AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

Previous Message Next Message
Message List New Topic Print View
|
Gregory Larkin
November 26, 2005 05:01PM
I'm trying to help someone read some old vision data into AFNI. I'm having some problems with to3d as I normally use it.

There are 32 (3mm) oblique slices collected from a surface coil from the back of the head

Here are the specs for the (spiral out) pulse sequence:
P63488.7.mag
TE 30
TR 2
nshots 1
frameperiod 2
FOV 200
matsize 64
inplane res [3.125 3.125]
nSlices 32
thick 3
totalFrames 201
#slices 6432

I tried to modify the to3d command as I normally use it to work with these data:
to3d -epan -prefix loc1 -xFOV 120R-L -yFOV 120A-P -zSLAB 116I-124S -time:tz 201 32 2.0s seqplus 3D:0:0:64:64:6432:'loc1'

It creates a file but it looks terrible and it's centered at 0,0,0. It should be anchored at the back of the head. I've never worked with oblique slices. Anyone see something obvious that I'm doing wrong?

Thanks!

Reply Quote
RSS
Subject Author Posted

oblique slices

Gregory Larkin November 26, 2005 05:01PM

Re: oblique slices

Rich Hammett November 27, 2005 07:16PM

Re: oblique slices

Godot November 27, 2005 09:26PM