tag:blogger.com,1999:blog-1405968300258104460.post3606706771033896567..comments2024-03-27T01:18:24.341-04:00Comments on Andy's Brain Blog: DTI Analysis, Steps 1 & 2: Distortion Correction and Eddy CorrectionAndrew Jahnhttp://www.blogger.com/profile/16435706598096921650noreply@blogger.comBlogger31125tag:blogger.com,1999:blog-1405968300258104460.post-71792026454469056172021-01-08T09:26:40.250-05:002021-01-08T09:26:40.250-05:00Error: data and bvals/bvecs do not contain the sam...Error: data and bvals/bvecs do not contain the same number of entries<br /><br />Does anybody know how to solve this issue while running dtifit in fsl?surenhttps://www.blogger.com/profile/11486579867689921309noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-2695927245453575982019-12-02T08:42:23.053-05:002019-12-02T08:42:23.053-05:00Any update on this? I am also wondering if there i...Any update on this? I am also wondering if there is any difference in running topup with 2 vs 10 b=0 volumes from each PE direction.IPhttps://www.blogger.com/profile/10903700720576833758noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-50818380843907220452019-07-05T06:38:15.491-04:002019-07-05T06:38:15.491-04:00Hi Andy,
I am a student researcher in the field of...Hi Andy,<br />I am a student researcher in the field of neuroimaging and I am beginner in the use of FSL, so I start with the correction of distortions with running topup command lines but my problem is that I do not get results i just obtain this file AP_PA_b0.topup_log but no corrected image,<br />do you have any idea about this kind of problem and how can i fix it please !!<br />thanks<br />TROUDI ABIRhttps://www.blogger.com/profile/13432071962169820656noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-22605359091655748012019-06-10T11:48:38.127-04:002019-06-10T11:48:38.127-04:00hey andy, I'm trying to see if I can use TORTO...hey andy, I'm trying to see if I can use TORTOISE to preprocess my data with my AP and PA scans merged? I'm having trouble finding a merged bvecs/bvals file for that merged scan though. Thanks!Anonymoushttps://www.blogger.com/profile/03410723048912831565noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-23692793086759713642019-04-01T08:36:56.589-04:002019-04-01T08:36:56.589-04:00Hi Andy, I'm newcomer in the neuro science fie...Hi Andy, I'm newcomer in the neuro science field. Your blog and youtube channel help me a lot. Anyway, I face a problem with handling fsl Dtifit. I'm trying to do Dtifit with UKBioBank data but it getting error which is saying 'bvals/ bvecs do not contain the same number of entries'. But as I checked, it has same number of entries.(150,150*3). My bvals file have 5 or 1995 (which is not 0 or 1000..). Can it be a problem?<br /><br />Thank you<br />woowonAnonymoushttps://www.blogger.com/profile/03532449766331546850noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-70808342326980428322017-08-08T06:40:02.929-04:002017-08-08T06:40:02.929-04:00Hey Andi, thank you for your support!
I have a que...Hey Andi, thank you for your support!<br />I have a question concerning topup/eddy on a data set measured on two seperate days.<br /><br />I did several dwi measurements on the same subject on two days. <br />Now I need to know either I have to merge all my files and do topup/eddy on all session or do I have to do it separately? When doing it separately do I have to register all dwi's to for example a mean image thus I can compare later on? If yes what happens with the bvecs file? I guess the b-matrix have to reorientate?<br /><br />Thank you<br />Cheers<br />MaxAnonymoushttps://www.blogger.com/profile/16108497164359138963noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-68501429133982976732017-07-13T08:13:04.175-04:002017-07-13T08:13:04.175-04:00There is also Brainsuite which is freely downloada...There is also Brainsuite which is freely downloadable and it offers registration based distortion correction:<br /><br />http://brainsuite.org/processing/diffusion/distortion-correction-and-co-registration/lrq3000https://www.blogger.com/profile/14275907715478948968noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-69204445063456134192017-06-26T11:52:45.923-04:002017-06-26T11:52:45.923-04:00I see. Well thank you for the insight!! I see. Well thank you for the insight!! steveghttps://www.blogger.com/profile/04475541993630397922noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-81490985521759093552017-06-24T16:40:24.500-04:002017-06-24T16:40:24.500-04:00Not necessarily; my understanding is that the dire...Not necessarily; my understanding is that the directions need to be opposite to each other, not for there to be different readtimes.<br /><br />I'm not an expert in this, so I would double-check with the FSL listserv to make sure.<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-5834063260611716072017-06-22T20:28:21.874-04:002017-06-22T20:28:21.874-04:00Rather, if I have one scan out of 6 in the shell w...Rather, if I have one scan out of 6 in the shell with a different calculated readout time in for the acqp file for topup (6 rows reading 0 1 0 x) for anterior to posterior aquisition but one row has a different x value then I should still be able to use TOPUP as one of the aquisitions was different? steveghttps://www.blogger.com/profile/04475541993630397922noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-59999471526627796542017-06-22T20:23:44.106-04:002017-06-22T20:23:44.106-04:00Thanks Andy!
So in referencing my PAR files, is &...Thanks Andy! <br />So in referencing my PAR files, is "phase encoding direction" synonymous with "preparation direction" designated by the PAR file? <br /><br />Or, must you really look at the FSL time series as you did in your video to visualize the distortions themselves in order to determine this?<br />steveghttps://www.blogger.com/profile/04475541993630397922noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-44963156748558729502017-06-21T11:28:22.900-04:002017-06-21T11:28:22.900-04:00Hi there,
I haven't used multishell DTI, so I...Hi there,<br /><br />I haven't used multishell DTI, so I can't say. However, my understanding is that topup requires images in opposite phase encoding directions - for example, one set of images collected A-P, and another set P-A. I don't think it would be appropriate in your case.<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-66735106696411694372017-06-19T18:37:16.996-04:002017-06-19T18:37:16.996-04:00Hi Andy,
If I am using a multishell DTI scheme wit...Hi Andy,<br />If I am using a multishell DTI scheme with 6 shells each with one b0 and 10 directions all acquired A-P is it still possible or beneficial to use topup? Do I need to reorganize my b-val file and volumes so that topup will extract all 6 b0 values first (such that the bval lists 000000,500,1000, etc)? Or does it require just one b0 followed by the number of volumes (in my case 6)?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-11935581668163408362017-06-19T15:24:43.293-04:002017-06-19T15:24:43.293-04:00This comment has been removed by the author.steveghttps://www.blogger.com/profile/04475541993630397922noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-44676115931325310592017-02-13T12:38:02.382-05:002017-02-13T12:38:02.382-05:00Hi Andy,
Will you be making a video or how-to tut...Hi Andy, <br />Will you be making a video or how-to tutorial on TORTOISE?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-25090285918545778232017-01-31T12:37:38.725-05:002017-01-31T12:37:38.725-05:00Hey there,
I would check out the featquery tool, ...Hey there,<br /><br />I would check out the featquery tool, either from the practical here:<br /><br />http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/feat1/<br /><br />Or the video here:<br /><br />https://www.youtube.com/watch?v=SNVt7smHLm8<br /><br />It should be similar to extracting parameter estimates like you would with any FMRI experiment; just give it a mask and the maps to extract from, and you should get the average MD across all the voxels in the mask.<br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-70464289181029557782017-01-31T03:11:26.275-05:002017-01-31T03:11:26.275-05:00Hi Andy,
Can you tell me how to extract Mea...Hi Andy,<br /> Can you tell me how to extract Mean Diffusivity (MD) values of each subject with the help of FSL tool ?<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-79885277036820505282016-12-16T11:05:02.371-05:002016-12-16T11:05:02.371-05:00Hi Danielle,
If you don't want to use topup, ...Hi Danielle,<br /><br />If you don't want to use topup, you can use another DTI preprocessing package like TORTOISE. The results are pretty good compared to FSL's preprocessing.<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-76100783466140480412016-12-14T09:35:42.483-05:002016-12-14T09:35:42.483-05:00Hi Andy,
What do you advise me to do to correct mo...Hi Andy,<br />What do you advise me to do to correct motion distortion? My patients have a lot of motion artifact ( because they are elderly). I am going to preprocess DTI data and don´t implement TOP UP so. <br />I would like to know if I can use any tool to better correct motion.Anonymoushttps://www.blogger.com/profile/12153322483415326787noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-47146819873465642712016-11-02T17:50:44.207-04:002016-11-02T17:50:44.207-04:00Which export option did you use from TORTOISE? I ...Which export option did you use from TORTOISE? I tend to use the FSL (sorted) one for TRACULA. Haven't had any problems... BUT, you may have to transpose the b-vectors and b-values to get them to play nice. Petehttps://www.blogger.com/profile/17830630319882851368noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-90812181505613490882016-08-31T10:17:44.885-04:002016-08-31T10:17:44.885-04:00Hi Marissa,
I'm not sure why that's happe...Hi Marissa,<br /><br />I'm not sure why that's happening; these days I use TORTOISE to preprocess my DTI data before running the analyses in Tracula, and I haven't had issues with that. Give that program a try and see if it fixes your problem.<br /><br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-79940686855057275632016-08-30T13:38:28.670-04:002016-08-30T13:38:28.670-04:00Hi Andy,
I've completed topop successfully, ...Hi Andy, <br /><br />I've completed topop successfully, but now I need to run a process through freesurfer called tracula, on this new combined AP/PA file. In order to run tracula I need the correct number of bvals and bvecs. I have these files, but they are for the AP and PA images separately. When I try to run the program, it tells me the number of images doesn't match the bvals and bvecs. I've tried just combining the files, copying AP into the same file as PA and running it that way but I still run into the same error. Do you know how I could get the proper bvals and bvecs for the new combined file?<br /><br />Thanks Anonymoushttps://www.blogger.com/profile/09437765672420565135noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-42197879904607433932016-02-25T00:12:49.323-05:002016-02-25T00:12:49.323-05:00I've been wondering the same thing about multi...I've been wondering the same thing about multiple b0 images. I have a dataset where there are 4 b0 AP scans and 1 b0 PA scan. What I've done is just pair each AP b0 scan with the 1 PA b0 scan (so my AP_PA_b0 file has 8 scans in it) and run top-up on that. Not sure if this is the right thing to do, though...Anonymoushttps://www.blogger.com/profile/01388016199082237496noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-44192430483522624372016-02-12T13:37:16.770-05:002016-02-12T13:37:16.770-05:00Thank you for getting back to me! Initially, I ter...Thank you for getting back to me! Initially, I terminated the process, because I thought that I did something wrong. However, I did rerun one person, and it ended up taking 1 hour and 20 minutes to run that person. I do have one more question. Our lab initially assumed that we should extract all 7 of our b0 volumes when creating the nodif image from our dwidata file, because we thought that would give us a more precise and clean image. However, entering only the first two b0 values, which are also the only b0 values not interrupted by any other value, is the only measure entered into the terminal which still actually provides the image of a brain in fslview. Adding any other b0 volume to this code: fslroi dwidata nodif 0 2 gives us an error. Therefore, is there no use for all of the b0 values together? Do they not produce better results when extracted all together? Thanks! Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-6957668532040241932016-02-05T12:41:51.170-05:002016-02-05T12:41:51.170-05:00Hey there,
It's difficult to say, given that ...Hey there,<br /><br />It's difficult to say, given that there are many differences between computers doing the processing. If you've written something incorrectly, it should either terminate with an error, or give you crazy output. Either way, I'm assuming that you've processed at least one person by now, so I'm curious how long it took?<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.com