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Hi,

Yes, as with the other subject, I concatenated bvals and bvecs values as Daniel showed me.

Kind regards,

Rosalia.

2015-10-06 21:17 GMT+02:00 [log in to unmask] <[log in to unmask]>:
Have you fixed the bvals and becs of the new subject?
Alexandre Manhães Savio
PhD, Medical Imaging, Machine Learning
ENGINE Project Wrocław University of Technology
home | email: [log in to unmask]


On 6 October 2015 at 21:12, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:
> Yes, and because I was having problems when running DTIFIT because number of
> bvecs and bvals does not match with the data....
>
> Now I am trying just the same with the other subject....and it is giving me
> problems. when I created the file data after fslmerge, the fslslize
> dimensions does not correspond to the same dimmensions as in the other
> subject...see:
>
> First problematic patient that did not give me more problems...
>
> rosalia@rosalia-PORTEGE-Z930:~$ cd
> /home/rosalia/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/jmsb_p3
> rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/jmsb_p3$
> fslsize data.nii.gz
> dim1           122
> dim2           122
> dim3           65
> dim4           62
> pixdim1        1.967213
> pixdim2        1.967213
> pixdim3        2.000000
> pixdim4        1.000000
> rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/jmsb_p3$
>
> Second problematic patient..fslsize for data.nii.gz before running
> eddy_correct:
>
> rosalia@rosalia-PORTEGE-Z930:~$ cd /home/rosalia/Desktop/dcs_p3
> rosalia@rosalia-PORTEGE-Z930:~/Desktop/dcs_p3$ fslsize data.nii.gz
> dim1           122
> dim2           122
> dim3           65
> dim4           62
> pixdim1        1.967213
> pixdim2        1.967213
> pixdim3        2.000000
> pixdim4        9.300000
> rosalia@rosalia-PORTEGE-Z930:~/Desktop/dcs_p3$
>
> I do not understand it...
>
> Rosalia.
>
> 2015-10-06 21:04 GMT+02:00 Daniel Kim <[log in to unmask]>:
>>
>> You mean dtifit - TBSS is completely different.
>> Should be no problem with both, although not sure at this point what your
>> original intentions were when concatenating two runs together.
>> Was it to get a better dtifit result?
>>
>> Danny Kim
>>
>> On 2015-10-06, at 11:57 AM, Rosalia Dacosta Aguayo wrote:
>>
>> So, there is no problem with the two different kind of dm4 from the tow
>> data? 31 and 62 for running TBSS?
>>
>> Thank you for your patience,
>>
>> Rosalia.
>>
>> 2015-10-06 20:54 GMT+02:00 Daniel Kim <[log in to unmask]>:
>>>
>>> Looks good.
>>> dim4 on the concatenated data simply indicates that now there are 62
>>> volumes instead of 31 - doubled because of the concatenation.
>>>
>>>
>>> On 2015-10-06, at 11:37 AM, Rosalia Dacosta Aguayo wrote:
>>>
>>> Hi Daniel,
>>>
>>> This is the report of the data of one of my patients I had no problems
>>> with DTIFIT
>>>
>>> rosalia@rosalia-PORTEGE-Z930:~$ cd
>>> /home/rosalia/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/adp_p3
>>>
>>> rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/adp_p3$
>>> fslsize data.nii.gz
>>> dim1           122
>>> dim2           122
>>> dim3           65
>>> dim4           31
>>> pixdim1        1.967213
>>> pixdim2        1.967213
>>> pixdim3        2.000000
>>> pixdim4        1.000000
>>>
>>> rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/adp_p3
>>>
>>> And this is the information after doing the new
>>> approach...concatenation....just the steps you describe:
>>>
>>> rosalia@rosalia-PORTEGE-Z930:~$ cd
>>> /home/rosalia/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/jmsb_p3
>>>
>>> rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/jmsb_p3$
>>> fslsize data.nii.gz
>>> dim1           122
>>> dim2           122
>>> dim3           65
>>> dim4           62
>>> pixdim1        1.967213
>>> pixdim2        1.967213
>>> pixdim3        2.000000
>>> pixdim4        1.000000
>>>
>>> rosalia@rosalia-PORTEGE-Z930:~/Desktop/ESTUDIO_DTI_BIOMARCADORES/PATIENTS/jmsb_p3$
>>>
>>> Should I be worried with this difference in dim4?
>>>
>>> Rosalia.
>>>
>>> 2015-10-06 20:30 GMT+02:00 Daniel Kim <[log in to unmask]>:
>>>>
>>>> Hmm... that does not sound good.
>>>> Maybe start from the beginning.
>>>> - Convert raw data using dcm2nii and obtain two raw dti nii.gz files:
>>>> name them dti1.nii.gz dti2.nii.gz
>>>> - concatenate nii.gz files to form one nii.gz file: fslmerge -t
>>>> dti_merged.nii.gz dti1.nii.gz dti2.nii.gz
>>>> - check dti_merged.nii.gz dimensions: fslsize dti_merged.nii.gz > this
>>>> should give you same x,y,z dimensions as dti1 and dti2 but a larger t
>>>> dimensions (if that's not the case, check dti1 and dti2 to make sure nothing
>>>> was corrupted during conversion).
>>>> - concatenate bvals and bvecs files (as mentioned before)
>>>> - run eddy_correct on dti_merged.nii.gz: eddy_correct dti_merged.nii.gz
>>>> data 0
>>>> - get brain mask from eddy corrected data.nii.gz: fslroi data nodif 0 1;
>>>> bet nodif nodif_brain -m
>>>> - run dtifit using concatenated bvals and bvecs on data.nii.gz
>>>>
>>>> hope that helps
>>>>
>>>> Danny Kim
>>>> On 2015-10-06, at 11:22 AM, Rosalia Dacosta Aguayo wrote:
>>>>
>>>> Hi Danny,
>>>>
>>>> Now, doing eddy_correct of my concatenated data I see that I have the
>>>> double of slices...I was used to average my two data sets...and now it
>>>> worries me that my ofther files have less directions that those two ones....
>>>>
>>>> Rosalia.
>>>>
>>>> 2015-10-06 20:18 GMT+02:00 Daniel Kim <[log in to unmask]>:
>>>>>
>>>>> No worries.
>>>>> It's also a good practice to look at the data before running dtifit and
>>>>> remove directions that are heavily corrupted with motion or artifacts.
>>>>>
>>>>> Good luck!
>>>>>
>>>>> Danny Kim
>>>>>
>>>>>
>>>>> On 2015-10-06, at 11:07 AM, Rosalia Dacosta Aguayo wrote:
>>>>>
>>>>> Thanks Daniel,
>>>>>
>>>>> This is more clear for me...when you have never done this before you
>>>>> feel very unsure about how to do it. Now it is perfect clear: paste 1 colum
>>>>> of first bvec with the first column of the second bvec and so on..with
>>>>> second and third columns...
>>>>>
>>>>> Thank you a lot.
>>>>>
>>>>> Now I feel more relieve.
>>>>>
>>>>> Warm regards,
>>>>>
>>>>> Rosalia
>>>>>
>>>>> 2015-10-06 19:58 GMT+02:00 Daniel Kim <[log in to unmask]>:
>>>>>>
>>>>>> Hi Rosalia
>>>>>>
>>>>>> Concatenating bvals and bvecs:
>>>>>>
>>>>>> Let's say bvals from DTI1: b11 b12 b13 b14 b15 ... b1n
>>>>>> and bvals from DTI2: b21 b22 b23 b24 b25 .... b2n
>>>>>>
>>>>>> then use a text editor to copy and paste DTI2's bvals to form a new
>>>>>> concatenated bvals: b11 b12 b13 ... b1n b21 b22 b23 ... b2n
>>>>>>
>>>>>> Same with bvecs - bvecs from DTI1:
>>>>>> v111 v112 v113 v114 v115 ... v11n
>>>>>> v121 v122 v123 v124 v125 ... v12n
>>>>>> v131 v132 v133 v134 v135 ... v13n
>>>>>>
>>>>>> And bvecs from DTI2:
>>>>>> v211 v212 v213 v214 v215 ... v21n
>>>>>> v221 v222 v223 v224 v225 ... v22n
>>>>>> v231 v232 v233 v234 v235 ... v23n
>>>>>>
>>>>>> Then use a text editor to concatenate bvecs to look like this:
>>>>>> v111 v112 v113 v114 v115 ... v11n v211 v212 v213 v214 v215 ... v21n
>>>>>> v121 v122 v123 v124 v125 ... v12n v221 v222 v223 v224 v225 ... v22n
>>>>>> v131 v132 v133 v134 v135 ... v13n v231 v232 v233 v234 v235 ... v23n
>>>>>>
>>>>>> Hope that helps.
>>>>>>
>>>>>> Danny Kim
>>>>>>
>>>>>> On 2015-10-06, at 10:41 AM, Rosalia Dacosta Aguayo wrote:
>>>>>>
>>>>>> I have concatenated first...but still with doubts regarding bvals and
>>>>>> bvecs files...please which is the next step? could you help me, please?
>>>>>>
>>>>>> 2015-10-06 19:18 GMT+02:00 Tibor Auer <[log in to unmask]>:
>>>>>>>
>>>>>>> I call data the output of the merge (before eddy_correct).
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> If you concatenate, then concatenation is the first step!
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Vale,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Auer, Tibor M.D. Ph.D.
>>>>>>>
>>>>>>> MRC Cognition and Brain Sciences Unit
>>>>>>> 15 Chaucer Road
>>>>>>> Cambridge
>>>>>>> CB2 7EF
>>>>>>>
>>>>>>> United Kingdom
>>>>>>>
>>>>>>> Phone/Work: +44-(0)1223-273613
>>>>>>>
>>>>>>> Mail: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>>>>> Behalf Of Rosalia Dacosta Aguayo
>>>>>>> Sent: Tuesday, October 06, 2015 6:16 PM
>>>>>>>
>>>>>>>
>>>>>>> To: [log in to unmask]
>>>>>>> Subject: Re: [FSL] Having problems with DTIFIT with only two
>>>>>>> subjects...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Just to know if we are speaking about the same:
>>>>>>>
>>>>>>> I call data to the results of first apply eddy_correct to dti_1 and
>>>>>>> dti_2 and then averaging the results with fslmaths.....
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2015-10-06 19:13 GMT+02:00 Tibor Auer <[log in to unmask]>:
>>>>>>>
>>>>>>> fslmerge –t data data_1 data_2
>>>>>>>
>>>>>>> should merge data_1 and data_2, so data will contain volumes of both
>>>>>>> both data_1 and data_2.
>>>>>>>
>>>>>>> fslsize data à dim4 should be fslsize data_1 à dim4 + fslsize data_2
>>>>>>> à dim4
>>>>>>>
>>>>>>> Vale,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Auer, Tibor M.D. Ph.D.
>>>>>>>
>>>>>>> MRC Cognition and Brain Sciences Unit
>>>>>>> 15 Chaucer Road
>>>>>>> Cambridge
>>>>>>> CB2 7EF
>>>>>>>
>>>>>>> United Kingdom
>>>>>>>
>>>>>>> Phone/Work: +44-(0)1223-273613
>>>>>>>
>>>>>>> Mail: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>>>>> Behalf Of Rosalia Dacosta Aguayo
>>>>>>> Sent: Tuesday, October 06, 2015 6:03 PM
>>>>>>>
>>>>>>>
>>>>>>> To: [log in to unmask]
>>>>>>> Subject: Re: [FSL] Having problems with DTIFIT with only two
>>>>>>> subjects...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> data or dti_1 and dti_2??
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2015-10-06 18:40 GMT+02:00 Tibor Auer <[log in to unmask]>:
>>>>>>>
>>>>>>> fslmerge –t data data_1 data_2
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Vale,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Auer, Tibor M.D. Ph.D.
>>>>>>>
>>>>>>> MRC Cognition and Brain Sciences Unit
>>>>>>> 15 Chaucer Road
>>>>>>> Cambridge
>>>>>>> CB2 7EF
>>>>>>>
>>>>>>> United Kingdom
>>>>>>>
>>>>>>> Phone/Work: +44-(0)1223-273613
>>>>>>>
>>>>>>> Mail: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>>>>>> Behalf Of Rosalia Dacosta Aguayo
>>>>>>> Sent: Tuesday, October 06, 2015 4:58 PM
>>>>>>> To: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>> Subject: Re: [FSL] Having problems with DTIFIT with only two
>>>>>>> subjects...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dear FSL experts and Michel,
>>>>>>>
>>>>>>>
>>>>>>> Sorry, when I try fslmerge to concatenate the two datasets acquired
>>>>>>> for the same subject in the same scanner.... I write:
>>>>>>>
>>>>>>> fslmerge data dti_1.nii.gz dti_2.nii.gz and nothing happens
>>>>>>>
>>>>>>> It tells the following I do not understand well:
>>>>>>>
>>>>>>> Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr
>>>>>>> value in seconds]
>>>>>>>
>>>>>>>      -t : concatenate images in time
>>>>>>>      -x : concatenate images in the x direction
>>>>>>>      -y : concatenate images in the y direction
>>>>>>>      -z : concatenate images in the z direction
>>>>>>>      -a : auto-choose: single slices -> volume, volumes -> 4D (time
>>>>>>> series)
>>>>>>>      -tr : concatenate images in time and set the output image tr to
>>>>>>> the final option value
>>>>>>>
>>>>>>> I guess I should use -t option but I am not sure...any one of you
>>>>>>> could help me with this?
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>>
>>>>>>> Rosalia.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2015-10-06 16:05 GMT+02:00 Rosalia Dacosta Aguayo
>>>>>>> <[log in to unmask]>:
>>>>>>>
>>>>>>> Hi Michael,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Thank you very much for your reply.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I will try this option too. There are remaining two new subjects and
>>>>>>> I would like to run TBSS as soon as possible.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Yours sincerely,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Rosalia.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> 2015-10-06 15:50 GMT+02:00 Harms, Michael <[log in to unmask]>:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Instead of coregistering/averaging maps after DTIFIT, the more
>>>>>>> typical approach would be to simply concatenate ('fslmerge') the two
>>>>>>> original runs, concatenate the bvals/bvecs files, and then just run
>>>>>>> eddy_correct and dtifit using those concatenated files (i.e., as if all the
>>>>>>> data was collected in a single run in the first place).
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> cheers,
>>>>>>>
>>>>>>> -MH
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> Michael Harms, Ph.D.
>>>>>>>
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>> Conte Center for the Neuroscience of Mental Disorders
>>>>>>>
>>>>>>> Washington University School of Medicine
>>>>>>>
>>>>>>> Department of Psychiatry, Box 8134
>>>>>>>
>>>>>>> 660 South Euclid Ave. Tel: 314-747-6173
>>>>>>>
>>>>>>> St. Louis, MO  63110 Email: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From: Tibor Auer <[log in to unmask]>
>>>>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>>> Date: Tuesday, October 6, 2015 5:38 AM
>>>>>>> To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>>> Subject: Re: [FSL] Having problems with DTIFIT with only two
>>>>>>> subjects...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dear Rosalia,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> How did you actually averaged the imagesin step e)? Are you sure
>>>>>>> there was no dimension reduction? Have you checked whether the output
>>>>>>> data.nii.gz is actually a 4D dataset with same amount of volumes as the
>>>>>>> number of entries in the bvals/bvecs.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> However, there are some more conceptual issues:
>>>>>>>
>>>>>>> 1.       In step d), you first registered data_1 to data_2 and data_2
>>>>>>> to data_1. So at the end, they are not aligned at all!
>>>>>>>
>>>>>>> 2.       Which bvals/bvecs have you used? The set from data_1 or from
>>>>>>> data_2?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> And more importantly:
>>>>>>>
>>>>>>> It is not advised to register raw DTI images, because then you
>>>>>>> disrupt the consistency between the geometry of the images and the geometry
>>>>>>> of the bvecs. One solution is to transform the bvecs, as well; but it is
>>>>>>> also suboptimal.
>>>>>>>
>>>>>>> My recommendation is to analyse the two datasets separately without
>>>>>>> any registration, and coregister+average the metric images (e.g. FA maps)
>>>>>>> after DTIFIT.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Vale,
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Auer, Tibor M.D. Ph.D.
>>>>>>>
>>>>>>> MRC Cognition and Brain Sciences Unit
>>>>>>> 15 Chaucer Road
>>>>>>> Cambridge
>>>>>>> CB2 7EF
>>>>>>>
>>>>>>> United Kingdom
>>>>>>>
>>>>>>> Phone/Work: +44-(0)1223-273613
>>>>>>>
>>>>>>> Mail: [log in to unmask]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> From: Rosalia Dacosta Aguayo [mailto:[log in to unmask]]
>>>>>>> Sent: Tuesday, October 06, 2015 11:05 AM
>>>>>>> To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>>>>> Subject: Having problems with DTIFIT with only two subjects...
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dear FSL team,
>>>>>>>
>>>>>>> I must be doing something wrong but I can not guess where is the
>>>>>>> problem. I have two groups of 12 subjects.
>>>>>>>
>>>>>>> 1. I have two DTI acquisitions (dti_1 and dti_2) from the same
>>>>>>> subject in the same scanner (the last two subjects to include in the study).
>>>>>>> And I did the following steps in order to prepare my two subjects.
>>>>>>>
>>>>>>> a) From DICOM to NIFTI (dcm2nii)
>>>>>>>
>>>>>>> b) eddy_correct dti_1 data_1 0
>>>>>>>
>>>>>>> c) eddy_correct dti_2 data_2 0
>>>>>>>
>>>>>>> d) Here I thing there is the problem...but I do not know to manage
>>>>>>> with them in order to ensure that both images are well aligned. I did the
>>>>>>> following for co-registration of the two images.
>>>>>>>
>>>>>>>
>>>>>>> - flirt -in data_2.nii.gz -ref data_1.nii.gz -out data_2_registered
>>>>>>> -bins 256 -cost corratio -searchrx 0 0 -searchry 0 0 -searchrz 0 0 -dof 6
>>>>>>> -interp trilinear
>>>>>>>
>>>>>>> - flirt -in data_1.nii.gz -ref data_2_registered.nii.gz -out
>>>>>>> data_1_registered -bins 256 -cost corratio -searchrx 0 0 -searchry 0 0
>>>>>>> -searchrz 0 0 -dof 6 -interp trilinear
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> e) Averaging of data_1_registered and data_2_registered  -out = data
>>>>>>>
>>>>>>> f) Creation of the nodif.nii.gz with fslroi from data
>>>>>>>
>>>>>>> g)Creation of nodif_brain_mask with BET
>>>>>>>
>>>>>>> h) FSL --> DTIFIT Reconstruct diffusion tensors --> specify files
>>>>>>> manually (data, nodif_brain_mask, bvecs and bvals).
>>>>>>>
>>>>>>> I get the following error message: Erros: Erro: data and bvals /
>>>>>>> bvecs do not contain the same number of entries
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I hope I have explained well all I have done in order to facilitate
>>>>>>> the finding of my error...
>>>>>>>
>>>>>>>  With my best regards,
>>>>>>>
>>>>>>> Rosalia.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ________________________________
>>>>>>>
>>>>>>> The materials in this message are private and may contain Protected
>>>>>>> Healthcare Information or other information of a sensitive nature. If you
>>>>>>> are not the intended recipient, be advised that any unauthorized use,
>>>>>>> disclosure, copying or the taking of any action in reliance on the contents
>>>>>>> of this information is strictly prohibited. If you have received this email
>>>>>>> in error, please immediately notify the sender via telephone or return mail.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>