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