* Scott, Doug the debabeler conversion now gives the same coordinates as
mri_convert for this image. thats great thanks a lot to you both.
* Doug Greve: Here's our C source file that has our code. There's a lot of stuff there, but hopefully you can piece it together.
* Hi Doug,Thanks for sharing; you've obviously invested a lot of time in figuring out what's going on.I've been reading through the set of rules you posted, but I don't have enough experience (or test files) to correct the Debabeler translation. I can see Y and Z corrections that involve dPhaseFOV * sNormal.dCor, but it is not clear to me how it all comes together.I was wondering if you'd be willing to share a snipet of code that explains how to code it?Thanks for considering this request,Scott
* Doug Greve: 20,32 is where the first vox would have been had you collected a single slice centered at the center of the mosaic. So if the mosaic is 1.2 meters wide, then the 1st vox will be centered 0.6m from the center of the mosaic (and so outside of the scanner). I have put the full set of rules that I use here:
http://www.nmr.mgh.harvard.edu/~greve/dicom-unpack
* Doug Greve: I put quite a bit of
effort into getting mri_convert to accurately reflect the geometry. The
way that I test this is to collect multiple volumes at different
resolutions, FoVs, and slice prescriptions. If the geometry is accurate
(and the subject has not moved), then the matrix to map one volume to
another can be completely predicted from the geometry of the volumes.
This can be checked with tkregister2:
I've run this hundreds of times, and it is always extremely accurate. I
consider this test to be definitive. If you do not consider this a good
test or find a place where it fails, then please let me know. Until
then, I will assume that debabler is incorrect (meaning that I will
leave y'all to resolve the differences :).
I can tell you one more thing to help you though. As you point out, the
offsets given by the debabbler below are way outside of the FOV. Am I
right in assuming that this is data from a Siemens scanner and that the
volume has been mosaiced? If so, then you should know that the location
of the first voxel (tag 20 32) is incorrect. That value is where the
first voxel would have been had you collected a single slice the size of
the mosaic.
* I am endeavouring to make a DICOM -> NIFTI file conversion. The Scanner is a SIEMENS 3T scanner and I am converting mosaiced images. I am using two tools: FreeSurfer / mri_convert - out of the box; LONI / debabler (V 2.5) - not out of the box. What we did was combine a Mapping file which handles our mosaics when converting to analyze and a Mapping file that handles our non-mosaiced images when converting to nifti into a mapping file that handles our mosaics for nifti. All we think we have done is deal with the framework, not the actual coordinate
conversion code.
The two conversions give different results regarding coordinates.
I'm very sorry for the delay of my answer. Honestly, I would like to thank you once again by all your efforts! I should have told you this almost two weeks ago... Please accept my apologies!
I am sorry that my efforts have proven insufficient for you. But I feel obligated to inform you about two aspects of your data: 1. The black voxels are occurring because the creator of the ANALYZE files made a mistake. For example, in the file you ftp'ed to me, the minimum and maximum pixel values are given as (-32768,32767) when the real minimum and maximum is (-32896, 32767). Further, the creator used 16-bit precision when writing the data, so if the values are -32767, -32768, -32769, -32770 then the values written are -32767, -32768, 32767, 32766. This means that you must manually correct all values less than -32768. For example, in the code I last emailed you, you can add the lines:
if (s < -32768) {
int diff = -(32768 + s);
s = -32768 + diff;
}
after the line: int s = (b1 << 8) + (b2 << 0);
2. The ANALYZE file format does not contain information about the orientation of the images (there is no way to know if the images are upside down because no information exists in the file to tell us). ANALYZE files are a bad way to store patient images because we do not know left from right. The ANALYZE to DICOM translation assumes the images are oriented according to the SPM standard. Therefore, if the images are upside down or in the wrong orientation, you will need to manually correct it (hopefully all of your images are in the same orientation, so you will only need to do this once). This can be done by changing the -1,0 in the Debabeler module "Image Orientation" (whichis in the "Create DICOM Images" module. The -1,0 refer to directional cosines and set the orientation of DICOM element (0020,0037). If you read up on directional cosines or experiment with values -1,0,1, you should be able to change the orientation to your preference. But I should point out that the ANALYZE file you ftp'ed me appears to be in SPM orientation (although I can't tell if the patient's left/right is correct). You will probably find that different DICOM viewers display the same DICOM data differently (so look for the coordinate axes). Because of these two reasons, I conclude that you will not find an automatic conversion from ANALYZE to DICOM. Again, my apologies for not offering you a better solution. But perhaps the above two points will help you find what you are looking for.
Thank you so much for your efforts, but please realize they continue to be almost useless for me. First, because I have 39 CDs (each one approximately with 45 pairs of ANALYZE files), and also because, even after trying your scrip for only one .img file, the correspondent DICOM images appear upside down and with black voxels scattered on them... Please be sure I realize your assistance means precious time for you... But, if you know a better alternative for the conversion I need, please let me know!
The reason the DICOM images are black is that the data in the ANALYZE file is signed (both negative and positive values). The ANALYZE to DICOM translation only handles unsigned data values. I've attached a java program you can use to convert your .img file from signed to unsigned. Then the translations should work. Instructions are below.
1. compile: javac SignedToUnsigned.java
2. run: java SignedToUnsigned 003.1001.25may99.3d.vol.img temp.img
3. use new img: mv temp.img 003.1001.25may99.3d.vol.img (unix)
I believe the ANALYZE 7.5 image data type is short (16 bits per voxel), but please find attached a pair of files to confirm this information.
What is the datatype (byte, short, float) of the ANALYZE image?
Sorry for bothering you again, but now that I found the output images and tried to see them with a DICOM viewer (I tried eFilm, DicomWorks, and Cheshire), they appear completely black... I can't find anything on them, even after trying to adjust the window level!...
Thank you very much! I already realized what's happened. My mistake...and some inexperience... Sorry!
The DICOM files should be in the same directory the ANALYZE files are in. Perhaps an error occurred during the translation? If you scroll through the message box at the bottom, there may be an error message.
I tried several times to convert Analyze 7.5 image files into DICOM files. I used Debabeler 2.3 on a Windows XP environment for that purpose. First, I chose the xml file AnalyzeToDicom_10Sep2004 from the load mappings box, then I selected the input files and the output source (DICOM), and finally ran the program. Apparently, the translation occurred successful, but I can't find the output files?!...
I'm afraid this error indicates to me that the java installation is not correct on your linux box. I would recommend deinstalling java and then reinstalling it.
I´m trying very hard to have Debabeler working on my linux 64-bit machine, without succeeding. The linux console always gives the (long!) error message. Any hint? I do appreciate your help. It goes fantastic on my Windows system, but I would prefer to use the linux machine. By the way, hereś the architecture: Linux neuron 2.6.16-1.2133_FC5 #1 SMP Tue Jun 6 00:51:53 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux
neuron/usr/local/Debabeler/debabeler_2_5> ./run.sh
Exception in thread "main" java.lang.ExceptionInInitializerError
at java.lang.Class.initializeClass(libgcj.so.7)
at java.lang.Class.forName(libgcj.so.7)
at
edu.ucla.loni.afni.plugin.AFNIImageWriterSpi.class$(AFNIImageWriterSpi.java:42)
at
edu.ucla.loni.afni.plugin.AFNIImageWriterSpi.<init>(AFNIImageWriterSpi.java:54)
at java.lang.Class.newInstance(libgcj.so.7)
at gnu.classpath.ServiceProviderLoadingAction.run(libgcj.so.7)
at java.security.AccessController.doPrivileged(libgcj.so.7)
at
gnu.classpath.ServiceFactory$ServiceIterator.loadNextServiceProvider(libgcj.so.7)
at gnu.classpath.ServiceFactory$ServiceIterator.<init>(libgcj.so.7)
at gnu.classpath.ServiceFactory.lookupProviders(libgcj.so.7)
at
javax.imageio.spi.IIORegistry.registerApplicationClasspathSpis(libgcj.so.7)
at javax.imageio.spi.IIORegistry.<init>(libgcj.so.7)
at javax.imageio.spi.IIORegistry.getDefaultInstance(libgcj.so.7)
at edu.ucla.loni.imageio.DualIO.getFileNameAssociators(DualIO.java:39)
at
edu.ucla.loni.debabel.events.engine.SourceFileManager.<init>(SourceFileManager.java:40)
at
edu.ucla.loni.debabel.events.engine.DebabelerEngine.<init>(DebabelerEngine.java:145)
at
edu.ucla.loni.debabel.events.engine.DebabelerEngine.<init>(DebabelerEngine.java:133)
at
edu.ucla.loni.debabel.events.engine.DebabelerEngine.<init>(DebabelerEngine.java:118)
at
edu.ucla.loni.debabel.events.engine.DebabelerViewEngine.<init>(DebabelerViewEngine.java:77)
at
edu.ucla.loni.debabel.events.FrameEventHandler.<init>(FrameEventHandler.java:96)
at
edu.ucla.loni.debabel.events.FrameEventHandler.<clinit>(FrameEventHandler.java:57)
at java.lang.Class.initializeClass(libgcj.so.7)
at
edu.ucla.loni.debabel.DebabelerFrameManager.<init>(DebabelerFrameManager.java:49)
at
edu.ucla.loni.debabel.DebabelerFrameManager.<clinit>(DebabelerFrameManager.java:41)
at java.lang.Class.initializeClass(libgcj.so.7)
at edu.ucla.loni.debabel.Debabeler.start(Debabeler.java:56)
at edu.ucla.loni.debabel.Debabeler.main(Debabeler.java:131)
Caused by: java.lang.IllegalArgumentException: wrong child policy
at javax.imageio.metadata.IIOMetadataFormatImpl.<init>(libgcj.so.7)
at
edu.ucla.loni.imageio.AppletFriendlyIIOMetadataFormat.<init>(AppletFriendlyIIOMetadataFormat.java:41)
at
edu.ucla.loni.afni.plugin.AFNIMetadataFormat.<init>(AFNIMetadataFormat.java:45)
at
edu.ucla.loni.afni.plugin.AFNIMetadataFormat.<clinit>(AFNIMetadataFormat.java:38)
at java.lang.Class.initializeClass(libgcj.so.7)
...26 more
It is true that the ANALYZE file header does not contain orientation information. However, the Debabeler translation assumes that the ANALYZE file has been written using the SPM orientation, and so adds an orientation to the NIFTI file it creates. MRIcro apparently does notadd an orientation.
Thanks again for your explanation. As you said, when converting dicom file to analyze format, it loses the information about orientation, etc. As a result, there should not be any orientatin information in an analyze file header. So If I convert an analyze pair to nifti format using Debabeler and FSL, both results should not contain any orientation information(I think the results should be the same). But why the retult files are different and MRIcro only shows warning messages when opening the nifti file created by Debabeler? I attached an analyze pair and two nifti files created by Debabeler and FSL. Could you please take a look? dicom-1.img and dicom-1.hdr are the analyze files for test. dicom-1_FSL.nii was converted by FSL avwchfiletype dicom-1_Debabeler.nii was converted by Debabeler using AnalyzeToNifti_18Feb2005.xml mapping file. Thank you very much.
Technically, both the Debabeler and FSL avwchfiletype programs are mapping the NIFTI fields correctly. The Debabeler uses the "recommended" method, whereas FSL avwchfiletype uses the old ANALYZE method (which created problems and motivated people to define NIFTI!). Please keep in mind that the ANALYZE file format does not contain information about the orientation of the scanned subject. When someone sends you an ANALYZE file, you cannot be sure which way the subject's right/left are. Yes, there is a hard-to-find implicit assumption as to what the orientation is, but in reality few people follow it (e.g., radiologists and neurologists flip right/left and create ANALYZE files the way they want to). I expect that the MRIcro warnings are telling you that you have some type of orientation problem with your data. When you created your ANALYZE file, you effectively removed the orientation and lost the ability to determine the subject's left/right. So you might get rid of the warnings by first converting to ANALYZE, but you may in effect be deceiving yourself by removing information that you should know. You can read more about the NIFTI standard by going to their web site and downloading the C source code (look at the comments in nifti1.h). For your convenience, I have attached to this email a segment from that file that I think is relevant here.
Thanks for your response. The nifti file converted with the mapping xml you sent me can be opened by fslview. However, MRICro(Windows version) still gives warning message. So I did the following test: I converted a dicom file to analzye format using debabler. Then I converted the analyze file to nifti format using both debabeler and avachfiletype(a tool in FSL). I found that the nifti file converted by FSL/avwchfiletype can be opened by MRICRO without any warning message while the one converted by debabeler can not. I checked the fields in the header of the two nifit files(converted with debabeler and FSL avwchfiletype). I found that the following fields are different: qform_code: 1(debabeler) 0(avwchfiletype) || scl_slope: 0(debabeler) 1(avwchfiletype) Does this indicate either debabeler or FSL avwchfiletype maps the fields in NIFTI header incorrectly?
I converted the Siemens Mosaic DICOM file you sent to NIFTI and tried it in FSLview. The message I saw was: This program has not been compiled for this data type Finished which means that FSLview doesn't support 16-bit unsigned short data. But your data doesn't need that precision. So I tried specifying it as 16-bit signed data and it worked for me; please see the attached. (If you compare the attached translation with the one you have, the only difference is that the "datatype" is now 4 instead of 512). As for MRIcro, I downloaded the linux version but I don't see any option to load a NIFTI file. At any rate, I think the message is warning you that you are attempting to combine two data sets that are not in the same 3d space. So it doesn't appear to be a file conversion issue.
I found that the Nifti file converted by using AnalyzeToNifti_18Feb2005.xml can not be opened with FSLview. Another viewer, MRICRO can open the file but shows some warning messages below: The Nifti file specifies an affine rotation [QForm>0]. MRICro will display the raw data. Warning: The nifti image includes a rotation transformation. You should reslice the data before attempting overlay the image. Also the same problem occurs when using DicomSiemensMosaicToOneFileNifti_05Apr2006.xml to convert Siemens Mosaic Dicom data to Nifti format. I have attached two dicom files I tried to convert. One is in standard dicom format, the other is in siemens mosaic dicom format. Could you please have a look?
Yes, you can specify it to be whatever you like. Please see the Debabeler_Usage.pdf in the doc directory, bottom of page 13.
Thank you for your help. DicomSiemensMosaicToAnalyze_10Sep2004.xml does not work for my data. It works when using xml/contrib/RogerMosaicAndRegular_24Nov2004.xml. Is there a way to change the default output files' location in RogerMosaicAndRegular_24Nov2004.xml?
Have you tried the translations: xml/contrib/RogerMosaicAndRegular_24Nov2004.xml xml/DicomSiemensMosaicToAnalyze_10Sep2004.xml in the Debabeler XML directory? If these don't work, I may have to ask you for a sample of your data to make a better determination.
I am trying to use LONI Debabler to convert EPI fMRI dicom data to analyze or nifti format. However I found that debabeler can not convert them correctly using the existing mappings. Is there a way to customize the mapping so that it can recognize and convert epi fMRI data or do you have any mapping xml file for epi fmri dicom conversion?
Fantastic!! Thank you. I will recommend your software to others. Really appreciate all your help!
That's a pretty big file; you will need to increase the memory to process it. If you go to your Debabeler directory, you need to edit the file called "run.bat". Open up an editor and change: -Xmx200M to -Xmx800M and try it again.
I can do that. I temporarily have access to a folder through ASU where I could upload the file and you could get it.
I guess I'd have to see the analyze file. Would you be willing to ftp it to me? Info below. Since there is very little info in the analyze file, producing DICOM files that work with your software seems unlikely, although I guess you can try.
Thanks, Scott. I did include all the textual output. It just ends there and doesn't seem to want to complete the translation. Any advice? Unfortunately, I don't have original DICOM files and the modeling software I'm using doesn't accept Analyze input, only DICOM.
It doesn't look like you included all the textual output, so I don't see any error (unless it just hung). In general, converting from ANALYZE to DICOM is a very bad thing to do. If you have access to the original DICOM files, I recommend that you use those.
Hi, I'm a researcher at Arizona State University and I'm trying desperately to convert Analyze files to DICOM format with your Debabeler, but I must be doing something wrong. I load the mappings for Analyze->DICOM and then I select the .hdr and .img files that are in Analyze format as the input files and then I select output as DICOM and then I press Debabel. These are the results I get and the files are not translated. HELP! Thank you!!
LONI Debabeler 2.5
Registered the mapping "Source Identification".
Registered the mapping "ANALYZE Group Assignment".
Registered the mapping "ANALYZE to DICOM Translation".
----------
BEGIN: Determine the names of the sources that produced the input
files.
Identified the source "analyze_source" for the files:
/C:/Documents and Settings/cschrei/WinRAR decomp Chimp
scans/pan_troglodytes_amnhL14CH2_rawvol.hdr
/C:/Documents and Settings/cschrei/WinRAR decomp Chimp
scans/pan_troglodytes_amnhL14CH2_rawvol.img
Number of successfully identified sources = 1.
END: Determine the names of the sources that produced the input files.
----------
BEGIN: Determine how the input files are grouped together.
Assigned the group id "/C:/Documents and Settings/cschrei/WinRAR decomp
Chimp scans/pan_troglodytes_amnhL14CH2_rawvol.hdr" to the files:
/C:/Documents and Settings/cschrei/WinRAR decomp Chimp
scans/pan_troglodytes_amnhL14CH2_rawvol.hdr
/C:/Documents and Settings/cschrei/WinRAR decomp Chimp
scans/pan_troglodytes_amnhL14CH2_rawvol.img
Number of group ids successfully assigned = 1.
END: Determine how the input files are grouped together.
----------
BEGIN: Convert the input file groups into output files of the target.
Number of groups to translate = 1.
It is unlikely because 99% of usage involves DICOM -> ANALYZE conversions (not ANALYZE -> DICOM). This is because scanners output DICOM and most people start with that. The conversion DICOM -> ANALYZE loses 95% of the information. So converting back to DICOM is somewhat difficult to do.
Thank you for your fast response. Do you think to develop this functionality in an immediate future?
That option is not currently available. Sorry for the inconvenience.
We would like to translate SPM files from fMRI experiments (450 volumes each of them 32 slices) to DICOM files We try your Analyze>DICOM translator but it outputs 450*32 dcm files (we expect 450 dcm files) Could you explain us how to parameterize the translator if the option is available
UPDATE: The Inspector is now available for viewing metadata from many different file formats.
Here are answers to your questions (in order):
1) The DiD removes the patient name and other strings from each file. The birthdate and study dates/times are not removed. Numbers are not removed if they are not stored as strings.
2) The image data is not modified in any way.
3) We typically use an in-house tool to view metadata. It has bugs and therefore is not available to the public. I don't know that much about other tools out there.
4) Type "java -jar loniDeidentifyDebablet.jar -help" for the command line options. Each time you run with command line options, each file you specify will receive the unique id you specify. To assign many unique ids, you must execute a command for each unique id.
I am using the LONI DiD bablet to de-identify GE Genesis files as well as ANALYZE files and have a few of questions:
1) Does the DiD algorithm only removes names from the header, not numbers? (i.e. birthdate)
2) What, if anything, does the DiD algorithm do to the image data?(Does is "scramble" the skull voxels?)
3) What tool do you recommend using to verify that all HIPPAA data has been removed from the header after running the DiD bablet?
4) How can I batch files to be de-identified and assign unique IDs to each file?
Sorry, I don't have a 4D translation. The images displayed in MRIcro are up to MRIcro; different viewers will show them differently.
Thanks, this works well. How about creating a 4D stack from the Siemens Mosaic Dicom volumes? BTW, when I look at the .nii files with MRIcro, they are upside down. Could you please explain?
Please give this a try.
Is there a DicomSiemensMosaictoOneFileNIFTI conversion available? I have read that SPM5 can read these.
It wasn't the file name, the number "-0.3842953174286 " was stuck in a DICOM field that is defined to be at most 16 characters (it has 17). I removed the 16 character check.
That did the trick. Do you think that the file name issue is peculiar to our Siemens equipment? Should I let them know? BTW, MRIcro shows the image rotated 180 degrees. I presume there is another viewer for NIFTI files..........
It looks like the space after that negative number is causing problems. I've removed the restriction on the size; please try the attachment.
I enclose the output from Debabeler from an attempt to translate one of the Siemens Mosaic files in Part 10 format to 2 file NIFTI. Any ideas? Do you need me to send one of the images?
LONI Debabeler 2.4
Registered the mapping "Source Identification".
Registered the mapping "Siemens Mosaic DICOM Group Assignment".
Registered the mapping "Siemens Mosaic DICOM to 2-File NIFTI Translation".
----------
BEGIN: Determine the names of the sources that produced the input files.
Identified the source "siemens_mosaic_dicom" for the files:
/C:/Documents and Settings/JAY/Desktop/Motor fMRI/03311143/27590773
Number of successfully identified sources = 1.
END: Determine the names of the sources that produced the input files.
----------
BEGIN: Determine how the input files are grouped together.
Assigned the group id "/C:/Documents and Settings/JAY/Desktop/Motor fMRI/03311143/27590773" to the files:
/C:/Documents and Settings/JAY/Desktop/Motor fMRI/03311143/27590773
Number of group ids successfully assigned = 1.
END: Determine how the input files are grouped together.
----------
BEGIN: Convert the input file groups into output files of the target.
Number of groups to translate = 1.
* Source Loading Error
...[ Unable to set data. ]...
...[ Could not map values from the DOM tree "edu_ucla_loni_jdicom_stream_1.0" to the Metadata Tree "edu_ucla_loni_jdicom_stream_1.0". ]...
...[ Could not map values from the DOM tree "DATA_SET" to the Metadata Tree "DATA_SET". ]...
...[ Could not map values from the DOM tree "00200037" to the Metadata Tree "00200037". ]...
...[ Could not map values from the DOM tree "VALUE" to the Metadata Tree "VALUE". ]...
...[ The value "-0.3842953174286 " does not satisfy the restriction "Range Restriction". ]...
* Unable to decode and read data for "siemens_mosaic_dicom" from the files:
...[ /C:/Documents and Settings/JAY/Desktop/Motor fMRI/03311143/27590773 ]...
* Group Translation Error
...[ Unable to load all the source data. ]...
* Unable to translate (siemens_mosaic_dicom) to (two_file_nifti) involving the files:
...[ /C:/Documents and Settings/JAY/Desktop/Motor fMRI/03311143/27590773 ]...
Number of successful translations = 0.
END: Convert the input file groups into output files of the target.
I've downloaded your Debabeler software to convert my Siemens mosaic fMRI data to NIFTI. It works fine if the input data is in the Siemens native .ima format, but not for the DICOM outputted format ( Part 10 I presume)which I burned to a CD with its Dicomdir. There are input errors during the translation phase. Can you please advise?
Statistics for Debabeler Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 8822 0 ...
Debabeler Web Preferences The following settings are web preferences of the Debabeler web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...
UPDATE: The Inspector is now available for viewing metadata from many different file formats. Here are answers to your questions (in order): 1) The !DiD removes the ...
Contact Information Scott Neu Laboratory of Neuro Imaging (LONI) Email: neu@loni.ucla.edu (Include the word "Debabeler" in the email subject line) NEVER email files ...
Scott, Doug the debabeler conversion now gives the same coordinates as mri convert for this image. thats great thanks a lot to you both. Doug Greve: Here's our C ...
I'm very sorry for the delay of my answer. Honestly, I would like to thank you once again by all your efforts! I should have told you this almost two weeks ago.. ...
Sorry, I don't have a 4D translation. The images displayed in MRIcro are up to MRIcro; different viewers will show them differently. Thanks, this works well. How ...
I'm afraid this error indicates to me that the java installation is not correct on your linux box. I would recommend deinstalling java and then reinstalling it. I ...
It is unlikely because 99 of usage involves DICOM ANALYZE conversions (not ANALYZE DICOM). This is because scanners output DICOM and most people start with that ...
It is true that the ANALYZE file header does not contain orientation information. However, the Debabeler translation assumes that the ANALYZE file has been written ...
Fantastic!! Thank you. I will recommend your software to others. Really appreciate all your help! That's a pretty big file; you will need to increase the memory to ...
This is a subscription service to be automatically notified by e-mail when topics change in this Debabeler web. This is a convenient service, so you do not have to ...
INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ...
TWiki's Debabeler web SCRIPTURL /view SCRIPTSUFFIX /Debabeler The Debabeler web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE ...
Scott, Doug the debabeler conversion now gives the same coordinates as mri convert for this image. thats great thanks a lot to you both. Doug Greve: Here's our C ...
I'm very sorry for the delay of my answer. Honestly, I would like to thank you once again by all your efforts! I should have told you this almost two weeks ago.. ...
I'm afraid this error indicates to me that the java installation is not correct on your linux box. I would recommend deinstalling java and then reinstalling it. I ...
It is true that the ANALYZE file header does not contain orientation information. However, the Debabeler translation assumes that the ANALYZE file has been written ...
Fantastic!! Thank you. I will recommend your software to others. Really appreciate all your help! That's a pretty big file; you will need to increase the memory to ...
It is unlikely because 99 of usage involves DICOM ANALYZE conversions (not ANALYZE DICOM). This is because scanners output DICOM and most people start with that ...
UPDATE: The Inspector is now available for viewing metadata from many different file formats. Here are answers to your questions (in order): 1) The !DiD removes the ...
Sorry, I don't have a 4D translation. The images displayed in MRIcro are up to MRIcro; different viewers will show them differently. Thanks, this works well. How ...
Contact Information Scott Neu Laboratory of Neuro Imaging (LONI) Email: neu@loni.ucla.edu (Include the word "Debabeler" in the email subject line) NEVER email files ...
INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ...
This is a subscription service to be automatically notified by e-mail when topics change in this Debabeler web. This is a convenient service, so you do not have to ...
Debabeler Web Preferences The following settings are web preferences of the Debabeler web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ...
TWiki's Debabeler web SCRIPTURL /view SCRIPTSUFFIX /Debabeler The Debabeler web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE ...
Statistics for Debabeler Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 8822 0 ...
This is a subscription service to be automatically notified by e-mail when topics change in this Debabeler web. This is a convenient service, so you do not have to come back and check all the time if something has changed. To subscribe, please add a bullet with your WikiName in alphabetical order to this list:
Format: TWiki handles entries in bullet list (<space><space><space>*) format containing the WikiName of a user; a WikiName with e-mail address; or a TWikiGroup. Examples:
Main.FredBloggs
Main.FredBloggs - secondary@home.com
Main.EngineeringGroup
The first entry is the default form, the notification gets sent to the e-mail address specified in the user's home page. The second entry lists an alternative e-mail address. The third entry specifies a group, the notification gets sent to each member of the group.
Related topics:WebChangesAlert, TWikiUsers, TWikiRegistration
The following settings are web preferences of the Debabeler web. These preferences overwrite the site-level preferences in TWikiPreferences, and can be overwritten by user preferences (your personal topic, eg: TWikiGuest in the Main web).
Preferences:
If yes, set SITEMAPLIST to on, do not set NOSEARCHALL, and add the "what" and "use to..." description for the site map. Make sure to list only links that include the name of the web, e.g. Debabeler.Topic links.
Set SITEMAPLIST = on
Set SITEMAPWHAT = Debabeler Site
Set SITEMAPUSETO = ...find information about the Debabeler
Exclude web from a web="all" search: (Set to on for hidden webs)
Set NOSEARCHALL =
Prevent automatic linking of WikiWords and acronyms (if set to on); link WikiWords (if empty); can be overwritten by web preferences:
Set NOAUTOLINK =
Note: Use the [[...][...]] syntax to link topics in case you disabled WikiWord linking. The <noautolink> ... </noautolink> syntax can be used to prevents links within a block of text.
Default template for new topics and form(s) for this web:
WebTopicEditTemplate?: Default template for new topics in this web. (Site-level is used if topic does not exist)
A preference is defined as: 6 spaces * Set NAME = value Example:
Set WEBBGCOLOR = #FFFFC0
Preferences are used as TWikiVariables by enclosing the name in percent signs. Example:
When you write variable %WEBBGCOLOR% , it gets expanded to #cc99cc .
The sequential order of the preference settings is significant. Define preferences that use other preferences first, i.e. set WEBCOPYRIGHT before WIKIWEBMASTER since %WEBCOPYRIGHT% uses the %WIKIWEBMASTER% variable.
You can introduce new preferences variables and use them in your topics and templates. There is no need to change the TWiki engine (Perl scripts).
TWiki's Debabeler web
http://www.loni.ucla.edu/twiki/bin/view/Debabeler
The Debabeler web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World.en-usCopyright 2009 Laboratory of Neuro Imaging, UCLA.TWiki Administrator [webmaster@loni.ucla.edu]TWiki Administrator [webmaster@loni.ucla.edu]TWikiTWiki.DebabelerLONI Wiki Home.Debabeler
http://www.loni.ucla.edu/twiki/bin/view/Debabeler
http://www.loni.ucla.edu/~dhasson/images/LONI_Collab_wh_60h.gifWebStatistics
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebStatistics?t=2009-11-22T13:18Z
Statistics for Debabeler Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and uploads: Nov 2009 8822 0 ... (last changed by guest)2009-11-22T13:18Zguest1.983updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebStatisticshttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebStatisticsWebPreferences
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebPreferences?t=2007-08-17T01:24Z
Debabeler Web Preferences The following settings are web preferences of the Debabeler web. These preferences overwrite the site-level preferences in TWIKIWEB . WIKIPREFSTOPIC ... (last changed by DavidHasson)2007-08-17T01:24Zdhasson1.11updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebPreferenceshttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebPreferences31_Jan_2007
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/31_Jan_2007?t=2007-07-24T15:56Z
UPDATE: The Inspector is now available for viewing metadata from many different file formats. Here are answers to your questions (in order): 1) The !DiD removes the ... (last changed by sneu)2007-07-24T15:56Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/31_Jan_2007http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/31_Jan_2007WebHome
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebHome?t=2007-07-24T15:42Z
Contact Information Scott Neu Laboratory of Neuro Imaging (LONI) Email: neu@loni.ucla.edu (Include the word "Debabeler" in the email subject line) NEVER email files ... (last changed by sneu)2007-07-24T15:42Zsneu1.6updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebHomehttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebHome14_Dec_2006
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/14_Dec_2006?t=2007-05-30T23:37Z
Scott, Doug the debabeler conversion now gives the same coordinates as mri convert for this image. thats great thanks a lot to you both. Doug Greve: Here's our C ... (last changed by sneu)2007-05-30T23:37Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/14_Dec_2006http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/14_Dec_200616_Nov_2005
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/16_Nov_2005?t=2006-07-27T22:51Z
I'm very sorry for the delay of my answer. Honestly, I would like to thank you once again by all your efforts! I should have told you this almost two weeks ago.. ... (last changed by sneu)2006-07-27T22:51Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/16_Nov_2005http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/16_Nov_200531_Mar_2006
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/31_Mar_2006?t=2006-07-27T22:27Z
Sorry, I don't have a 4D translation. The images displayed in MRIcro are up to MRIcro; different viewers will show them differently. Thanks, this works well. How ... (last changed by sneu)2006-07-27T22:27Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/31_Mar_2006http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/31_Mar_200619_Jun_2006
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/19_Jun_2006?t=2006-07-27T22:15Z
I'm afraid this error indicates to me that the java installation is not correct on your linux box. I would recommend deinstalling java and then reinstalling it. I ... (last changed by sneu)2006-07-27T22:15Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/19_Jun_2006http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/19_Jun_200630_Jun_2006
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/30_Jun_2006?t=2006-07-27T22:10Z
It is unlikely because 99 of usage involves DICOM ANALYZE conversions (not ANALYZE DICOM). This is because scanners output DICOM and most people start with that ... (last changed by sneu)2006-07-27T22:10Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/30_Jun_2006http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/30_Jun_200621_Jun_2006
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/21_Jun_2006?t=2006-07-27T21:59Z
It is true that the ANALYZE file header does not contain orientation information. However, the Debabeler translation assumes that the ANALYZE file has been written ... (last changed by sneu)2006-07-27T21:59Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/21_Jun_2006http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/21_Jun_200627_Jul_2006
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/27_Jul_2006?t=2006-07-27T21:32Z
Fantastic!! Thank you. I will recommend your software to others. Really appreciate all your help! That's a pretty big file; you will need to increase the memory to ... (last changed by sneu)2006-07-27T21:32Zsneu1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/27_Jul_2006http://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/27_Jul_2006WebNotify
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebNotify?t=2004-08-28T07:30Z
This is a subscription service to be automatically notified by e-mail when topics change in this Debabeler web. This is a convenient service, so you do not have to ... (last changed by PeterThoeny)2004-08-28T07:30ZPeterThoeny1.4updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebNotifyhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebNotifyWebLeftBar
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebLeftBar?t=2004-08-16T05:52Z
INCLUDINGWEB Web INCLUDINGWEB Web Home Changes Index Search Webs WEBLIST{" $name" separator ""} INCLUDE{" MAINWEB . WIKINAME LeftBar" warn "Create personal sidebar ... (last changed by ArthurClemens)2004-08-16T05:52ZArthurClemens1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebLeftBarhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebLeftBarWebRss
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebRss?t=2004-08-16T03:27Z
TWiki's Debabeler web SCRIPTURL /view SCRIPTSUFFIX /Debabeler The Debabeler web of TWiki. TWiki is a Web-Based Collaboration Platform for the Corporate World. INCLUDE ... (last changed by PeterThoeny)2004-08-16T03:27ZPeterThoeny1.2updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebRsshttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebRssWebSearchAdvanced
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebSearchAdvanced?t=2004-01-18T10:52Z
INCLUDE{" TWIKIWEB .WebSearchAdvanced"} (last changed by PeterThoeny)2004-01-18T10:52ZPeterThoeny1.1updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebSearchAdvancedhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebSearchAdvancedWebIndex
http://www.loni.ucla.edu/twiki/bin/view/Debabeler/WebIndex?t=2001-11-24T11:41Z
SEARCH{"\. " scope "topic" regex "on" nosearch "on"} See also the faster WebTopicList (last changed by PeterThoeny)2001-11-24T11:41ZPeterThoeny1.2updatedmajorhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebIndexhttp://www.loni.ucla.edu/twiki/bin/rdiff/Debabeler/WebIndex
