[Mristudio-users] Using processed data

Wed Dec 16 23:11:38 EST 2009

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-----Original Message-----
From: gjmuro at optonline.net
Date: Thu, 17 Dec 2009 03:45:19 
To: DTI Studio, ROI Editor,	Landmarker Questions/Support<mristudio-users at mristudio.org>
Subject: Re: [Mristudio-users] Using processed data

T
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-----Original Message-----
From: "Mark A. Pinsk" <mpinsk at gmail.com>
Date: Wed, 16 Dec 2009 22:40:25 
To: DTI Studio, ROI Editor, Landmarker Questions/Support<mristudio-users at mristudio.org>
Subject: Re: [Mristudio-users] Using processed data

Still no luck.  In the DTI Mapping parameters window, there is no
lower left field for the number "65" to appear.  I only see that in
the MRIView3D parameters window.

I am beginning to wonder if I'm having a more low-level problem?  I'm
running the latest DTI-Studio 3.0.1 beta x64 on Windows 7 64bit.   I
also tried DTI-Studio 3.0.1 beta x86.

Anyone interested in having a copy of my 4D Nifti file and seeing if
they can import it?

thanks
Mark

On Wed, Dec 16, 2009 at 8:46 PM, susumu mori <susumu at mri.jhu.edu> wrote:
> Hi Mark,
>
> Please try Philips REC format. This is a 4D raw format with integer. For
> both "raw" and "Philips REC", DtiStudio expect you to have 4D raw
> (no-header) file, not a bunch of 3D files. In your case, you need a single
> raw file that contains all 65 volume data (65 x 96 x 128 x 47) in one file.
>
> For this conversion, you can read 4D Nifty or 4D analyze (depending on the
> version of DtiStudio) by MriView3D and save all the images at once as a
> "raw" format. Then, the images are ready for DtiMapping. In DtiMapping, as I
> mentioned, open it as Philips REC. In the opening window, specify;
>
> 96x128x47
>
> Then you should get "65" as the number of the 3D images correctly calculated
> from the file size at the left bottom of the window. Also choose
> gradient-by-gradient for the order of the file. If you have a correct table
> with 65 lines, you should not get the error message.
>
> If you have the 4D analyze file, the *.img file of the Analyze format can
> also be directly read as "Philips REC". However, you have to be careful
> because if the Analyze is in Neurology convention (default setup) and read
> the *.img as "Philips REC", the images may be inverted because DtiStudio
> uses Radiology convention.
>
> I hope it helps.
>
> Susumu
>
>
>
> On Wed, Dec 16, 2009 at 7:39 PM, Mark A. Pinsk <mpinsk at gmail.com> wrote:
>>
>> No luck.  Let me outline my steps here:
>>
>> 1. I start with a 4D NIFTI file that contains 65 volumes (60 DWI + 5 B0).
>> The image dimensions are 96x128, 47 slices per volume.
>> Slice orientation is Coronal.  FOV is 96x128.  Pixels are 1x1x1.1.
>>
>> 2. I split the 4D NIFTI file into 65 3D NIFTI files using this FSL
>> command:
>> fslsplit input.nii.gz
>>
>> 3. I convert each of the 65 3D NIFTI files to ANALYZE format:
>> fslchfiletype ANALYZE vol0000.nii.gz
>> [..]
>> fslchfiletype ANALYZE vol0064.nii.gz
>>
>> 4. I am able to successfully import the ANALYZE files in MRIView3D by
>> choosing Analyze format (but no luck with Raw format).
>>
>> 5. I have no luck importing the ANALYZE files in DTI Mapping choosing
>> Raw format.  I get this message:
>> "Number of files in this fold is less than expected:
>> (Img_Slices*Img_Blocks).
>>
>> Any suggestions?  Thanks for all your help!
>> Mark
>>
>>
>>
>>
>> On Wed, Dec 16, 2009 at 1:34 PM, darshan pai <darshanp20 at yahoo.com> wrote:
>> > 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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