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Author: Lee Friedman (---.hsd1.nm.comcast.net)
Date: 12-31-06 13:19
It looks like @SUMA_AlignToExperiment does not like nifti.
Is SUMA all afni-file-type based?
Lee
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Author: Lee Friedman (---.hsd1.nm.comcast.net)
Date: 12-31-06 13:30
Ziad,
Here is what I have as input to SUMA:
A freesurfer analysis (through autorecon2) of a single T1 image taken during the same session as the functional data.
The functional data have already been completely processed in nifti form, including spatial normalization to an MNI EPI template (in MNI space) using SPM5.
It consists of 3 key files:
sub1_Intercept - the model intercept which is like a average EPI image.
sub1_PerChg - an image in percent change units.
sub1_PerNoise - an image in percent noise units.
These are 4x4x4mm.
I am willing to resample but want to use a nearest neighbor method to minimize additional smoothing.
These are all nifti and they are already in MNI space (qform_code = 4).
What are the steps for me to get the surfaces from freesurfer and the functional stuff aligned?
I suppose I could simply run a 3dvolreg aligning the freesurfer stuff to the functional stuff.
Lee
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Author: Ziad Saad (---.res.east.verizon.net)
Date: 01-02-07 14:07
Hi Lee,
How did @SUMA_AlignToExperiment fail?
It should work with nifti datasets but I never actually tested it as it predates that world. Send me the SurfVol and the ExpVol datasets and I'll look into it.
cheers,
-ziad
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Author: Lee Friedman (---.hsd1.nm.comcast.net)
Date: 01-02-07 15:12
Ziad,
Happy new year to you!
I think before I send you files, this following will help.
I have a little script called run_AlignToExperiment.csh
@SUMA_AlignToExperiment -exp_anat 000900369824_HRF_Intercept_mag_ef.nii -surf_anat 000900369824_HRF_Intercept_mag_ef.nii
Both files are in the directory in which I run the command.
Here is what I get:
source run_AlignToExperiment.csh
Error: No Experiment Anatomy 000900369824_HRF_Intercept_mag_ef.nii (.HEAD or .BRIK) in current directory
Lee
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Author: Ziad Saad (---.nimh.nih.gov)
Date: 01-03-07 15:48
Hi Lee,
It is too much of a pain to modify these large csh scripts to work with both AFNI and NIFTI datasets. We are developing a python library that will allow a better handling of various types for scripting purposes and someday I plan to port @SUMA_AlignToExperiment to python.
In the meanwhile, how about adding to your script two lines, one on top to convert the -exp_anat and -surf_anat to afni dsets with 3dNIFTItoAFNI, run the script, then use 3dAFNItoNIFTI to convert the output.
The script is meant to align datasets with rigid body transformations between datasets of the same nature (within modality) but in your case you need some stretching and scaling action. The -wd option should allow you to do that. Also, you don't need the entire EPI time series for -exp_anat and -surf_anat, the first sub-brick should suffice.
cheers,
-ziad
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Author: rick reynolds (---.nimh.nih.gov)
Date: 01-03-07 17:10
Note that there is no 3dNIFTItoAFNI program.
To make such a conversion, it is enough to
use 3dcopy.
e.g. 3dcopy dset.nii dset
That would make dset+orig from dset.nii (though
maybe it is dangerous not to change the name).
- rick
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