sdm-help-list
sdm-help-list > RE: visualizing VBM results
Jan 24, 2018 11:01 AM | Anton Albajes-Eizagirre - FIDMAG - Germanes Hospitalaries
RE: visualizing VBM results
Dear Collen,
We just uploaded to the web an updated version of SdmGui for OSX. This should fix the issue at the time of launching viewers (MRICron and FSLView). However, please take into account that MRICron for OSX doesn't let us directly load overlays, so you'll have to add them manually in order to obtain the same image you would obtain in Linux or Windows. FSLView works the same in any host OS.
Could you please let us know if you had the chance to try it, and to confirm it solves the problem?
Thanks,
Anton
Originally posted by Anton Albajes-Eizagirre:
We just uploaded to the web an updated version of SdmGui for OSX. This should fix the issue at the time of launching viewers (MRICron and FSLView). However, please take into account that MRICron for OSX doesn't let us directly load overlays, so you'll have to add them manually in order to obtain the same image you would obtain in Linux or Windows. FSLView works the same in any host OS.
Could you please let us know if you had the chance to try it, and to confirm it solves the problem?
Thanks,
Anton
Originally posted by Anton Albajes-Eizagirre:
Dear Collen,
Another user reported a problem with the MRICron launch while using Sierra. We are working on it, preparing an updated version fixing the issue.
The masks for peaks are just masks with the voxel of the peak valued at 1 and the rest valued at 0. The masks for the blobs are masks with 1 for the cluster, 0 elsewhere. Therefore, concatenating peak masks or blob masks would only give you the map of peak locations for the former or the shape of all the clusters for the later. But all 1 and 0 images.
Yes, the file MyMean_z_p_0.00500_1.000_10_p.nii.gz is already thresholded,being 0.005 the threshold valued used, 1.000 the peak height threshold and 10 the extent threshold.
Best regards,
Anton
Originally posted by Colleen Rollins:
Another user reported a problem with the MRICron launch while using Sierra. We are working on it, preparing an updated version fixing the issue.
The masks for peaks are just masks with the voxel of the peak valued at 1 and the rest valued at 0. The masks for the blobs are masks with 1 for the cluster, 0 elsewhere. Therefore, concatenating peak masks or blob masks would only give you the map of peak locations for the former or the shape of all the clusters for the later. But all 1 and 0 images.
Yes, the file MyMean_z_p_0.00500_1.000_10_p.nii.gz is already thresholded,being 0.005 the threshold valued used, 1.000 the peak height threshold and 10 the extent threshold.
Best regards,
Anton
Originally posted by Colleen Rollins:
Dear Anton,
Many thanks for your quick reply. I'm using MacOS High Sierra v10.13.2 and SDM v5.141.
Are the overlays concatenations of the peak files? (Ie. would MyMean_z_p_0.00500_1.000_10_p.nii.gz be equivalent to each of the mask_MyMean_z_p_0.00500_1.000_10_peak1.nii.gz files being loaded?) I'm just trying to clarify what the other nifty files show. Also, I just wanted to confirm that MyMean_z_p_0.00500_1.000_10_p.nii.gz (and neg) are already thresholded, or is any more correction/thresholding required?
Thanks again,
Colleen
Many thanks for your quick reply. I'm using MacOS High Sierra v10.13.2 and SDM v5.141.
Are the overlays concatenations of the peak files? (Ie. would MyMean_z_p_0.00500_1.000_10_p.nii.gz be equivalent to each of the mask_MyMean_z_p_0.00500_1.000_10_peak1.nii.gz files being loaded?) I'm just trying to clarify what the other nifty files show. Also, I just wanted to confirm that MyMean_z_p_0.00500_1.000_10_p.nii.gz (and neg) are already thresholded, or is any more correction/thresholding required?
Thanks again,
Colleen
Threaded View
| Title | Author | Date |
|---|---|---|
| Colleen Rollins | Jan 15, 2018 | |
| Anton Albajes-Eizagirre | Jan 15, 2018 | |
| Colleen Rollins | Jan 15, 2018 | |
| Anton Albajes-Eizagirre | Jan 21, 2018 | |
| Anton Albajes-Eizagirre | Jan 24, 2018 | |
| Layla Lavallé | Jun 5, 2020 | |
| Colleen Rollins | Jan 29, 2018 | |