[Mristudio-users] Using processed data

Wed Dec 16 19:39:40 EST 2009

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
>>>>>> _______________________________________________
>>>>>> Mristudio-users mailing list
>>>>>> Mristudio-users at mristudio.org
>>>>>> http://lists.mristudio.org/mailman/listinfo/
>>>>>> Unsubscribe, send a blank email to:
>>>>>> Mristudio-users-unsubscribe at mristudio.org
>>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Mristudio-users mailing list
>>>> Mristudio-users at mristudio.org
>>>> http://lists.mristudio.org/mailman/listinfo/
>>>> Unsubscribe, send a blank email to:
>>>> Mristudio-users-unsubscribe at mristudio.org
>>>>
>>>
>>
>
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org
>
>
>
>
>
> _______________________________________________
> Mristudio-users mailing list
> Mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to: Mristudio-users-unsubscribe at mristudio.org
>