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
On Wed, Jul 11, 2018 at 11:17 AM, VA Research <[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]> 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]> on behalf of VA Research <n.n.di.methyl.tryptamine1@GMAIL.COM >
Sent: Tuesday, July 10, 2018 6:17 PMI 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 = -Yepi_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]x.ac.uk> wrote:
HiWhatever 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.
CheersStam
On 10 Jul 2018, at 22:42, VA Research <n.n.di.methyl.tryptamine1@GMAIL.COM > 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_REGdata_type INT16dim1 110dim2 110dim3 65dim4 69datatype 4pixdim1 2.000000pixdim2 2.000000pixdim3 2.000000pixdim4 11.700000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+
DTI AFTER RUNNING THOSE PREPROCESSING
data_type FLOAT32dim1 192dim2 256dim3 256dim4 69datatype 16pixdim1 1.000000pixdim2 1.000000pixdim3 1.000000pixdim4 1.000000cal_max 0.0000cal_min 0.0000file_type NIFTI-1+
On Tue, Jul 10, 2018 at 1:56 PM, Stamatios Sotiropoulos <[log in to unmask]x.ac.uk> 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.
CheersStam
On 10 Jul 2018, at 20:29, Krieger, Donald N. <[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]> on behalf of VA Research <n.n.di.methyl.tryptamine1@GMAIL.COM >
Sent: Tuesday, July 10, 2018 1:58:25 PM
To: [log in to unmask]
Subject: Re: [FSL] BEDPOSTX - Still Running After 5 DaysEvery 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]> 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 – DonFrom: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Moises Hernandez
Sent: Monday, July 9, 2018 10:45 PM
To: [log in to unmask]
Subject: Re: [FSL] BEDPOSTX - Still Running After 5 DaysHi 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:Moises.On 9 July 2018 at 21:39, VA Research <n.n.di.methyl.tryptamine1@gmail.com > wrote:Hello Experts,Any ideas, why it would be taking this long to complete one DTI image?Thanks so much,Joseph Veliz
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