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help > RE: CONN output space different from input space
Mar 29, 2023 10:03 AM | Alfonso Nieto-Castanon - Boston University
RE: CONN output space different from input space
Hi Ryan,
The exported files are all in the same MNI-space as your data, they are only being cropped (just to save storage space) to only include voxels covering the analysis mask. When the files are cropped the header information of the file is also modified to indicate so, always keeping the proper orientation/space of your NIFTI files (e.g. this is indicated by the mat header field containing the appropriate voxel-to-world mapping indicating the position of each voxel in MNI-space) so all software packages including SPM should be able to properly display those NIFTI files in MNI coordinates despite their different bounding-box dimensions. In any case if you want to skip this cropping operation I believe you can do so by changing in the file conn_display.m the line that reads:
DOCROP=true;
(this should be around line # 179) to read instead:
DOCROP=false;
That will make the files created by the 'export mask' tool have the same dimensions as your analysis mask (91x109x91)
Hope this helps
Alfonso
Originally posted by ryanw412:
The exported files are all in the same MNI-space as your data, they are only being cropped (just to save storage space) to only include voxels covering the analysis mask. When the files are cropped the header information of the file is also modified to indicate so, always keeping the proper orientation/space of your NIFTI files (e.g. this is indicated by the mat header field containing the appropriate voxel-to-world mapping indicating the position of each voxel in MNI-space) so all software packages including SPM should be able to properly display those NIFTI files in MNI coordinates despite their different bounding-box dimensions. In any case if you want to skip this cropping operation I believe you can do so by changing in the file conn_display.m the line that reads:
DOCROP=true;
(this should be around line # 179) to read instead:
DOCROP=false;
That will make the files created by the 'export mask' tool have the same dimensions as your analysis mask (91x109x91)
Hope this helps
Alfonso
Originally posted by ryanw412:
Hello,
I was viewing my results and I wanted to extract the mask of a significant cluster. After clicking the "Export mask" tool, I noticed that the [given_roi_name].nii had the dimensions 74x92x78. When I opened the CONN files in SPM and extracted the cluster through SPM instead, the dimensions of the cluster mask were 91x109x91, which I believe is the standard MNI output space .
Both of these output spaces are different than the original space of my input images (MNI152NLin2009cAsym, with dimensions of 97x115x97.
My question is: Does CONN resample the original input images to be in MNI space? Is there a convenient way to convert the output images back into my original input space? I found a way using AFNI's 3dresample, but I was wondering if there was an option to do this within CONN.
Additionally, why was the original cluster mask using CONN's "Export mask" tool in a different space than MNI space?
Thank you for the clarification!
Best,
Ryan
I was viewing my results and I wanted to extract the mask of a significant cluster. After clicking the "Export mask" tool, I noticed that the [given_roi_name].nii had the dimensions 74x92x78. When I opened the CONN files in SPM and extracted the cluster through SPM instead, the dimensions of the cluster mask were 91x109x91, which I believe is the standard MNI output space .
Both of these output spaces are different than the original space of my input images (MNI152NLin2009cAsym, with dimensions of 97x115x97.
My question is: Does CONN resample the original input images to be in MNI space? Is there a convenient way to convert the output images back into my original input space? I found a way using AFNI's 3dresample, but I was wondering if there was an option to do this within CONN.
Additionally, why was the original cluster mask using CONN's "Export mask" tool in a different space than MNI space?
Thank you for the clarification!
Best,
Ryan
Threaded View
| Title | Author | Date |
|---|---|---|
| ryanw412 | Mar 24, 2023 | |
| Alfonso Nieto-Castanon | Mar 29, 2023 | |