tag:blogger.com,1999:blog-1405968300258104460.post8177375081046771219..comments2024-03-27T01:18:24.341-04:00Comments on Andy's Brain Blog: FSL Tutorial: Part 1 (of many)Andrew Jahnhttp://www.blogger.com/profile/16435706598096921650noreply@blogger.comBlogger25125tag:blogger.com,1999:blog-1405968300258104460.post-36987487784416622722019-08-21T10:17:58.321-04:002019-08-21T10:17:58.321-04:00in FSL can you measure the activity with a ROI ?in FSL can you measure the activity with a ROI ?cvv4x4https://www.blogger.com/profile/16538156007407779871noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-90688278786986393862018-06-13T16:37:36.525-04:002018-06-13T16:37:36.525-04:00Hey Andy,
I hope you're doing well. The link ...Hey Andy,<br /><br />I hope you're doing well. The link for the example data does not seem to work:<br /><br />mypage.iu.edu/~ajahn<br /><br />What can be done about this? I would greatly like to follow these videos!Anonymoushttps://www.blogger.com/profile/00544507069081112072noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-90621117496422497242018-03-10T16:46:49.616-05:002018-03-10T16:46:49.616-05:00Hi Andrew,
The link for downloading sample FSL dat...Hi Andrew,<br />The link for downloading sample FSL data doesn't seem to work. Is there any other link I can use to download your sample data folder?<br />Thanks!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-68206740097718087742017-12-20T13:12:45.800-05:002017-12-20T13:12:45.800-05:00Hi Andy
I downloaded a dmri data from ppmi-info.or...Hi Andy<br />I downloaded a dmri data from ppmi-info.org. In each subject's folder there are bvals,bvects and dmri data. The problem is there is just one bval=0 in data, but with my knowledge at least there should be two volumes with zero b-values in different PE directions to do topup. How can I solve this problem?<br />thanksAnonymoushttps://www.blogger.com/profile/01044599063421469644noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-61128141695916165852017-05-30T09:15:18.717-04:002017-05-30T09:15:18.717-04:00Hi David,
I don't know if you can override th...Hi David,<br /><br />I don't know if you can override the "run" flag, but you can merge them after you've converted them using something like FSL's fslmerge or AFNI's 3dTcat. For example:<br /><br />fslmerge -t oneRun.nii run1.nii run2.nii run3.nii<br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-6696086357113027962017-05-29T19:35:40.039-04:002017-05-29T19:35:40.039-04:00Hi Andy,
When converting dicom files into a 4d ni...Hi Andy,<br /><br />When converting dicom files into a 4d nifti (.nii), do you know how to convert over multiple runs? I'm using mri_convert but it automatically detects the run of the input file and only converts that specific run. I need to convert several runs into one nifti but I'm not sure how to override the 'run' detector, I can't seem to find a flag for this. Any ideas?<br /><br />Cheers,<br />DavidDavidhttps://www.blogger.com/profile/05783886466213580903noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-73359741220054147102016-09-27T17:55:42.208-04:002016-09-27T17:55:42.208-04:00Hi,
I am having the same problem on a new MacMin...Hi, <br /><br />I am having the same problem on a new MacMini with OS El Capital version 10.11.6. I tried reinstalling XQuartz, like some other forums have suggested, but I still get the error "[Warning] Unsupported OS (apple darwin 15.6). This version of the OS has not been fully tested." <br /><br />Have you or anyone else found a solution?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-79145452202350085992016-09-23T13:06:02.770-04:002016-09-23T13:06:02.770-04:00Hi Safal,
Unfortunately I haven't done much a...Hi Safal,<br /><br />Unfortunately I haven't done much analysis of perfusion data (that was six years ago, and even then I wasn't sure I was doing it right). Best of luck with your search, and if I do start to learn something, I'll let you know!<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-53046024706303624712016-09-20T11:19:18.684-04:002016-09-20T11:19:18.684-04:00Hi Andy,
Thank you so much for all your hard work...Hi Andy,<br /><br />Thank you so much for all your hard work and all those great tutorials! I would not have done anything if it was not for your help! I am working as a post-doc on neuroimaging but I am just getting things started with fMRI analysis with no guidance (my previous work focused only on DTI analysis). I use Human Connectome Project data so I am lucky that HCP already provides the parameters for FSL analysis. Based on your tutorials I saw that this was adequate for me to obtain a good depiction of the hand motor area using the motor task fMRI datasets.<br /><br />The only problem is that I wanted to try the method described in this recent paper http://www.nature.com/articles/srep20170#f2 (the author was so kind to send me his toolbox which only works in SPM though). Do you think there is a way to use my FSL produced data in SPM for such an analysis to produce maps of inter-subject variability? Also after that would I be able to extract some ROIs from SPM for single subjects in order to combine them using a script I have with my previously used DTI ROIs to optimize the tracking of the hand motor area in the subjects or there is no point and I should use FSL based on your tutorials for ROI extraction based on the activation I got? <br /><br />Sorry about all those questions..I may be asking for a lot here but if you have any pieces of information that may be helpful or if you could provide me with any guidance I would be more than grateful. <br /><br />In any case thank you very much for your wonderful work! I appreciate it!<br /><br />Best regards,<br />Magda.Anonymoushttps://www.blogger.com/profile/15862516365210269930noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-3496365088215208272016-09-17T06:56:36.631-04:002016-09-17T06:56:36.631-04:00Hi Andrew. Great tutorials. Really helpful, especi...Hi Andrew. Great tutorials. Really helpful, especially for someone like me who is just getting into MRI analysis. Any chance that you have gone through perfusion data analysis in SPM or FSL? It's been a real struggle with perfusion data at the moment and so would greatly appreciate your help. <br /><br />Thanks for all these insightful videos.<br /><br />Regards!Safalnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-80330617169012759852016-09-17T06:53:56.667-04:002016-09-17T06:53:56.667-04:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/17055560829827904448noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-16860495995941766532016-09-09T16:11:47.387-04:002016-09-09T16:11:47.387-04:00Hi,
Great tutorials, really helpful when I needed ...Hi,<br />Great tutorials, really helpful when I needed to create ROIs.<br />I recently bought a MacBook Pro with OS El Capitan, and I am having trouble installing FSL.<br />After asking me for the place to install, the terminal says: Unsupported OS (apple darwin 15.6). This version of the OS has not been fully tested.<br />Thanks for your help!pandonaudehttps://www.blogger.com/profile/16879143114872586790noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-75125110336749883842015-09-25T05:23:48.307-04:002015-09-25T05:23:48.307-04:00Great Tutorials. Thank you very much Andy!Great Tutorials. Thank you very much Andy!Adham Elshahabihttp://adham.elshahabi.comnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-36283062786619158732015-01-08T07:53:59.765-05:002015-01-08T07:53:59.765-05:00Unfortunately, no; not yet! There may be one in th...Unfortunately, no; not yet! There may be one in the future.<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-91524129092776913712015-01-07T19:13:59.017-05:002015-01-07T19:13:59.017-05:00Hello! Thanks for this great blog. Do you have a t...Hello! Thanks for this great blog. Do you have a tutorial for FS-FAST? Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-13335105685210902662014-11-13T06:27:49.760-05:002014-11-13T06:27:49.760-05:00This comment has been removed by the author.Anonymoushttps://www.blogger.com/profile/17265062163886654621noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-71470075067488622872014-07-29T03:37:55.780-04:002014-07-29T03:37:55.780-04:00thanks for the help!thanks for the help!Anonymoushttps://www.blogger.com/profile/05914769487727517633noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-66437820382243959592014-05-07T20:04:45.667-04:002014-05-07T20:04:45.667-04:00Hey Nathan, thanks for pointing that out. I think ...Hey Nathan, thanks for pointing that out. I think I reference the link in a later post, but I will update it on this post for easier reference.<br /><br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-24786494690477504662014-05-06T13:01:16.545-04:002014-05-06T13:01:16.545-04:00Example data is at following: mypage.iu.edu/~ajahn...Example data is at following: mypage.iu.edu/~ajahnnathanhutchesonhttps://www.blogger.com/profile/12940867648413963621noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-69223825100044817812014-04-23T15:03:04.986-04:002014-04-23T15:03:04.986-04:00Hi Sanket,
I don't have an algorithm specific...Hi Sanket,<br /><br />I don't have an algorithm specifically for what you are describing - and I haven't worked that much with DTI data, although conceptually it should be similar to basic resting state analyses - but I have one question: When you say you got to the 59th time series and that the given data was the same as the test data, what does that mean exactly? And what is the test data? I need a few more details.<br /><br />Thanks,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-88173458168442018832014-04-18T12:31:25.062-04:002014-04-18T12:31:25.062-04:00Given a resting state fMRI dataset and a parcellat...Given a resting state fMRI dataset and a parcellated brain volume image in DTI space, please design an algorithm to measure the functional connectivity between those parcellated brain regions. <br /><br />1) The data is already transformed to the same DTI space.<br />2) The brain volume is parcellated into anatomical regions based on the HAMMER algorithm. It is based on the MNI atlas. Each brain region should be treated as a graph node.<br />3) The measured connectivity should be represented as a graph edge. Create the final constructed graph of the structural connectivity map and rendering of the connectivity map<br /> 4) the Brain regions are given in the text file with their intensities.<br /><br />I tried loading the nifty file in matlab then comparing the test data (atlas) with 150 time series after this I got at the 59th time series the given data is same to test data. Now I dont understand how to deal with the image and map the data to get the fiber connectivity ?<br /><br />I am dealing with all this stuff for the first. If you have any suggestions or ideas please help me out. Thanks!!Anonymoushttps://www.blogger.com/profile/11176457995381683851noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-37966577124723715762014-04-15T11:11:14.324-04:002014-04-15T11:11:14.324-04:00Hi Sanket,
If you have a path pointing to the FSL...Hi Sanket,<br /><br />If you have a path pointing to the FSL libraries (which should be done as part of a typical installation), then you should be able to launch the GUI by just typing "fsl".<br /><br />Best,<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-25105834328068891442014-04-13T20:04:54.137-04:002014-04-13T20:04:54.137-04:00how to get the fsl GUI ? I mean i have installed t...how to get the fsl GUI ? I mean i have installed the fsl and thats it. I tried writing commands in the terminal but I couldn't. I am new to this. Please do let me know if you have a manual of commands or something . Thanks!<br />Anonymoushttps://www.blogger.com/profile/11176457995381683851noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-77114525754091405822013-09-10T12:56:32.276-04:002013-09-10T12:56:32.276-04:00Hi,
Can you provide any more details on when the ...Hi,<br /><br />Can you provide any more details on when the error occurred, and what error output it gives, if any?<br /><br />-AndyAndrew Jahnhttps://www.blogger.com/profile/16435706598096921650noreply@blogger.comtag:blogger.com,1999:blog-1405968300258104460.post-48245166746905945492013-08-31T02:32:56.068-04:002013-08-31T02:32:56.068-04:00SOOOOO happy when I found your web site and about ...SOOOOO happy when I found your web site and about to follow you along but unfortunately, I got "An error occurred, please try again later".<br /><br />What give?<br /><br />thanksAnonymousnoreply@blogger.com