[Kenneth Chan]

Here is a mod install file, please test. [file name=install_vista_7.gz size=1633]http://www.maldi-msi.org/images/fbfiles/files/install_vista_7.gz[/file]

Never mind, 7 would not let me have access to C:\Program Files\BioMap 🙁

Attachments:

• install_vista_7.gz

[Kenneth Chan]

Yep, don’t tell me, let me guess, you unzip the file and you try to run it normal, but it told you that you don’t have the privilege, so you try running it as admin, but you get the below error….

That’s because when you try to run a script as admin in Vista and 7, windows default your working directory to windows\system32 which is not where you want to be.

Here is my work around:[ol][li]Make sure you have admin privilege[/li][li]unzip BioMap to some directory[/li][li]Delete your current C:\Program File\BioMap, it must likely have lots of junk in it (req admin)[/li][li]make a NEW C:\Program File\BioMap (req admin)[/li][li]copy everything form the unzip BioMap folder and copy it into C:\Program File\BioMap (req admin)[/li][li]Run install-win.bat from inside C:\Program File\BioMap to complete the install(req admin)[/li][li]Run BioMap and get the licenserc by e-mail[/li][li]copy it to C:\Program File\BioMap (req admin)[/li][/ol]
Good luck

[Kenneth Chan]

Markus wrote:
[quote]Yes, we are currently building a tool for the FlashQuant systems which will output imzML. This code might then be ported to the 4000 Series software, if there should be a demand…[/quote]
demand! We actually consider FlashQuant for imaging, but didn’t have money + it will eat up time on our one and only 4000 trap. That said, we will have to port some of our ANALYZE codes:(

KC

[Kenneth Chan]

O, boy. Okay here is what you do.
[ol]
[li]open your file.[/li][li]Analysis > Plot > Point[/li][li]You will get the spectrum in the plot tool window.[/li][li]zoom into the m/z region you want to substract (190 for you)[/li][li]MIDDLE BUTTON click and drag on the matrix peak. A green bar will appear over your matrix peak.(middle button might be your scroll wheel)[/li][li]An pop up window will appear. You could play around with the Analysis Mode (I use Mean) And for the Output window, pick an empty window. That’s where your mean image (in your case the matrix divisor) will go. [/li][li]You should see a new image appear in the window you speced. On the bottom you should see something like “(mean:189.3432-191.3324)[/li][li]close the spectrum “Plot tool” window[/li][li]Here is the part I get wrong all the time. Highlight the file you open in step 1. This is your numerator. [/li][li]Tools > Calculation > Divide and the divide window will pop up[/li][li]Your Reference is the window with your matrix image. Output to an empty window. [/li][li]Wait.[/li][/ol]
Hope this is what you were looking for. If it works, send beer.

KC

[Kenneth Chan]

Hi LuLu,

Just woundering if m/z 190 is of a full scan data or if it is an extracted ion image (EII).

Because I think one of “value” in the division operation must be a “EII”. That is you can not divide 2 full data set. Hope it helps.

KC

[Kenneth Chan]

Like Markus said, get some training. Know what you are getting into. Take it from someone who has been bashing his head for the pass 2 year (off and on). The state of MSI is more art then science as especially when it comes to sample prep, you need a teacher to guide you in your first few steps.

I’ve went to the ASMS training course this year and learn more in those 2 days then I did the pass years. If you are lucky enough to be in the EU I think they have hands on training.

Good luck.

KC

[Kenneth Chan]

Yes it is!

I’ve ran BioMap on XP x64 & I am using Windows 7×64 right now. Plus I’ve seen it run on SUSE, but had permission issues.

KC

PS I didn’t write BioMap, just use it B)

[Kenneth Chan]

By lower do you mean the section that is run earlier? It might be matrix evaporation. In long runs (> 2hrs) matrix begins to sublimate this gives a “graded” intensity shift. It happen to us when we were using 2,6 DHA.

We sometime observe a sudden shift in intensity, making a “break” in intensity i.e. a bottom half is lighter than the top half for example. We can’t proof it, but we think it’s an instrument problem.

Hope it helps

[Kenneth Chan]

Check to see if there are any “.” in your file path.

[i]ie c:\desktop\brain[b][color=#FF0000].[/color][/b]1\slice.img[/i]

.net interpret this as a file and it gets confused; hence your [i]no valid header error[/i]
the work around is not to use any “.” in your file path. Hope it helps.

KC

[Kenneth Chan]

I’ve got the solution. use double quotes. Search and replace these two lines:

rem check if BioMap is installed in local directory
if "%ldir%"=="%bdir%" goto usave

if not "%ldir%"=="%SYSTEMROOT%" goto aask

[Kenneth Chan]

Hello everyone,

The problem is how windows batch files handles spaces. When windows encounters a space in the condition of an if statement, it expects to see an operator… even if it is around quotation marks. Open a command line window and try this:

Type :

If ‘bob’==’bob’ echo true

Then try:

If ‘bob is’==’bob is’ echo it will never work

The only work around is to make sure all the files are at the right place, rem out the first if statement and add the line goto usave

I’m sure there is another way to do this ie. Some env switch that will use short names, but I can’t find it….

KC

PS My message box is tiny!!!!

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