[Mristudio-users] Using processed data

[darshan pai]

when you say a 4D file I assume that you have a Analyze file with an entry on the number of volumes , Is it? . If it is then try to make it a 3D file with all the 65 slices added in the z direction and see if it helps..

Regards     

Dp    



----- Original Message ----
From: Mark A. Pinsk <mpinsk at gmail.com>
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <mristudio-users at mristudio.org>
Sent: Wed, December 16, 2009 12:13:42 AM
Subject: Re: [Mristudio-users] Using processed data

Also, I should mention that the Analyze file loads just fine using
"MRI View3D" and "Analyze" file format.


On Wed, Dec 16, 2009 at 12:09 AM, Mark A. Pinsk <mpinsk at gmail.com> wrote:
> Thanks for your help, I'll do my best to answer them...
>
> FYI: these are small volumes from animal scans ( 1 x 1 x 1.1 mm resolution):
>
> Image Dimensions: 96 Width, 128 Height, 47 slices
> Slice Orientation: Axial
> Slice Sequencing: Inferior-Superior
> FOV: 96 Width, 128 Height, 1.1 Slice Thickness
> Pixel Size: 1.000 Width, 1.000 Height
> Slices to be processed: 0 to 46, All Slices
> Image Sequence: Gradient By Gradient
> b_Value: 1000
>
> My gradient table has 65 entries.  The first 5 entries are B0 images,
> the remaining 60 are for the 60 directions.  There is no mean image at
> the end of my data.   I can discard 4 of the B0 images, but that does
> not seem to make a difference on my error message.  I have several B0
> images in accord with recent work that suggests having a ratio of 6:1
> diffusion to non-diffusion weighted images (Zhu et al. NeuroImage
> 2008).
>
>
>
> On Tue, Dec 15, 2009 at 11:42 PM, Gonzalo Rojas <grojasy at puc.cl> wrote:
>> Hi Mark:
>>
>>  Many questions:
>>
>> i) do you specify correctly the "image slices" quantity in "iamge dimension"
>> ?... that value is the quantitry of axial slices in each gradient
>> direction...
>>
>> ii) and the "image width" and "image height" in "image dimension" ?... did
>> you checked that values ?...
>>
>> ii) in "lice orientation" did you specify "axial" ?..
>>
>> iii) and in "Voxel Size", "Field of View-width" and "Field of View-Heigth"
>> did you specifiy the FOV value correctly ?...
>>
>> iv) you could check the previos values looking at "Pixel Size-Width" and
>> "Pixel Size-Height"...
>>
>> v) in "Slices to be processed" it must appears 0-(image slices-1)
>>
>> vi) in gradient table you must put the 61 (0-60) directions... in your 4D
>> analyze file is included the "mean" of all the 60 directions at the end of
>> the file ?... if it is, you must put "100,100,100" as the last gradient
>> direction to skip that image in the computation...
>>
>> vii) in "Image secuence" you must select "Gradient by Gradient" option...
>>
>> viii) in "Raw-BIN Files folder you must specify the IMG file of the Analyze
>> pair...
>>
>> ix) why you have 5 b0 volumes ?... to compute tractography, you must have
>> only one b0 volume... you must put "100,100,100" in "Gradient Table" for
>> each of the 4 b0 slices to skipt them...
>>
>>  Sincerely,
>>
>>
>> Gonzalo Rojas Costa
>> Department of Radiology
>> Las Condes Clinic
>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>> Tel: 56-2-2105170
>> Cel: 56-9-97771785
>> www.clc.cl
>>
>> El 16-12-2009 1:07, Mark A. Pinsk escribió:
>>>
>>> Thanks !
>>>
>>> I converted by 4D NIFTI file to a 4D ANALYZE file as you suggested.
>>>
>>> I attempt to read it in as RAW, but it seems to get stuck...
>>>
>>> I specify the file in the Raw-BIN Files Folder field, but I get this
>>> message:
>>> "Number of files in this fold is less than expected:
>>> (Img_Slices*Img_Blocks)."
>>>
>>> I only have a single .img/.hdr pair in my folder since it is a 4D file
>>> (i.e. it contains 65 volumes (5 b0 volumes + 60 directions)).
>>>
>>> Sorry, any help would be greatly appreciated.
>>> Thanks
>>> Mark
>>>
>>>
>>>
>>>
>>> On Tue, Dec 15, 2009 at 10:29 PM, Gonzalo Rojas<grojasy at puc.cl>  wrote:
>>>>
>>>> Hi Mark:
>>>>
>>>>  Yes... you could do all the processing that you mentioned (in FSL), and
>>>> bring it to dti-studio... the FSL output file format is NIFTI.GZ... you
>>>> must
>>>> convert it to ANALYZE 4D, and then you must load that ANALYZE 4D file as
>>>> a
>>>> RAW data file format in DTI-STUDIO...
>>>>
>>>>  Sincerely,
>>>>
>>>>
>>>> Gonzalo Rojas Costa
>>>> Department of Radiology
>>>> Las Condes Clinic
>>>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>>>> Tel: 56-2-2105170
>>>> Cel: 56-9-97771785
>>>> www.clc.cl
>>>>
>>>> El 15-12-2009 23:37, Mark A. Pinsk escribió:
>>>>>
>>>>> Hi, someone asked this a while ago in the archives but I didn't see a
>>>>> reply.   Can I use data that I've processed in FSL (eddy current
>>>>> correction, motion correction, and field map-based undistortion) and
>>>>> bring it into dti-studio?   The data is in one large 4D nifti file.  I
>>>>> don't see where I can do this, is it not possible?
>>>>>
>>>>> thanks
>>>>> mark
>>>>> _______________________________________________
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>

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