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Dichter
BIAC Faculty
190 Posts |
 Posted - Mar 26 2007 : 10:57:21 AM
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Sorry if this was covered in another post already...
I am trying to load FSL output (e.g., "cope1.nii.gz") into showsrs2 as an overlay on anathalf.bxh, but am getting an interpolation error ("Overlay interpolation must use an integer scale factor"). I've added the path '\\gall\programs\User_Scripts\BIAC_matlab_ver3.1.0_test' to my startup.m file already.
Thanks for any help,
-Gabriel |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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petty
BIAC Staff
USA
453 Posts |
Posted - Mar 26 2007 : 11:23:43 AM
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thats because your FSL data is 91x109x91 and 2x2x2 and the anatHalf is likely 90x108x78 at 1.75x1.75x1.75.
if you want a template brain that looks good use the canonical SPM brain, they are in the same space:
\\Gall\Programs\MATLAB\spm5\canonical\single_subj_T1.nii
or use your bg_image ... thats the one thats relevant to your specific data set. |
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Dichter
BIAC Faculty
190 Posts |
Posted - Mar 26 2007 : 11:37:12 AM
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| Thanks, Chris. However, I still get the interpolation error for both single_subj_T1.nii and bg_image.nii.gz. The overlay I'm trying to load is is pe1.nii.gz. Per Syam's recent post, I'm using the latest BXH tools release. Thanks. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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petty
BIAC Staff
USA
453 Posts |
Posted - Mar 26 2007 : 11:52:47 AM
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| is your map empty perhaps? |
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Dichter
BIAC Faculty
190 Posts |
Posted - Mar 26 2007 : 12:58:28 PM
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Nope.
I am able to load the overlay on its own, but not over an anatomical image. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 26 2007 : 1:18:22 PM
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| Can you verify that the dimensions of both images are the same? (i.e. what shows up in the readmr GUI when you open each image?) |
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Dichter
BIAC Faculty
190 Posts |
Posted - Mar 26 2007 : 4:17:30 PM
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OK, that's it:
bg_image.nii.gz: 91x109x91, voxel size 2x2x2
pe2.nii.gz: 64x64x34, voxel size 3.75 x 3.75 x 3.8
So, which anatomical image are people using to display their FSL data? |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 26 2007 : 4:27:33 PM
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| OK, am I to understand that these images are the results of a single run analysis? If so, these are likely not transformed into standard space. Even if you run registration, FSL only stores the transformation matrices until it needs to stamp out registered brains (like across runs/subjects analysis). If you want registered data at the first level, you need to explicitly run featregapply on the .feat directory. It will then send images to reg_standard... |
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Dichter
BIAC Faculty
190 Posts |
Posted - Mar 27 2007 : 09:48:00 AM
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| OK - I can load the 2nd-level output fine on bg_image.nii.gz. Thanks, Syam & Chris. |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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syam.gadde
BIAC Staff
USA
421 Posts |
Posted - Mar 27 2007 : 10:13:28 AM
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| Also, if you have already run higher-level analyses, FEAT probably did create registered pe/cope/etc. images in reg_standard. If your .fsf file had sscleanup_yn set to "n", then these won't be deleted after the second-level analyses are done. (in case you were interested in seeing the first-level images) |
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Dichter
BIAC Faculty
190 Posts |
Posted - Apr 02 2007 : 1:10:46 PM
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| I am now unable to load Analyze7.5_SPM files with readmr. I am trying to load tstat1.nii.gz from under the \stats output folder, and get an error that "tstat1.nii.gz is not an Analyze7.5_SPM file". |
Gabriel S. Dichter, PhD
UNC Departments of Psychiatry & Psychology
http://www.can.unc.edu/ |
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petty
BIAC Staff
USA
453 Posts |
Posted - Apr 02 2007 : 1:42:25 PM
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| fslwrapbxh is your friend |
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Topic |
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loading cope1.nii.gz files in showsrs2
