open-discussion
open-discussion > RE: Too many gradients excluded by "default"
May 11, 2017 02:05 PM | Martin Styner
RE: Too many gradients excluded by "default"
This indeed looks like an issue for
DWIConvert. Which version are you using, as earlier version had a
known bug with multi-b-value images to go from NRRD to NIFTI (and
back)? You may want to download it with the newest version of
Slicer (maybe even a nightly build), or compile it
yourself: https://github.com/BRAINSia/BRAINSTools/tree/master/DWIConvert
Btw, we do not maintain DWIConvert, it's a Slicer/BRAINS tool that we use (just like FSL's bet2)
Also, can you double-check the header of the NRRD file, whether the first DWI gradient is 0 0 0? This would narrow it down to see which of the 2 conversions messes things up.
Best
Martin
Originally posted by Minchul Kim:
Btw, we do not maintain DWIConvert, it's a Slicer/BRAINS tool that we use (just like FSL's bet2)
Also, can you double-check the header of the NRRD file, whether the first DWI gradient is 0 0 0? This would narrow it down to see which of the 2 conversions messes things up.
Best
Martin
Originally posted by Minchul Kim:
Hello , Martin
I got into another problem of DTIPrep excluding the initial B0 gradient dataset.
And I think it's due to "DWIConvert" module.
My DWI data is in nifti format and I tried to convert the data into NRRD format.
I used "DWIConvert" I could convert my data, but faced a problem of unwanted change of b-values.
I used "FSLtoNRRD" command and gave input b-value text file with one B0 and B1000, 1500 and 2000 values.
The given txt. file is " 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 "
After converting, I re-converted NRRD file into Nifti format to check everything is fine.(because DTIPrep kept on excluding initial B0 gradient).
But the B-value cameout with Nifti file is not same as I gave as input.
The numbers were ramdomly changed.
The b-value text file cameout is
"569.14677169328775
1210.4240156296401
2394.278657453659
2064.6115111473659
2436.8009231442984
1705.7749517509521
1516.4484019703827
1514.1840056875694
1719.9054732742741
2824.3546439594234
2039.8874449352959
1211.1570127685525
2394.0072468217677
2064.9339802438881
2437.7675224831487
1705.874096430357
1516.5357335934659
1514.0713333670778
1719.814571234273
2824.4174183001828
2040.1616777009938
1210.592447597332
2394.3981996158004
2064.7939236817956
2437.6351466971118
1706.1506126118095
1516.6813482354526
1514.5959658969289
1719.3471588181069
2824.4694227411933
2214.1862132865399
1818.5253904163474
2379.8818229158201
1534.0663695825635
2377.2198780491276
1531.6037871520705
2376.2974797197626
1533.6721350225935
3030.4495159553903
1497.819497263901
1139.6441598187059
1817.9113032772889
2379.4458786272944
1533.8076305638847
2377.341528007285
1532.092919034837
2376.8870089482484
1533.7763507339953
3030.39438321854
1497.4963034622233
1139.4844454853051
1817.60332523135
2379.0966775756933
1533.7479203686992
2377.114705937805
1532.9149473982216
2376.9214811331449
1533.496245336315
3030.1965392951452
1497.2164576375399
485.30360327283682
2963.2369306481619
1239.161593096693
2396.5764449663329
1660.7085313620228
1508.0419153094763
1896.0191813079648
3153.7796491840281
730.87428877886327
1942.1368712267449
1008.437730083243
2963.446215401349
1240.038375975256
2397.1494366414922
1659.3181504339971
1507.376482833866
1894.6606209606766
3153.9309149673081
730.16050594589706
1942.6741487412278
1007.5010623141499
2963.5995044988094
1240.5890343827225
2397.4182379207482
1659.6068556891951
1507.0685735595321
1894.0214419438767
3153.877208544558
730.13306594795426
1943.4686143768183
1007.4178745724701"
And no B-value of "0", which should be resistration template.
I think when converting nifti to NRRD, unintented b-value change occurs.
I have tired with other datasets from other subjects and found this always occurs.
This maybe a problem with DWIConvert module, but I just want to ask have you ever faced and fixed this problem.
Or could I send you a sample dataset of mine for you to take a look?
Minchul
I got into another problem of DTIPrep excluding the initial B0 gradient dataset.
And I think it's due to "DWIConvert" module.
My DWI data is in nifti format and I tried to convert the data into NRRD format.
I used "DWIConvert" I could convert my data, but faced a problem of unwanted change of b-values.
I used "FSLtoNRRD" command and gave input b-value text file with one B0 and B1000, 1500 and 2000 values.
The given txt. file is " 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 1500 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 "
After converting, I re-converted NRRD file into Nifti format to check everything is fine.(because DTIPrep kept on excluding initial B0 gradient).
But the B-value cameout with Nifti file is not same as I gave as input.
The numbers were ramdomly changed.
The b-value text file cameout is
"569.14677169328775
1210.4240156296401
2394.278657453659
2064.6115111473659
2436.8009231442984
1705.7749517509521
1516.4484019703827
1514.1840056875694
1719.9054732742741
2824.3546439594234
2039.8874449352959
1211.1570127685525
2394.0072468217677
2064.9339802438881
2437.7675224831487
1705.874096430357
1516.5357335934659
1514.0713333670778
1719.814571234273
2824.4174183001828
2040.1616777009938
1210.592447597332
2394.3981996158004
2064.7939236817956
2437.6351466971118
1706.1506126118095
1516.6813482354526
1514.5959658969289
1719.3471588181069
2824.4694227411933
2214.1862132865399
1818.5253904163474
2379.8818229158201
1534.0663695825635
2377.2198780491276
1531.6037871520705
2376.2974797197626
1533.6721350225935
3030.4495159553903
1497.819497263901
1139.6441598187059
1817.9113032772889
2379.4458786272944
1533.8076305638847
2377.341528007285
1532.092919034837
2376.8870089482484
1533.7763507339953
3030.39438321854
1497.4963034622233
1139.4844454853051
1817.60332523135
2379.0966775756933
1533.7479203686992
2377.114705937805
1532.9149473982216
2376.9214811331449
1533.496245336315
3030.1965392951452
1497.2164576375399
485.30360327283682
2963.2369306481619
1239.161593096693
2396.5764449663329
1660.7085313620228
1508.0419153094763
1896.0191813079648
3153.7796491840281
730.87428877886327
1942.1368712267449
1008.437730083243
2963.446215401349
1240.038375975256
2397.1494366414922
1659.3181504339971
1507.376482833866
1894.6606209606766
3153.9309149673081
730.16050594589706
1942.6741487412278
1007.5010623141499
2963.5995044988094
1240.5890343827225
2397.4182379207482
1659.6068556891951
1507.0685735595321
1894.0214419438767
3153.877208544558
730.13306594795426
1943.4686143768183
1007.4178745724701"
And no B-value of "0", which should be resistration template.
I think when converting nifti to NRRD, unintented b-value change occurs.
I have tired with other datasets from other subjects and found this always occurs.
This maybe a problem with DWIConvert module, but I just want to ask have you ever faced and fixed this problem.
Or could I send you a sample dataset of mine for you to take a look?
Minchul
Threaded View
| Title | Author | Date |
|---|---|---|
| minchulusa | Apr 19, 2017 | |
| Martin Styner | Apr 19, 2017 | |
| minchulusa | Apr 20, 2017 | |
| Martin Styner | Apr 20, 2017 | |
| minchulusa | Apr 20, 2017 | |
| Martin Styner | Apr 20, 2017 | |
| minchulusa | May 11, 2017 | |
| minchulusa | May 18, 2017 | |
| Martin Styner | May 18, 2017 | |
| Martin Styner | May 11, 2017 | |