Hi Taylor,
Below is the command:
lesion_filling -i ~/Documents/all-baseline/WMmasks/C0101S01.nii -l ~/Documents/all-baseline/ship-masks/C0101S01.nii -w ~/Documents/all-baseline/WMmasks/C0101S01_seg_1.nii -o ~/Documents/all-baseline/filled/C0101S01.nii -v
The output I provided earlier is the verbose output: I did not want to give all the samples values, because there are a lot. Here it is again, but omitting a bunch of sample values in the middle:
Read in images
Counted lesions in mask : total = 14
Calculated outer border mask
Calculated outer border components
Calculated inner border and region masks
Component 1 of 14
Cols = 1 and rows = 42
Calculating cummulative distribution
Random sampling...
Putting samples back into image
Values are : 1370.959961 1185.339966 1349.890015 1344.780029 1359.369995 1118.849976 1153.140015 1318.500000 1165.099976 1231.770020 1236.089966 1278.300049 1201.439941 1243.109985 1358.800049 1371.150024 1279.780029 1287.839966 1122.699951 1264.979980 962.000000 1128.300049 1094.650024 1307.550049 1074.849976 1194.540039 1110.050049 1021.950012 1360.130005 1084.750000 ...................... 1243.380005 1279.040039 1357.469971 1158.660034 1230.959961 1297.329956 1363.550049 1097.400024 1287.839966 1308.280029 1139.339966 1041.569946 1092.449951 1355.949951 1032.849976 1103.449951 1043.750000 1137.500000 1043.750000 1324.339966 1243.920044 1362.219971 1278.670044 1230.150024 1024.130005 1139.800049 1183.040039 1355.380005 1098.500000 1241.489990 1203.739990 1313.390015 1113.900024 1163.719971 977.260010 1300.250000 965.270020 1027.400024 1369.060059 1357.089966 1352.810059 1126.920044 1371.150024 1361.839966 1075.400024 1015.409973 1123.250000 1164.180054 1160.500000 1109.500000 962.000000 1368.489990 970.719971 1256.469971 1178.900024 1032.849976 1366.589966 1311.199951 1035.030029 973.989990 1183.959961 1227.449951 1322.150024 1219.079956 1294.410034
Image Exception : #4 :: Incompatible number of mask positions and matrix columns
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
Abort trap: 6
Thank you!
Mariya
Mariya Cherkasova, PhD
CIHR and MSFHR/LJHFM Fellow
Pacific Parkinson's Research Centre
University of British Columbia
2221 Westbrook Mall, rm M46C
Vancouver, BC V6T 2B5
phone: 604-822-3428
fax: 604-822-7866
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Taylor Hanayik [[log in to unmask]]
Sent: March-08-19 4:53 AM
To: [log in to unmask]
Subject: Re: [FSL] Error in lesion_filling
Hi Mariya,
Could you provide the whole command that you are running?
Also, could you try running again with the -v (verbose) option, and provide the text output?
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]<mailto:[log in to unmask]>
On 7 Mar 2019, at 17:57, Mariya Cherkasova <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi, I am still experiencing the issue below. I would really appreciate some help/ advice on this.
Thank you,
Mariya
Hello,
I am getting errors when I run the lesion_filling script on T1 scans from MS patients.
It looks like the script gets as far as producing fill values for the lesion voxels:
Read in images
Counted lesions in mask : total = 14
Calculated outer border mask
Calculated outer border components
Calculated inner border and region masks
Component 1 of 14
Cols = 1 and rows = 55
Calculating cummulative distribution
Random sampling...
putting samples back into image
Values are : 1396.680054 1225.829956 1372.670044 1371.339966 1380.209961 1166.020020 ....
BUT THEN I GET THE ERROR:
Image Exception : #4 :: Incompatible number of mask positions and matrix columns
libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
Abort trap:
Please advise.
Many thanks,
Mariya
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
________________________________
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|