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]
>>>> <[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.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>
>
