Hi All,

I am trying to run LesionToads on T1 SPGR and Flair for MS lesion segmentation, and when I click "Ok" it pops up with "Atlas File - No Lesion - T1 Only: Value None is invalid." Can any one please suggest where am I going wrong. I have not changed any default options. Am I suppose to provide any atlas related *.txt file under "Atlas Files" tab option?

Thanks,
Sneha

Hi Sneha,

Did you get response related to your query?
Can you please clarify what  *txt files in Atlas you used for Atlas file with lesions, no lesion T1 and flair and no lesion T1 only?

Thanks!

Hi Ankita,

No one has responded to this query yet and thank you for your response.

I am selecting following files as my inputs:

Main inputs:
1. T1_SPGR and Flair image
2. Atlas to use: No lesions
3. Output images: hard segmentations+memberships
4. Output max membership classification/ Correct inhomogeneity/ Output inhomogeneity field: unchecked

Atlas file:
By default Atlas file with lesions, no lesion T1 and flair fields had pre-selected *.txt files and no lesion T1 only was empty. I kept the default *txt for Atlas file with lesions, no lesion T1 and flair and selected "/mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt" file for no lesion T1 only. Following are all the files
1. Atlas file - With lesions: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-lesiontoads2012.tx
2. Atlas file - No lesions - T1 and Flair: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt
3. Atlas File- no lesion - T1 only: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt

For lesion options and Advance options tabs I have kept the defaults.

Can you please suggest if I have entered wrong inputs or if anything is missing?

Thanks,
Sneha

Hi Sneha

Thanks for your response. Are you looking at healthy subjects ?
I am changing few parameters for depending upon healthy or diseased population.

Hi Anikta,

No these are MS patients.

Thanks,
Sneha

Hi Sneha,

Sorry for the delayed response. I am surprised how are you getting any lesion quantification in MS by using "no lesion" atlas? I tried that but when i use "no lesion atlas" my Toad cruise lesion output comes out to be empty.

Please note that I am referring to the following step:

Atlas to use: No lesions

Dear Ankita,

Thank you for your response. I am not able to succeed until I choose *.txt file as it gives me an error that no atlas has been chosen. If I select with lesions option can you please suggect which *txt files in Atlas to use for Atlas file with lesions, no lesion T1 and flair and no lesion T1 only?

I selected following .txt files and I do not get any output.
1. Atlas file - With lesions: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-lesiontoads2012.tx
2. Atlas file - No lesions - T1 and Flair: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt
3. Atlas File- no lesion - T1 only: /mipav/plugins/Atlas/lesionToads-atlas-2012/cruise-atlas-12obj-toads2012.txt

For main inputs I have selected:
1. Output images: hard segmentations+memberships
2. Output max membership classification/ Correct inhomogeneity/ Output inhomogeneity field: unchecked

All I get is lesion+toads.input output.

Thanks,
Sneha

Dear Sneha Pandya,

I am pretty new to MIPAV. May I ask what "atlas list" means? Where can I get or download it?
while trying to run spectre, I am required to provide "atlas list" 
I would really appreciate it if someone can help me out.

Thanks,
Hank

If I remember correctly, the atlas list should contain the names of a group of T1 images and corresponding binary masks that have been modified to include only brain tissue. These images will be registered to your input scan to create a probability mask, basically using info from the atlas volumes to inform segmentation of brain from dura and other intracranial structures. It should be included in TOADS-CRUISE, but you can also download the atlas and text file here: http://www.nitrc.org/frs/?group_id=271 (save the file named SPECTRE_ATLASES-v2.tar.gz, as the others do not seem to work). When SPECTRE asks for an atlas file, point it to the text file and corresponding directory of atlas images.

I hope that helps!

Jen

Dear Jen,

thanks for your quick reply! I successfully download it.

Hank

Great! I hope SPECTRE works well for you!

Jen

Hi Jen,

please let me ask some more questions.

I can run SPECTRE after I chose a T1 image as a input, and send in "oasis-3-v2.txt" in the file you asked me to download for Atlas List.
But I can get any output result. Something wrong with system? We are supposed to get a stripped image after we finish SPECTRE?

Thanks,
Hank

Hi Hank,

I have passed your question to a colleague who may be able to help you more quickly than I can. If not, I will take a look at this and try to help you when I get home.

Jen

Originally posted by Hsiu-Wei Yang: