you Bruse. Actually i converted the input into RAI orientati

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

External Email - Use Caution Thank you Bruse. Actually i converted the input into RAI orientation using mri_convert --out_orientation and gave RAI input the free-surfer through recon-all. The results are not generated. My goal is to run free-surfer with RAI orientation and resul

[Freesurfer] Differences between qdec display and summary file for monte carlo corrected results

External Email - Use Caution Hi, experts, I used qdec to do some analysis on my data and tried to correct for multiple comparisons using the button in qdec of monte carlo simulation. I saw only one big cluster in the display window of qdec. However, I saw three clusters in the

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh no, not really. What is your goal? We should handle any input orientation as long as it is specified in the headers. cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote: >External Email - Use Caution > > Hello Team, > > As i know free-surfer generates the output with follo

[Freesurfer] run recon all with forced orientation, spacing and dimension

External Email - Use Caution Hello Team, As i know free-surfer generates the output with following: 1) Dimensions : 256*256*256 2) Spacing : 1, 1,1 mm 3) Orientation : LIA Is there any way to run free-surfer with user specified orientation, spacing and dimension ? Thanks, Rites