Freesurfer October 2009

freesurfer@nmr.mgh.harvard.edu

99 participants
151 discussions

running motion correction
by Ahmed, F, Me <fahmed＠sun.ac.za> 21 Oct '09

21 Oct '09

Hello, I'm currently converting my dicom images into the mgz format and I was wondering, I only have one acquisition per subject, therefore do I have to run the motion correction step before running autorecon1? Or can I just go straight into running autorecon1? From the tutorial, I'd imagine I must run the motion correction step as it says that autorecon1 uses the output from the motion correction step, so I'm just a little confused. Thank you, Fatima

2 1

subcortical gray matter segmentation
by asaf achiron 21 Oct '09

21 Oct '09

when conducting a subcortical gray matter segmentation, the volume of the cerebral cortex is also measured . how this is performed? is it also based upon the probabilistic atlas ? thank you Asaf

2 1

{Disarmed} Re: mgz file is tilted
by Jay Ives 20 Oct '09

20 Oct '09

2 1

TIV corrected
by Guang Zeng 20 Oct '09

20 Oct '09

Hi, there, Have those volume of ROIs in aseg.stats been TIV corrected? Thanks a lot! Guang _________________________________________________________________ Hotmail: Free, trusted and rich email service. http://clk.atdmt.com/GBL/go/171222984/direct/01/

3 4

T1 scanning parameters and mean curvature
by Narly A Golestani 20 Oct '09

20 Oct '09

Hello all, I would like to know whether the T1 parameters such as TR, TE, TI, and flip angle can systematically influence mean curvature values obtained by recon-all -all. I have processed 2 data sets with the following T1 parameters, and am noticing that the mean curvature values systematically bigger in the former compared to the latter data set in 78% of the brain regions segmented in the default (Desikan) atlas. data set 1: TR=12.24, TE=3.56, TI=530.00, flip angle=23.00 Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels data set 2: TR=20.66, TE=8.42, TI=640.00, flip angle=25.00 Original Data has (1, 1, 1) mm size and (224, 256, 176) voxels More generally, I would like to confirm that it's not recommended to combine data based on different scanning parameters in one study, due to possible systematic differences in the segmentation output related to scanning parameters. thanks in advance and all the best, Narly.

2 1

optseq2 questions
by 杨宏宇 20 Oct '09

20 Oct '09

Hi list, I am using optseq2 to design my fMRI study. These are my scripts: optseq2 --ntp 500 --tr 2 --psdwin 0 40 1 --ev star 12 9 --ev star 13 8 --ev star 14 8 --ev diamond 12 9 --ev diamond 13 8 --ev diamond 14 8 --tnullmin 5 --tnullmax 7 --nkeep 3 --o ex.event12.13.14s --nsearch 5000 I have 2 events, which last for 12,13, and 14s. I found that the schedule documents I got had many null events more than 7s, however, I have set the maximam as 7s. In the sum logfile, I found that my script was recorded correctly, so could you please tell me the reason, and how to solve the problem? Many thanks, Hongyu Division on Addiction, Psychiatry Department, UT Southwestern Medical Center

3 3

Creating FSGD file
by Weisinger, Brian (NIH/OD) [E] 20 Oct '09

20 Oct '09

I am trying to follow the directions to create a FSGD file put I am having trouble. I used open office to make the file which looks like the one in the example. Is this where I am supposed to create it? Do I create it in as a text file? Do I save it as an .odt file? If all this is correct I have a question of where do I place the file so when I put in mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff It finds it? Thanks for the help.

2 1

mgz file is tilted
by Jay Ives 20 Oct '09

20 Oct '09

2 1

out of space
by Ahmed, F, Me <fahmed＠sun.ac.za> 20 Oct '09

20 Oct '09

Hello, I'm trying to get my dicom images into my VMware desktop but I have run out of space so can't continue to copy files over. I am trying desperately to make space on the desktop and had a question regarding that. I have 2 freesurfer folders; 1 is on my desktop and 1 is located in /usr/local. I'm wondering if I need to have both, or if I can delete the one on my desktop (as it's taking up space) and if so, will that cause any problems in using fs? Any advice you can give will be greatly appreciated. Thank you, Fatima

4 3

mri_motion_correction to average DTI sequences?
by Francisco Costela 20 Oct '09

20 Oct '09

Hi all, I want to get the average DTI from 2 DTI sequences (obtained from the same subject with the same configuration data). I am using mri_motion_correct to get it but I wonder whether I can apply the original diffusion direction file to this average image or I need to rotate the diffusion direction accordingly (due to the motion introduced). Thanks for your help, Francisco

2 1

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Freesurfer October 2009