http://cmrm.med.jhmi.edu/cmrm/forumMRI/ Diffusion Tensor Imaging en Thu, 17 May 2012 08:35:11 +0000 http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=118#post-222 Mon, 07 May 2012 14:48:44 +0000 JHMI_Hangyi 222@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>in "fiber" tab, you cannot open a ROI saved under "ROI" tab, they have different format. </p> 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-219 Thu, 01 Dec 2011 15:21:48 +0000 JHMI_Hangyi 219@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>IQC Flag file Output (.flg file) file is designed for saving the image quality checking results (of manually quality checking and/or automatic outlier slice-rejection), so the users don't have to do the same work repeatedly for a data set. when you re-loading the same dataset with the .flg file using "DTI Mapping" command, the bad image slices will be crossed out automatically based on the work you had did before (so you don't have to repeat image quality checking again). </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=115#post-218 Thu, 01 Dec 2011 15:01:09 +0000 JHMI_Hangyi 218@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>you can use TRACE, instead of Mean_ADC (Mean_ADC = TRACE/3) </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-214 Wed, 27 Jul 2011 02:18:16 +0000 chasiubao73 214@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hi Kenichi,</p> <p>Thank you for your response. Yes, we use affine 12. We will try adjusting the contrast of our subject and template images before applying AIR Linear in Diffeomap. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=113#post-213 Tue, 26 Jul 2011 15:54:22 +0000 koishi 213@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Dear chasiubao73,</p> <p>If you chose 6-parameter rigid, the result is identical to the Eve, in terms of the size and shape. Rigid transformation just change the position and angle of the image.<br /> If you chose 9- or 12- parameter affine, and still the result is identical to the Eve, please try the followings.<br /> 1) Before you apply AIR, match the image centers of the template (your image) and the subject (Eve). The center of Eve is located in the upper edge of the body of the fornix. The "shift" function of the Diffeomap is useful to match the centers.<br /> 2) Please make sure that the image contrast of your image and that of the Eve are close enough. You can modify the image contrast before you apply AIR.<br /> Hope this helps.</p> <p>Best regards,</p> <p>Kenichi Oishi </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-211 Tue, 26 Apr 2011 16:08:27 +0000 xin 211@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>"isotropic image" means that the voxel of the image has the same size in three dimensions. If you load an image into DiffeoMap, this means that "pixel size - width", "pixel size - height" and "slice thickness" in the image parameter pop-up window should be the same. </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-208 Fri, 11 Feb 2011 15:27:44 +0000 xin 208@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>In the folder "ROIEditor", there are three text files in \Images\JHU_MNI_SS. They give you the names of each ROI. There are also three ROI files in the same folder, JHU_MNI_SS_WMPM_TypeI.dat, JHU_MNI_SS_WMPM_TypeII.dat and JHU_MNI_SS_WMPM_TypeIII.dat. ROIEditor can let you load them as ROIEditor-defined-format ROI files not as images. Then you can see a detailed atlas with the names. </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-205 Thu, 09 Dec 2010 21:03:31 +0000 xin 205@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Replied </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=64#post-204 Wed, 08 Dec 2010 21:47:46 +0000 rwrigh21 204@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Could you also send me the executables? </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=108#post-203 Tue, 02 Nov 2010 19:25:47 +0000 xin 203@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hello chasiubao73,</p> <p>DiffeoMap requires all the images loaded in the same window have the same parameters, such as the same dimensions, the same FOV width, the same FOV height, the same slice thickness.</p> <p>For example, you cannot load a 256*256*50 image and a 181*217*181 image to the same window. </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=64#post-198 Mon, 13 Sep 2010 13:54:36 +0000 xin 198@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Replied </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=106#post-197 Mon, 13 Sep 2010 13:46:57 +0000 JHMI_Hangyi 197@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>what do you plan to use your ROIs (for fiber-selection, statistics, or viewing)?<br /> for viewing, please used "File-&gt;MriView3D".. or "Image Load" of the "image" tab. for fiber selection, please using "Image save" of the "image" tab to convert it as RAW file before you do fiber selection... </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-195 Tue, 07 Sep 2010 14:00:00 +0000 susumu 195@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hi Yong,</p> <p>Sorry for my slow response.<br /> I believe any registration inevitably leads to interpolation and resultant smoothing (SNR goes up but resolution goes down). You can see noticeable SNR improvement and smoothing as you observed. I think there is no way to avoid it.</p> <p>Susumu </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=64#post-194 Mon, 30 Aug 2010 17:17:49 +0000 churnd 194@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>I am interested as well...? </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=67#post-192 Thu, 19 Aug 2010 06:55:19 +0000 christineb1979 192@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Thanks for this... i will try to use this... </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=105#post-191 Wed, 18 Aug 2010 12:50:26 +0000 JHMI_Hangyi 191@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>the program follows radiological convention, image's right is subject's left. </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=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=103#post-188 Wed, 04 Aug 2010 14:29:22 +0000 yongzhangdti 188@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Got your paper. Thank you very much, Hangyi!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=103#post-187 Wed, 04 Aug 2010 14:18:20 +0000 JHMI_Hangyi 187@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>the program will use "each image", not "each measurement" (I suppose that you mean "each repetition") individually. </p> <p>if a repetition has one B0+6DWIs, for 2 repetition, the program will use them just as a dataset with 2B0s+12DWIs. mathematically, one repetition results in a 6-equations system, two repetitions result in a 12-equations system. as long as the system has at least 6 uncorrelated equations, we can find out the 6 unknowns of the tensor elements and then one FA, not 2FAs. the more equations you have, the better SNR you get. </p> <p>for details of tensor calculation, please refer to: DtiStudio: resource program for diffusion tensor computation and fiber bundle tracking. Comput. Methods Programs Biomed. 2006 Feb;81(2):106-16. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=103#post-186 Tue, 03 Aug 2010 19:05:44 +0000 yongzhangdti 186@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Hi Hangyi,</p> <p>Many thanks for your reply! Say we have four repeated measurements. If the program uses each measurement individually, we should have four FA maps from the different measurements. However, DTIStudio provides only one FA map even if a user specifies multiple repeated measurements. Just wonder how the program combines the FA map from each measurement. Thanks again!</p> <p>Yong </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=103#post-185 Tue, 03 Aug 2010 18:50:30 +0000 JHMI_Hangyi 185@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>for multiple repetition dataset, the program will use each image individually, without averaging. for AIR, no smoothing performed internally. the FA dropping is not expected after AIR. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=103#post-184 Mon, 02 Aug 2010 22:22:28 +0000 yongzhangdti 184@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Is there any additional smoothing step involved in rigid body registration which may decrease FA?</p> <p>Yong </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-182 Thu, 29 Jul 2010 16:04:25 +0000 GRGlenn 182@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>Thank you very much for your help. </p> http://cmrm.med.jhmi.edu/cmrm/forumMRI/topic.php?id=102#post-181 Thu, 29 Jul 2010 14:38:11 +0000 JHMI_Hangyi 181@http://cmrm.med.jhmi.edu/cmrm/forumMRI/ <p>after AIR, the image may rotated. so the gradient should be adjusted accordingly. that is the purpose of the option "adjusting gradient..". </p>