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Dear Joseph, I think eddy needs - I think I got the acqp.txt and index.txt part values right but what to put into --field_mat ? I have to make a .mat file like the following? fsl_prepare_fieldmap SIEMENS dtiFMphase.nii.gz dtiFMmag_brain dtiFMrads 2.46 flirt -ref first_Vol_in_Dti -in dtiFMrads -init my_matfile -applyxfm so my eddy command will look like this? eddy --imain=DTI64 --mask=first_Vol_in_Dti_mask --index=index.txt --acqp=acqp.txt \ --bvecs=bvec --bvals=bval --field=dtiFMrads --field_mat=my_mat_file --out=DTI64_EDY if you do a google search on “eddy fieldmap” you should find the help page where this is described. In general the eddy online help is quite good, so it makes sense to take a look there if you have a problem. https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/UsersGuide#A--field As you can see there there are two important caveats when using a dual-echo fieldmap with eddy. There is actually a third one too, which is that the resulting voxel-displacement-map has to be invertible. Because of these caveats we are getting a lot of reports from people who are having problems with using a measured fieldmap. I am currently working on a tool that will “massage” a measured fieldmap into a format that works with eddy. But we _strongly_ recommend acquiring a reverse-PE-polarity fieldmap instead of a dual-echo fieldmap. Jesper On Wed, Jul 11, 2018 at 11:17 AM, VA Research <[log in to unmask]<mailto:[log in to unmask]>> wrote: Agreed, I am trying to figure out how to do that right now. On Wed, Jul 11, 2018 at 11:01 AM, Danny Kim <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Why use epi_reg? Why not just use eddy and specifying the field map you collected to do distortion correction? Danny Kim ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of VA Research <[log in to unmask]<mailto:[log in to unmask]>> Sent: Tuesday, July 10, 2018 6:17 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] BEDPOSTX - Still Running After 5 Days I think epi_reg is the culprit - after eddy correction - run epi_reg with fieldmaps to unwarp - which works but yes it does upsample like crazy by registering my dti to my mprage Can I use epi_reg to remove warping WITHOUT registering to the T1? # UNWARP WITH FIELMAPS & REGISTER DTI64 TO MPRAGE # EFFECTIVE ECHO SPACING FOR DTI = 0.69 ms # PHASE ENCODING DIRECTION FOR DTI64 = ANTERIOR >>> POSTERIOR = -Y epi_reg --echospacing=0.00069 --wmseg=T1_wmseg --fmap=dtiFMrads --fmapmag=dtiFMmag --fmapmagbrain=dtiFMmag_brain --pedir=-y --epi=DTI64_EDY --t1=oMPRAGE --t1brain=oMPRAGE_brain --out=EDCOR_FUNC2STRUCT On Tue, Jul 10, 2018 at 3:01 PM, Stamatios Sotiropoulos <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Whatever you have done in “Preprocessing” has massively and unnecessarily upsampled your data, which is why bedpostx now takes ages (you go from a 110x110 matrix and 65 slices to 192x256 matrix with 256 slices). This looks wrong, so before worrying about bedpostx you should get your preprocessing right, there is no need for any upsampling when you do distortion correction. Cheers Stam On 10 Jul 2018, at 22:42, VA Research <[log in to unmask]<mailto:[log in to unmask]>> wrote: DTI IN 64 DIRECTIONS AFTER RUNNING PREPROCESSING I JUST USE THE DEFAULT bedpostx DTI (no options) DTI BEFORE RUNNING EDDY AND UNWARPING WITH FIELDMAPS EPI_REG data_type INT16 dim1 110 dim2 110 dim3 65 dim4 69 datatype 4 pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 pixdim4 11.700000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ DTI AFTER RUNNING THOSE PREPROCESSING data_type FLOAT32 dim1 192 dim2 256 dim3 256 dim4 69 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ On Tue, Jul 10, 2018 at 1:56 PM, Stamatios Sotiropoulos <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Joseph What is the resolution of your data and how many directions do you have? And how do you call bedpostx? Bedpostx is not multi-threaded. It can only use multiple cores via SGE or similar cluster scheduler. If you do not have that, every slice will be processed serially on a single core, so for high resolution data and depending on how many MCMC iterations/model type you have asked this can take very long. Which is why we developed a GPU version, as Moises pointed out. Cheers Stam On 10 Jul 2018, at 20:29, Krieger, Donald N. <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hopefully one of the FSL people will weight in on this. I'm interested to hear what they say. When I saw something comparable, I just assumed there was something wrong with the scan which was tripping FSL up. Best - Don ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of VA Research <[log in to unmask]<mailto:[log in to unmask]>> Sent: Tuesday, July 10, 2018 1:58:25 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] BEDPOSTX - Still Running After 5 Days Every slice seems to be taking 3+ hours to complete. I have plenty of cores(12) and ram (64gb) available. looking the activity monitor xfibres 156MB of ram On Tue, Jul 10, 2018 at 3:24 AM, Krieger, Donald N. <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Joseph, If it’s still running take a look at how much memory it is using, both resident and virtual. I have seen bedpostx jobs run interminably on a single core when I had more than two jobs running on a multi-core device which shares 8 GBytes of memory. I a lot of virtual memory is in use, the job is likely going to the disk often for memory space which slows things down by more than an order of magnitude. I also have had jobs which ran interminably for no reason that I could identify but I presumed that there was a problem with the scan quality which was causing the problem. I hope this is helpful. Best – Don From: FSL - FMRIB's Software Library [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of Moises Hernandez Sent: Monday, July 9, 2018 10:45 PM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] BEDPOSTX - Still Running After 5 Days Hi Joseph, It is possible that something did not work correctly, but bedpostx can take 1 or 2 days if you use a single CPU core, or even more if your data is high resolution. Do you get any message at all? An alternative is to use an NVIDIA gpu: https://users.fmrib.ox.ac.uk/~moisesf/Bedpostx_GPU/ Moises. On 9 July 2018 at 21:39, VA Research <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello Experts, Any ideas, why it would be taking this long to complete one DTI image? Thanks so much, Joseph Veliz ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1