RE: Right- left handed information

max keuken — Wed, 31 May 2023 19:25:46 GMT

Hi Federico,
Thank you for your interest in this dataset. I am sorry to say that we did not record this information at the time and we have no way of collecting it now. 
Best, 
Max
Originally posted by Federico Biafore:
<blockquote>
Hi, I would like to know if it is possible to know the distribution of left-handed and right-handed people in the sample. 
 
Thanks!
</blockquote>

Right- left handed information

Federico Biafore — Wed, 31 May 2023 18:02:38 GMT

Hi, I would like to know if it is possible to know the distribution of left-handed and right-handed people in the sample. 
 
Thanks!

RE: Data in DICOM format

max keuken — Wed, 29 Nov 2017 7:13:17 GMT

Hi Thibo,
No sorry about that, for this project we only prepared the NIFTI data format.
Best,
Max

RE: 3T DWI test-retest reliability dataset

max keuken — Wed, 29 Nov 2017 7:11:01 GMT

Hi Thibo,
Thank you for your interest, and sorry for the slow response as I was traveling.
Regarding the missing T1, for Subject "pp20" - "pp34" these are all missing as they were part of a new batch of subjects, in which the extra T1 measurements were dropped. This was done to optimize total scan duration since a single t1 image was sufficient for registration purposes.
Best regards
Max

RE: 3T DWI test-retest reliability dataset

Thibo Billiet — Thu, 23 Nov 2017 9:51:28 GMT

Hi,

Related to this, could it be that the pp20_t1_B folder is missing?
Maybe this is also related to upload issues, or perhaps there was no T1 acquisition for the retest case?

Kind regards,

Thibo

Data in DICOM format

Thibo Billiet — Thu, 09 Nov 2017 16:56:36 GMT

Hi,

Thank you for this great initiative. Would the data be also available in DICOM format?

Kind regards,

T

New version due to error in affine matrix

max keuken — Tue, 17 Oct 2017 11:37:54 GMT

###########################################################################
###########################################################################
# #
# Error in the affine matrix #
# #
###########################################################################
###########################################################################

#############################
# Description of the error #
#############################
It has come to our attention (thanks to Eleftherios Garyfallidis) that there is a mismatch
between the voxel size as given by the pixel resolution and the voxel size if you extract
it using the affine information for the diffusion weighted data (DWI) which has been made
available on:

https://www.nitrc.org/frs/?group_id=990

and is described in the following publication:
Boekel, W., Forstmann, B.U., Keuken, M.C., (2017). A test-retest reliability analysis of
diffusion measures of white matter tracts relevant for cognitive control.
Psychophysiology 54 (1): 24-33.

The DWI data was acquired with the following sequence:
www.spinozacentre.nl/wiki/index.php/NeuroWiki:Sequences#DTI32_SENSE2

and this sequence should have resulted in 2mm isotropic voxels.
However there is a mismatch in the header of the shared files. More specifically, in python using nibabel:

import nibabel as nib
# loading the data as exported by V2.6 (version 1.1 on nitric):
img1 = nib.load('pp01_dwi_run01_A.nii.gz')
# Give me the voxel size based on the affine info
nib.affines.voxel_sizes(img1.affine)
# output:
# array([ 2.00000002, 1.99999997, [b]3.73333342[/b]])
# Give me the voxel size based on the header info
img1.header.get_zooms()[:3]
# output:
# (2.0, 2.0, 2.0)

Based on the header info the data is 2mm isotropic, whereas according to the affine info the voxel size in the z-dimension is 3.733mm which is incorrect.

The question is whether the data was actually acquired with a z voxel size of 3.7mm, and then resliced OR whether the tool that was used to export the data damaged the header info and that the affine matrix info is not correct?

###################################
# Where does the error come from ? #
###################################
I went back to the raw data which were backed up by the first author. The raw data that was exported from the scanner were par/rec files.
This is in Philips proprietary format and can be used instead of the DICOM format.

# Par/rec stage?
The par/rec file of pp01_dwi_run01_A has the following header info (as read by MIPAV):
Image information
Dimension 0: 112
Dimension 1: 112
Dimension 2: 60
Dimension 3: 34
Type: Float
Min: 0.0
Max: 1072259.625
Modality: Magnetic Resonance
Slice origin upper left corner of image - right hand rule
Origin X (left to right) : -0.0
Origin Y (top to bottom) : -0.0
Origin Z:(into the screen): 58.0
Origin T:(time): 0.0
Orientation: Axial
X axis orientation: right to left
Y axis orientation: anterior to posterior
Z axis orientation: inferior to superior
Pixel resolution 0: 2.0 Millimeters
Pixel resolution 1: 2.0 Millimeters
Pixel resolution 2: 2.0 Millimeters
Pixel resolution 3: 7542.096 Milliseconds
Slice thickness: 0.0
Endianess: Little Endian
Matrix:
1.0000 0.0000 0.0000 0.0000
0.0000 1.0000 0.0000 0.0000
0.0000 0.0000 1.0000 0.0000
0.0000 0.0000 0.0000 1.0000
Other information
Description = Magnetic Resonance
Voxel Offset = 352.0
Intent code = No intention
X,Y,Z Coordinate system = Scanner-based anatomical
Source type = FLOAT
Slope scale = 1.0
Added offset = 0.0
Frequency encoding direction = none
Phase encoding direction = none
Slice acquisition direction = none
Axis: x-orientation = Right to Left
Axis: y-orientation = Anterior to Posterior
Axis: z-orientation = Inferior to Superior
X Origin: -0.0
Y Origin: -0.0
Z Origin: 58.0
cal_min = 0.0
cal_max = 0.0
Bits per Pixel = 32
Name or meaning of data =
No extended header is present
Qform Matrix =
2.0000 -0.0000 -0.0000 -0.0000
-0.0000 2.0000 -0.0000 -0.0000
0.0000 0.0000 2.0000 -0.0000
0.0000 0.0000 0.0000 1.0000

Based on this information, the par/rec has the expected dimensions (2mm isotropic).
So the error does not come from the data acquisition side of things.

# Par/rec -> nifti stage?
The par/rec files were initially exported to Nifti's using an open source tool called r2agui (v 2.6. https://sourceforge.net/projects/r2agui/ ).
When checking the voxel size using nibabel I get the exact same output as when I would use the images that were uploaded to nitrc.org.
So it seems that the r2agui software did not interpret the DWI par/rec data correctly and damaged the affine info.

###################################
# Solution #
###################################
In the 5 years that passed between acquiring and exporting the par/rec data to nifti there has been a new release of the r2agui software.
Using r2agui (v 2.7. which addressed issues with exporting DWI data) I exported the par/rec file again.

Now in python I get the following:

# loading the data as exported by V2.7:
img2 = nib.load('pp01_dwi_run01_A_v27.nii.gz')
# Give me the voxel size based on the affine info
nib.affines.voxel_sizes(img2.affine)
# output:
# array([ 2.00000002, 1.99999997, 1.99999995])
# Give me the voxel size based on the header info
img2.header.get_zooms()[:3]
# output:
# (2.0, 2.0, 2.0)

So using the updated version of r2agui (V 2.7) the data is now exported in such a way that the affine voxel sizes correspond to the voxel sizes that were acquired at the scanner.

All structural scans have been re-exported, de-faced with the identical mask, and re-uploaded into a new data release (V2.0)

RE: 3T DWI test-retest reliability dataset

Aimee Wang — Thu, 23 Jun 2016 21:21:52 GMT

Thank you!

RE: 3T DWI test-retest reliability dataset

max keuken — Thu, 23 Jun 2016 20:32:58 GMT

Hi Aimee,
Thanks for the heads up!
This seems to ba a technical issue with uploading the data to NITRC. I'll upload those subjects again and email you once they are available.

Best regards,
Max

3T DWI test-retest reliability dataset

Aimee Wang — Thu, 23 Jun 2016 20:26:34 GMT

I can't help noticing that subject"pp07"and "pp16"are not available for downloading .
Is it a technical issue or they were omitted?

And could you telll me the reason?

Thanks

NITRC 3T DWI test-retest reliability dataset Forum: open-discussion

RE: Right- left handed information

Right- left handed information

RE: Data in DICOM format

RE: 3T DWI test-retest reliability dataset

RE: 3T DWI test-retest reliability dataset

Data in DICOM format

New version due to error in affine matrix

RE: 3T DWI test-retest reliability dataset

RE: 3T DWI test-retest reliability dataset

3T DWI test-retest reliability dataset