http://cmrm.med.jhmi.edu/cmrm/forumMRI/ Diffusion Tensor Imaging en Thu, 17 May 2012 08:35:35 +0000 http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=118#post-221 Sun, 06 May 2012 21:15:11 +0000 JDH37 221@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>After saving a region of interest drawn in the 'ROI tab' (I've been saving as graphic compatible and binary images), how do you then open that file in the 'Fiber tab'?</p> <p>Thanks in advance for the help. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=116#post-217 Tue, 29 Nov 2011 21:03:24 +0000 necessca 217@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello,</p> <p>Would someone provide me with guidance on interpreting the IQC Flag file Output from DTI Studio?</p> <p>Thanks in advance,<br /> Abbie </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=115#post-216 Thu, 01 Sep 2011 16:36:45 +0000 chasiubao73 216@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Greetings,</p> <p>When I calculate the ADC map, it seems the ADC map mean has disappeared from the drop down menu. A few of my colleagues has also experienced this. Has anybody else encounter.</p> <p>Thank you for any suggestions and all your hard work. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=114#post-215 Wed, 03 Aug 2011 17:48:55 +0000 Zhipeng 215@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p><a href="http://162.129.247.245/Protocol/DTS/Tutorial/iPad.htm" rel="nofollow">http://162.129.247.245/Protocol/DTS/Tutorial/iPad.htm</a> </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=113#post-212 Fri, 22 Jul 2011 20:08:40 +0000 chasiubao73 212@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Greetings,</p> <p>We have a question about the AIR Linear co-registration step that we perform. We are doing an atlas (Eve)to subject AIR Linear transformation. What happens is that we have noticed that the resultant brain image is almost identical to the original Eve atlas brain. </p> <p>We have done the necessary pre-processing steps to ensure that the background noise and skull stripping are as matched closely to one another as much as possible.</p> <p>Any suggestions as to why our atlas to subject registration yields a resultant image almost identical to the original starting Eve brain?</p> <p>Thank you for all your assistance in our research endeavors. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=112#post-210 Tue, 19 Apr 2011 18:54:04 +0000 rwrigh21 210@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>I would like to register an image to a T1-MRI template using the Volume LDDMM in DiffeoMap, but when I click on the Single channel button, I get the following error: "The template should be an isotropic image". What does this mean?</p> <p>Thanks,<br /> Rika </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=110#post-207 Sat, 05 Feb 2011 23:46:53 +0000 chasiubao73 207@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Greetings,</p> <p>Thank you for the wonderful forum site and software. I am wondering if there is a detailed atlas with the name of neuroanatomical structure that corresponds to each of the region of the ROI parcellated WMPM maps that we see in ROIeditor. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=64#post-94 Tue, 11 May 2010 22:35:45 +0000 yongzhangdti 94@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hi,</p> <p>According to the user manual, we need to build makeaheader.exe, alignlinear.exe and align_warp.exe by ourselves in order to use Automatic Image Registration in DiffeoMap. Just wonder if there are pre-compiled binary files for those who don't have access to Microsoft Visual C++. Many thanks for any relevant information!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=108#post-202 Tue, 02 Nov 2010 14:45:59 +0000 chasiubao73 202@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Greetings,</p> <p>I am having a bit of difficulty loading the my images into DIFFEO Map. I saved the DICOM files as raw data and when I try to load my images inti DIFFEO Map, I get the following error:</p> <p>"The image you want to load must have the same dimensions and orientations as the other images in the image list."</p> <p>My image parameters are correct. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=106#post-196 Fri, 10 Sep 2010 17:12:38 +0000 shaan2k11 196@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello, </p> <p>I have certain pre-defined ROIs in NIFTI file format that I want to use as ROI in DTI Studio. But I did not find any option for loading it in the ROI panel. I tried converting the NIFTI file into Raw data and using the ROI panel load function. But, it did not work either. Could you please suggest a workaround?</p> <p>Thanks,<br /> Shantanu </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=104#post-189 Wed, 11 Aug 2010 17:25:53 +0000 yongzhangdti 189@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Dear everyone,</p> <p>We performed the AIR-based rigid-body registration before tensor calculation. There was not much translation (~0.2-0.5 mm) and rotation as we observed from the saved transformation file. However, the registered raw diffusion weighted images were a lot smoother and had much less contrast compared to those without registration. Hangyi mentioned there was no internal smoothing associated with the rigid-body registration. Just wonder if the tri-linear interpolation alone can cause this. Our raw diffusion weighted images were acquired with a 128x128 matrix and the in-plane resolution is 1.5x1.5 mm. </p> <p>We observed ~16% decrease in FA,~15% decrease in Eigen Value 0, ~12% decrease in Eigen Value 1, ~19% increase in Eigen Value 2. Just wonder if anybody else experienced the same issue. We also tried the gradient adjustment option but there was not much change. So far we suspect that the interpolation associated with registration could be a major cause. Any suggestion will be greatly appreciated!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=67#post-103 Fri, 14 May 2010 02:26:33 +0000 wayne_qin 103@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello, every one. I encounter a question about the gradient vetors. The individual vectors extracted from the DICOM data seem some what different with the standard vectors provided by company. I have tried to use them to calculate the diffusion indices such as FA and MD,respectively. Diversities ranging from 0.5% to 5% were also manifested. My question are: what's the reason and which is best for the tensor calculation?<br /> Thanks! </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=105#post-190 Wed, 18 Aug 2010 01:34:45 +0000 chasiubao73 190@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hi,</p> <p>Does the generated FA map follow neurological (left to left and right to right) or radiological convention (left to right and right to left)in DtiStudio. I am asking just to confirm because I am having matching FA values on DtiStudio where the left FA value matches to the right FA value on another generated FA map. Neither FA maps has undergone any sort of processing via another software. The FA maps were generated from DICOM. I was under the assumption that DtiStudio follows a radiological convention.</p> <p>Thanks all for the great software </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=103#post-183 Mon, 02 Aug 2010 20:21:48 +0000 yongzhangdti 183@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Dear everyone,</p> <p>Repeated measurements are usually performed in DTI to improve SNR. Just wonder how DTIStuodio deals with the repeated measurements. My first guess is FA will be calculated based on each measurement and then the arithmetic mean of FA will be calculated across the multiple measurements or raw diffusion weighted images will be averaged first and the average images will be used to calculate FA.</p> <p>Also we would like to perform rigid body registration with Automatic Image Registration (AIR) to correct any potential motion artifact. Raw diffusion weighted images with different gradient directions applied are registered to B0 image. It seems that calculated FA values decrease for about 10-20% as compared to those without AIR registration. Just wonder if the difference is expectable and reasonable.</p> <p>Thank you very much for your help!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=102#post-179 Wed, 28 Jul 2010 22:30:57 +0000 GRGlenn 179@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hey, </p> <p>In the Automatic Image Registration tool, what does the Adjusting the gradients for DWIs if applicable checkbox do? By checking this box, the FA values calculated for a patient with multiple runs apparently increases. Is this something that I should do? </p> <p>Thanks, </p> <p>Russell Glenn </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=101#post-176 Tue, 27 Jul 2010 21:14:34 +0000 GRGlenn 176@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hey, </p> <p>I have been using DTIStudio to process a lot of data, and the FA maps generated by DTIStudio have significantly lower values than the FA maps generated by Siemens software and spm (on the order of 15 to 30% lower in the cortical spinal tract and medial lemniscus, for example). My method is to load the images using DTI Mapping, then do AIR to the first b0 image without creating new images in DTIStudio. I always check every slice for corrupted images, and then I do the tensor calculations using default settings. Is there something I am doing wrong? Do you have any ideas for why the FA maps would be so much lower? </p> <p>Thanks, </p> <p>Russell Glenn </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=69#post-114 Mon, 17 May 2010 22:55:33 +0000 yongzhangdti 114@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello,</p> <p>Many thanks for the great help from this forum! I've successfully performed an affine transform for a DTI dataset. As suggested by the user manual, I normalized a tensor file and then re-calculated the FA map. Now I have linearly co-registed FA, eigenvectors, eigenvalues and colormaps. But what should I do with a ADC map? It seems there is no re-created ADC map from the AIR affine transform. Should I normalize the ADC map directly or I can built it on any other co-registered image? Any hint will be greatly appreciated!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=59#post-81 Thu, 06 May 2010 00:22:59 +0000 yongzhangdti 81@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hi everyone,</p> <p>I repeate DTI measurement for four times and I've used the AIR registration tool provided in the DTI Studio to co-register the four datasets in the DICOM format from Siemens. However, it seems the tensor calculation is still done on the datasets without registration. Just wonder how we can tell the DTI Studio to work on the registered datasets. Any suggestion will be greatly appreciated!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=10#post-17 Tue, 28 Jul 2009 20:50:43 +0000 Muhammad 17@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>I would like to know How to define region of interest in dti studio, Actually I want to Fibertrack already segmented data , So before that I want to define the Region of interest . How would i do that? </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=100#post-171 Mon, 12 Jul 2010 19:28:18 +0000 DTIJoy 171@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello,<br /> I have been attempting to run the Automatic Image Registration, but after choosing a reference file (the first non-b0 image), noise level, and images to be registered, I receive a error stating that the "MriView3D MFC Application has stopped working" and the program shuts down. </p> <p>Has anyone else experienced this problem and/or know of any solutions?</p> <p>Thank you! </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=98#post-166 Wed, 07 Jul 2010 16:17:31 +0000 yongzhangdti 166@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Dear everybody,</p> <p>I am interested in the slice-by-slice statistics along the fiber tracks in the brainstem. I've registered individual DTI images to the JHU_MNI_SS atlas using DiffeoMap. But only the average across each whole fiber track can be calculated using ROIEditor with JHU_MNI_SS_WMPM_TypeIII as the WMPM type. Just wonder if there is any option so that we can convert the JHU_MNI_SS_WMPM_TypeIII map into individual ROIs so that I can have slice-by-slice statistics in the axial orientation. I did see the pre-defined fiber tracks provided by ROIEditor. But they don't include all the fiber tracks in the brainstem and they are not ROIs either. So no slice-by-slice statistics can be extracted using these pre-defined fiber tracks. Any help will be greatly appreciated!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=99#post-167 Wed, 07 Jul 2010 17:12:15 +0000 chasiubao73 167@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Greetings,</p> <p>How would one handle multiple b0 values in generating the FA map, color map, ADC map and etc etc.</p> <p>Currently I have deciphered the gradient table to look like this:</p> <p>0: 0, 0, 0<br /> 1: -1, -0.166, 0.11<br /> 2: -0.901, 0.169, 0.815<br /> 3: -0.656, -0.582, -0.9<br /> 4: -0.693, -0.357, -0.543<br /> 5: 0.525, 0.639, 0.33<br /> 6: 0.524, -0.609, -0.22<br /> 7: 0.004, 0.511, -0.414<br /> 8: 0.679, -0.884, -0.262<br /> 9:-0.088, -0.294, -0.887<br /> 10: -0.257, -0.086, -0.863<br /> 11: 0, 0, 0<br /> 12: 0, 0.986, 0.664<br /> 13: -0.419, -0.601, -0.386<br /> 14: 0.366, 0.8, 0.259<br /> 15: -0.698, -0.924, -0.488<br /> 16: -0.396, 0.689, -0.013<br /> 17: -0.783, -0.065, -0.233<br /> 18: -0.91, 0.627, 0.737<br /> 19: 0.139, -0.296, 0.432<br /> 20: 0.185, -0.907, -0.089<br /> 21: -0.443, 0.867, 0.504<br /> 22: 0, 0, 0<br /> 23: 0, 0, 0.74<br /> 24: -0.11, 0.781, 0.433<br /> 25: 0.66, 0.143, 0.35<br /> 26: 0.178, -0.14, -0.683<br /> 27: 0.753, 0.341, -0.944<br /> 28: 0.335, -0.791, -0.947<br /> 29: -0.415, -0.589, 0.535<br /> 30: -0.721, 0.362, 0.863<br /> 31: -0.979, 0.302, -0.453<br /> 32: 0.859, -0.491, -0.025 </p> <p>The generated FA map looks good however the color map is way off. Any assistance would be greatly appreciated. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=97#post-162 Wed, 30 Jun 2010 15:34:01 +0000 GRGlenn 162@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hey, </p> <p>When you calculate the statistics for Images along selected fibers, it seems like you have weighted the voxel values by the number of fibers that pass through the voxel. I have a few questions about this. (1) What are the reasons for fiber weighting? (2) Is there a way to see how many fibers go through each voxel so that I can integrate over certain regions of a tract and recalculate the mean and std without generating new tracts? </p> <p>Thanks, </p> <p>Russell Glenn </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=95#post-158 Wed, 23 Jun 2010 16:05:46 +0000 yongzhangdti 158@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello,</p> <p>Many thanks for the great support from this forum! I have a question about pediatric brain templates because currently I am working on the pediatric subjects. Just wonder if it will be proper to just use the brain templates derived from adults for linear or non-linear normalization. I saw some pictures of FA colormap from pediatric brains under Research-&gt;Human-&gt;Database on the DTIStudio website. Is there any pediatric atlas under construction? Thanks again! </p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=94#post-156 Mon, 21 Jun 2010 15:32:20 +0000 GRGlenn 156@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hey, </p> <p>I am working on some programs in MATLAB for processing images created by DTIStudio, and I am just curious about how DTIStudio creates the colormap image. I can load all of the images fine, but if I try to recreate the colormap image by multiplying each element of the 1st eigenvector image by any of the DTI parameters, e.g. FA, I get an image that is much more pixelated than the one created by DTIStudio. Do you apply any sort of interpolation algorithm in the image processing, or is it a simple element-by-element multiplication? I am ultimately interested in investigating fiber tracking algorithms. </p> <p>Thanks, </p> <p>Russell Glenn </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=75#post-135 Mon, 14 Jun 2010 23:12:50 +0000 saba 135@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello,<br /> I was wondering if you have any registered volumes to the JHU_MINI_SS atlas? I want to use the segmented ROI map with other volumes rather than just the provided atlas. </p> <p>Thanks<br /> Saba </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=74#post-130 Thu, 10 Jun 2010 18:09:02 +0000 psych 130@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Dear All,<br /> We are trying to run Dtistudio for the first time on one of our users PC running Windows XP.<br /> When we double click on DTISTUDIO to run, the following error pops up:<br /> “This application failed to start because the application configuration is incorrect. Reinstalling the application may fix this problem.”</p> <p>Do I need to install any Microsoft Visual Studio tools, if yes please let us know which one?<br /> Thanks for any help.</p> <p>Abrahim </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=73#post-129 Thu, 10 Jun 2010 15:04:06 +0000 yln 129@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>In DTIStudio,when i save the result of fiber tracking,Once saved in binary image form, information about streamline (or direction) will be lost.the output is useful for statistical analysis.But how to find the information about direction on fiber? How to convert 2D to 3D format? How does colormap color on vector map? thank you! </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=72#post-127 Tue, 08 Jun 2010 15:24:20 +0000 FuJinxi 127@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hey, </p> <p>I am attempting to perform DTI computations, but I am having a very difficult time working with DICOM files. In DTI Studio, how do you extract gradient tables from DICOM metadata? I cannot find this information anywhere, even in the Private tags. It is some great mystery to me. We are using a SIEMENS MAGNETOM Trio, A Tim System with syngo MR B15 software.</p> <p>Thanks!<br /> - Jinxi </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=71#post-125 Tue, 01 Jun 2010 14:38:08 +0000 yln 125@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>hello! I have three questions to ask you! thanks!<br /> I used the version of DtiStudio-latest-x86.exe at the first time and i have seen the user manual of version 2.40. In the version manual, it mentioned the button of DTI map and Mean-STD ,but i cannot find them. Where are they?<br /> In the version of DtiStudio-latest-x86.exe,it has the button of "get eigen-values/vectors,color map,FA map and so on,from the tensor image ",but i donnot know where the results are saved?<br /> What can AIR do?指令引用内存不能为“read”，why？and what should i do?<br /> thank you very much！ </p>