Hi Taylor,
I have uploaded the lesion mask and the WM mask files.
1. The lesion mask file is called 101_mask.nii
2. The WM mask file as outputted by FAST is called ccsvi_101_t1brain_seg_3.nii
3. The WM mask including both lesioned and non-lesioned WM is called 101_fullmask.nii.
I hope this provides enough information for you to identify the problem (as I am not including the original t1 scan).
Thanks for your help!
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 Cherkasova, Mariya [[log in to unmask]]
Sent: March-11-19 10:32 AM
To: [log in to unmask]
Subject: Re: [FSL] Error in lesion_filling
Hi Taylor,
Let me check with my co-investigators regarding confidentiality issues and get back to you.
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-11-19 10:21 AM
To: [log in to unmask]
Subject: Re: [FSL] Error in lesion_filling
Hi Mariya,
Could you zip and share your images that you’re trying to run (just the relevant files necessary for running lesion_filling)? Maybe one working subject, and one not working subject?
You can upload your images securely to OxFile at this link:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=690991047F8A89D9F1
Cheers,
Taylor Hanayik
Taylor Hanayik PhD
FMRIB, John Radcliffe Hospital
University of Oxford
[log in to unmask]
> On 11 Mar 2019, at 16:45, Cherkasova, Mariya <[log in to unmask]> wrote:
>
> Hi Taylor,
> I'm not sure if it's helpful information, but just in case: the only time the script runs successfully is on a patient who does not have any WM lesions: i.e. the mask is empty:
>
> lesion_filling -i ~/Documents/all-baseline/WMmasks/C0253S01.nii -l ~/Documents/all-baseline/ship-masks/C0253S01.nii -w ~/Documents/all-baseline/WMmasks/C0253S01_seg_2.nii -o /Users/filled/C0253S01.nii -v
> Read in images
> Counted lesions in mask : total = 0
> Calculated outer border mask
> Calculated outer border components
> Calculated inner border and region masks
>
> In this case, it creates two volumes in the output folder: C0253S01_inneronly.nii.gz and C0253S01.nii.gz, which are identical. This demonstrates that this is not some sort of a system issue where the script is unable to write files to a directory on my computer. It appears to be something about the filling of lesions.
> Best wishes,
> 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 Cherkasova, Mariya [[log in to unmask]]
> Sent: March-08-19 8:48 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Error in lesion_filling
>
> Hi Taylor,
> I've checked all my masks (example images attached). Incidentally, if I run this with seg2 instead of seg1, I get the same error, just different sample values:
>
> lesion_filling -i ~/Documents/all-baseline/WMmasks/C0101S01.nii -l ~/Documents/all-baseline/ship-masks/C0101S01.nii -w ~/Documents/all-baseline/WMmasks/C0101S01_seg_2.nii -o ~/Documents/all-baseline/filled/C0101S01.nii -v
> 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 = 44
> Calculating cummulative distribution
> Random sampling...
> Putting samples back into image
> Values are : 1700.119995 1492.560059 1681.150024 1700.479980 1689.140015 1397.489990 1511.760010 1657.500000 1463.050049 1561.459961 1568.819946 1625.400024 1514.959961 1580.780029 1688.599976 1700.300049 1627.239990 1634.400024 1399.380005 1608.839966 1319.000000 1404.650024 1385.609985 1691.300049 1375.890015 1505.359985 1393.170044 1349.250000 1689.859985 1380.750000 1554.560059 .... 1685.359985 1387.500000 1578.020020 1569.739990 1653.650024 1395.060059 1526.479980 1326.699951 1643.750000 1320.650024 1352.000000 1698.319946 1686.979980 1683.349976 1402.459961 1700.300049 1691.479980 1376.160034 1345.949951 1399.650024 1461.589966 1455.750000 1392.900024 1319.000000 1697.780029 1323.400024 1598.260010 1544.900024 1391.550049 1695.979980 1692.199951 1355.849976 1325.050049 1490.640015 1554.099976 1660.250000 1539.839966 1688.060059
>
> 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
>
> I wonder if this sheds any light on things. Also, I've tried creating masks (with FAST) using both 3 and 4 tissue classes (4th being lesions), considering the extensive WM lesions in these patients. It does not seem to make a difference. And I've also made sure all the files I'm using align.
>
> Thanks again,
> 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 8:17 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Error in lesion_filling
>
> Hi,
>
> Judging from your file names, it’s possible that your white matter mask image is actually a grey matter mask. Depending on how you segmented (i.e. brain extraction first) then the _seg_1_ file is usually grey matter and _seg_2_ is the white matter mask.
>
> Can you verify visually (open in FSLeyes)?
>
>
>
> Cheers,
>
> Taylor Hanayik
>
>
> Taylor Hanayik PhD
> FMRIB, John Radcliffe Hospital
> University of Oxford
> [log in to unmask]<mailto:[log in to unmask]>
>
>
>
>
>
> On 8 Mar 2019, at 16:07, Cherkasova, Mariya <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>
> 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]<mailto:[log in to unmask]>] on behalf of Taylor Hanayik [[log in to unmask]<mailto:[log in to unmask]>]
> Sent: March-08-19 4:53 AM
> To: [log in to unmask]<mailto:[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]><mailto:[log in to unmask]>
>
>
>
>
>
> On 7 Mar 2019, at 17:57, Mariya Cherkasova <[log in to unmask]<mailto:[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
>
>
> ________________________________
>
> 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
########################################################################
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
|
