Dear All,
I am trying to batch script roi extraction from image (nii) to then perform ROI analysis over multiple ROIs and subjects.
So, I am trying to batch script roi extraction from image (nii) to then perform ROI analysis over multiple ROIs and subjects.
I am using the example lines provided:
fname = roi_list{1}; roi = maroi_image(fname);
I got an error early on while loading the roi:
maroi_image ERROR (line 34) params.vol = spm_vol(params);
-I have seen a couple of posts that resolved a similar issue by adding marsbar('on'). It didn't work for me.
-I tried to versions of matlab: 2016b and 2019a - same error
So I tried a workaround by using
fname = spm_vol(roi_list{i1}); % instead of fname = 'image.nii' roi = maroi_image(fname); roi = maroi_matrix(roi);
the script now runs without errors and roi.mat is generated.
However, when I attempt to visualize the rois from marsbar - roi definition - view
They do not appear in the gui in the folder where they are. Thus I understand that marsbar does not recognize them.
Does anyone have a clue?
I noticed that the there is one difference between the roi build via scripting and via gui:
the label field is empty:
val = [maroi_matrix - 11 - binarized] label: '' source: 'C:\path-to-roi\11_roi.mat' binarize: 1 roithresh: 0.5000 spm_hold: 1 dat: [158×190×136 double] mat: [4×4 double] maroi: [1×1 maroi]
Can this be the problem?
Please help!!!
Thanks!
Ilaria
Sorry - I'm afraid I don't monitor this forum. Could you post to the mailing list instead?
Cheers,
Matthew
My apologies!
I thought they were the same thing.
Thanks for catching this promptly.
Best,
Ilaria
Ilaria Sani, PhD
Postdoctoral Fellow, Freiwald Lab
The Rockefeller University
1230 York Ave., New York, NY 10065.
Phone: (212) 327 7699
Fax: (212) 327 7698
Email: isani01@rockefeller.eduhttps://rumail.rockefeller.edu/owa/redir.aspx?C=Kqhy3ohui0OLc6NBHS0gx_jC9yHmUtEIuvMTV8kpl1lEP6utIV_5LPRr35l0-k2eSQyLqrMn4XI.&URL=mailto%3assadagopan%40rockefeller.edu
From: Matthew Brett matthewbrett@users.sourceforge.net
Sent: Monday, July 13, 2020 6:39 AM
To: [marsbar:support-requests] 6@support-requests.marsbar.p.re.sourceforge.net
Subject: [marsbar:support-requests] #6 unable to buid roi from image (batch)
Sorry - I'm afraid I don't monitor this forum. Could you post to the mailing list instead?
Cheers,
Matthew
[support-requests:#6]https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_p_marsbar_support-2Drequests_6_&d=DwMGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=d4z88RzwDKeicDL3VVuTqQcuSf1y8Z7V7XewX20Ubmk&m=mMEodBmvRnBYtLWljmqCxrVFepyryc5yi4L92Iultdk&s=5iDH-MnZpZ7KzKE0ag7mruCF5RJRuuYsZmquytm210c&e= unable to buid roi from image (batch)
Status: open
Group: v1.0 (example)
Labels: batch roi-build nii
Created: Mon Jul 13, 2020 01:15 PM UTC by ilaria sani
Last Updated: Mon Jul 13, 2020 01:15 PM UTC
Owner: nobody
Dear All,
I am trying to batch script roi extraction from image (nii) to then perform ROI analysis over multiple ROIs and subjects.
So, I am trying to batch script roi extraction from image (nii) to then perform ROI analysis over multiple ROIs and subjects.
I am using the example lines provided:
fname = roi_list{1};
roi = maroi_image(fname);
I got an error early on while loading the roi:
maroi_image ERROR (line 34) params.vol = spm_vol(params);
-I have seen a couple of posts that resolved a similar issue by adding marsbar('on'). It didn't work for me.
-I tried to versions of matlab: 2016b and 2019a - same error
So I tried a workaround by using
fname = spm_vol(roi_list{i1}); % instead of fname = 'image.nii'
roi = maroi_image(fname);
roi = maroi_matrix(roi);
the script now runs without errors and roi.mat is generated.
However, when I attempt to visualize the rois from marsbar - roi definition - view
They do not appear in the gui in the folder where they are. Thus I understand that marsbar does not recognize them.
Does anyone have a clue?
I noticed that the there is one difference between the roi build via scripting and via gui:
the label field is empty:
val =
[maroi_matrix - 11 - binarized]
label: ''
source: 'C:\path-to-roi\11_roi.mat'
binarize: 1
roithresh: 0.5000
spm_hold: 1
dat: [158×190×136 double]
mat: [4×4 double]
maroi: [1×1 maroi]
Can this be the problem?
Please help!!!
Thanks!
Ilaria
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