Text archives Help
- From: eschn1@umbc.edu
- To: seg3d@sci.utah.edu
- Subject: [Seg3D] Re: Re: Re: Re: Re: Re: Mask Data Filter
- Date: Mon, 21 Jun 2010 10:39:26 -0400 (EDT)
- Importance: Normal
Hi Kris,
I wanna try ftping you two files (one session with an .img file that works
and another session with .tiff that doesn't) to your folder but right now
I do not have any login id for your ftp server so I am not authorized to
upload files. It also won't let me login anonymously. It there a way that
I can gain authorization to your ftp server so I can upload the two
sessions?
Elizabeth
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Hi Elizabeth,
>
I'm not really sure what is going on. It almost appears as though
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the mask you have created happens to grab values from the original image
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that are all the same value of 33195. Your window/level screenshot is a
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little perplexing to me as I am used to seeing a histogram plot at the
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top of the window/level tool panel and didn't see that in your
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screenshot. At this point there are a few things you can try, but these
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are guesses on my part:
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1. Try downloading the latest Seg3D 1.13 (I made a bad attempt at
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releasing 1.13 on April 16, that resided on the web for a few days until
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being resolved on April 22) and see if that helps at all.
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2. Try saving as some other file format from ImageJ or see what options
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are given when saving from ImageJ, maybe this is doing something
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unexpected to your data.
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3. Take the same set of requested screenshots and get the unmasked,
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segmentation and masked data volume information when working with a .img
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file that is successful, maybe we can see a difference between a data
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set that works for you and one that doesn't. Preferably, you could do
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this for the same data set using both the .img and the .tiff files.
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-Kris
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On 6/16/10 2:53 PM, eschn1@umbc.edu wrote:
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> Kris,
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> The info for the mask data volume is:
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> This is a data volume.
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> Origin: 0 0 0
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> Spacing: 1 1 1
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> Size: 148 120 120
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> Space: Unknown
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> Volume: 2.1312e+006
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> Min/Max: 0 33195
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>
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> I tried to ftp the session to you but the computer I work at won't allow
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> it, so I included the screen shot you asked for. Also, I adjusted the
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> window/level was to get it to show some of the different gray values.
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> Another thing to add about the scan I was working with: The CT scan was
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> originally a .img file but I needed to reorient it in ImageJ and then
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> saved it as a series of .tiff files( .img wasn't a save option). Seg3D
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> is
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> only doing this to files that I first altered in ImageJ and saved as a
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> series of .tiff files.
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>
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> Thanks again for your help.
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>
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> Elizabeth
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>> Hi Elizabeth,
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>> One other thing I forgot to ask for, can you also send the info
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>> for
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>> the masked data volume? As far as I can tell from what you've sent so
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>> far everything looks like it should be working. My current guess is
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>> that there are a very few discrete values in the masked data so that
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>> Seg3D applies a color map coloring these few discrete values the same
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>> and having the data appear to be binary. Would you mind saving your
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>> Seg3D session and ftp'ing to ftp.sci.utah.edu ? From there, please put
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>> the session file in upload/ForKris . If this is not possible, please
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>> select your masked data volume, open Tools->Window/Level Tool, and take
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>> a screenshot of the full Seg3D window. I'm hoping the histogram
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>> displayed by Window/Level Tool may give us some clues. You may also
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>> try
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>> adjusting the window/level yourself to see whether the masked data
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>> really is binary or is just being displayed that way.
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>>
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>> Thanks!
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>> Kris
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>>
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>> On 6/16/10 11:38 AM, eschn1@umbc.edu wrote:
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>>
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>>> Hi Kris,
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>>>
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>>> Thanks for your response. I use the exact same process that you use
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>>> for
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>>> Mask Data Filter so I don't have any different or additional steps to
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>>> add.
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>>>
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>>> The info for my label volume says:
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>>>
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>>> This is a label volume.
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>>> Origin: 0 0 0
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>>> Spacing: 1 1 1
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>>> Size: 148 120 120
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>>> Space: Unknown
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>>> Volume: 2.1312e+006
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>>> Label Count: 45284
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>>> Label Volume: 45284
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>>> Label Volume Percentage: 2.12481
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>>>
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>>> The info for my data volume says:
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>>>
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>>> This is a data volume.
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>>> Origin: 0 0 0
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>>> Spacing: 1 1 1
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>>> Size: 148 120 120
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>>> Space: Unknown
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>>> Volume: 2.1312e+006
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>>> Min/Max: 30451 37939
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>>>
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>>> I have also included some screen shots. Let me know if you need
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>>> anymore
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>>> information and thanks again for the help.
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>>>
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>>> Elizabeth Schneider
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>>>
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>>>
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>>>
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>>>
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>>>> Hello,
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>>>> I will need some more information to help troubleshoot this
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>>>> issue.
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>>>> Would you please click on the "i" button on the right-hand Volumes
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>>>> panel
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>>>> for both the label volume and data volume you are using and email the
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>>>> contents of the Volume Information that is displayed? I am
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>>>> specifically
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>>>> interested in the type of volume (it should say either "This is a
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>>>> data
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>>>> volume." or "This is a label volume.") and the Min/Max values.
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>>>>
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>>>> Here is the process I use for Mask Data Filter:
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>>>> 1. Create segmentation of data (will be stored in a label volume)
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>>>> 2. Open Mask Data Filter
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>>>> 3. Select the label volume containing the segmented data
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>>>> 4. Either click the Set Mask Label button from the Mask Data panel OR
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>>>> go
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>>>> to the Edit menu -> Set Mask Label
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>>>> 5. Select the data volume containing the data to be masked
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>>>>
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>>>> At this point, you should have the label volume highlighted in a
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>>>> salmon/pinkish color and the data volume highlighted in a purple
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>>>> color.
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>>>>
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>>>> 6. Click the Start button on the Mask Data panel
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>>>>
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>>>> Does this match what you are doing? If not, please also email the
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>>>> exact
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>>>> steps you perform related to using the Mask Data Filter.
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>>>> It also may be helpful if you can email four screenshots: one
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>>>> showing
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>>>> the segmented data, one showing the data that you want to mask, one
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>>>> showing the entire Seg3D window just before you click the Start
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>>>> button
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>>>> on the Mask Data panel, and one showing the result of the mask data.
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>>>>
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>>>> -Kris
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>>>>
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>>>> On 6/14/10 9:27 AM, eschn1@umbc.edu wrote:
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>>>>
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>>>>
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>>>>> Hello,
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>>>>>
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>>>>> I am having a problem with the Mask Data Filter. I am currently
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>>>>> using
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>>>>> Seg3D
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>>>>> version 1.13.0 and am still new to the program. My task is to
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>>>>> segment
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>>>>> pig
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>>>>> hearts from CT scans and create a gray scale mask of the pig heart.
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>>>>> I
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>>>>> have been
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>>>>> using the Mask Data filter to create my final mask of the heart but
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>>>>> the
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>>>>> weirdest thing keeps happening. The tutorial I have says that Mask
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>>>>> Data
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>>>>> is
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>>>>> supposed to create a gray scale mask but it will alternate between
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>>>>> giving me a
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>>>>> gray scale mask and a binary mask. I don't know what cause it to
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>>>>> switch
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>>>>> back
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>>>>> and forth. Right now all it's producing is binary masks when I use
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>>>>> it.
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>>>>>
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>>>>> Does anyone know how to get Mask Data to only create a gray scale
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>>>>> mask
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>>>>> (and no
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>>>>> binary masks) ?
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>>>>>
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>>>>>
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>>>>>
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>>>>
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>>>>
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>>>>
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>>
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>>
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>>
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- [Seg3D] Mask Data Filter, eschn1, 06/14/2010
- [Seg3D] Re: Mask Data Filter, Kristen Zygmunt, 06/15/2010
- [Seg3D] Re: Re: Mask Data Filter, eschn1, 06/16/2010
- [Seg3D] Re: Re: Re: Mask Data Filter, Kristen Zygmunt, 06/16/2010
- [Seg3D] Re: Re: Re: Re: Mask Data Filter, eschn1, 06/16/2010
- [Seg3D] Re: Re: Re: Re: Re: Mask Data Filter, Kristen Zygmunt, 06/18/2010
- [Seg3D] Re: Re: Re: Re: Re: Re: Mask Data Filter, eschn1, 06/21/2010
- [Seg3D] Re: Re: Re: Re: Re: Re: Re: Mask Data Filter, Kristen Zygmunt, 06/21/2010
- [Seg3D] Re: Re: Re: Re: Re: Re: Re: Re: Mask Data Filter, eschn1, 06/21/2010
- [Seg3D] Re: Re: Re: Re: Re: Re: Re: Re: Re: Mask Data Filter, Kristen Zygmunt, 06/21/2010
- [Seg3D] Re: Re: Re: Re: Re: Re: Re: Re: Re: Re: Mask Data Filter, Kristen Zygmunt, 06/22/2010
- [Seg3D] Re: Re: Re: Re: Re: Re: Re: Re: Re: Re: Re: Mask Data Filter, eschn1, 06/22/2010
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