Sorry, I should have asked earlier which scanner platform you acquired the data on. I was assuming (for no good reason) that this was Siemens data -- I can't be of much help with Philips data. Hopefully someone with experience with angulated acquisitions on Philips will chime in. Otherwise, posting to the MRICON list might be more appropriate.
The reason this is complicated is that there is no standardized way across vendors (to my knowledge) for storing diffusion gradient directions in the DICOMs.So, there is an interaction between (1) how Philips actually does the acquisition, (2) what Philips stores in the DICOMs, and (3) what 'dcm2nii' (or another DICOM conversion tool) does with that DICOM data.
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: "Raphael F.C." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, May 8, 2015 11:00 AM
I also tried doing that by command line. But there is no message telling me bvecs are being corrected.I pasted below the output of: $ dcm2nii CTR001
Chris Rorden's dcm2nii :: 4AUGUST2014 (Debian) 64bit BSD License
reading preferences file /home/nf04/.dcm2nii/dcm2nii.ini
0 files in working directory /media/nf04/0628596A28595A2F/Raphael/DTI/Teste
Data will be exported to /media/nf04/0628596A28595A2F/Raphael/DTI/Teste
Validating 1 potential DICOM images.
*User: check slice thickness. Possible Philips R3.2.2 bug - scanner can report different 0020,0032 values for the same slice.
Found 1 DICOM images.
Converting 1/1 volumes: 1
CTR001->20141213_162702Reg256DTIhighiso20SENSEs1151a1011.nii
4D Philips DTI data 2380
Swizzling: XYTZ -> XYZT
brightest voxel was 1601: data will be saved as 16-bit signed integer.
GZip...20141213_162702Reg256DTIhighiso20SENSEs1151a1011.nii.gz
Number of diffusion directions = 34
GZip...x20141213_162702Reg256DTIhighiso20SENSEs1151a1011.nii.gz
Removed DWI from DTI scan - saving volumes 1..33
2015-05-08 12:31 GMT-03:00 Harms, Michael <[log in to unmask]>:
Sorry, I always use 'dcm2nii' at the Linux command line, not a GUI version. What platform are you using?
'dtifit' will not perform any correction for angulation. That needs to be done by 'dcm2nii'. But again, I'm used to that being the default setting anyway (at least at the command line). Don't you get output to the terminal indicating that the bvecs are being rotated?
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: "Raphael F.C." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, May 8, 2015 10:21 AM
In dcm2nii, Help->Preferences, there is the checkbox 'Reorient large images to the nearest orthogonal plane'. And it says that it will not have any effect on DTI images to avoid 'disrupting interpretation of the principle vectors'.Thank you, Michael!Just to understand it better:
Does this mean that I can either check or uncheck this box, and this will not affect the DTI?
"If your acquisition was angled, then yes, you want to account for that in the bvecs if using 'dtifit'"
Does it mean that bvec file will be corrected after transformation so that I don't need to worry with converted DTI images, i.e., that I can just input these images into dtifit? O should I expect dtifit to perform that correction (The later is what I understood from the quotation above).
2015-04-28 11:09 GMT-03:00 Harms, Michael <[log in to unmask]>:
Hi,
If you are using the default settings, then yes, 'dcm2nii' should correct the bvecs for the slice angulation. If you pay attention to the output to the terminal (if using command line 'dcm2nii') you can confirm that this is indeed the case.
If your acquisition was angled, then yes, you want to account for that in the bvecs if using 'dtifit'.
cheers,-MH
--Michael Harms, Ph.D.-----------------------------------------------------------Conte Center for the Neuroscience of Mental DisordersWashington University School of MedicineDepartment of Psychiatry, Box 8134660 South Euclid Ave. Tel: 314-747-6173
From: "Raphael F.C." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Tuesday, April 28, 2015 6:26 AM
To: FSL - FMRIB's Software Library <[log in to unmask]>
Subject: Re: [FSL] TBSS - FOV angulation
Dear Andreas,
Just to be crystal clear:
1) dcm2nii will correct the gradient table by the angulation used in the FOV. Is that right? Is there any special option that I need to check in order to do so? Because I have already converted DICOM images to nifti used mricron (dcm2nii), but I didn't check any option box in particular.
2) If I don't do it, do you think there is going to be any problem?
Thank once more,Raphael
2014-12-11 9:54 GMT-02:00 Andreas Bartsch <[log in to unmask]>:
No, dtifit itself doesn't. You may do that with the DICOM to NIFTI conversion, e.g. using dcm2nii or MRIConvert.Cheers,Andreas
Von: "Raphael F.C." <[log in to unmask]>
Antworten an: FSL - FMRIB's Software Library <[log in to unmask]>
Datum: Donnerstag, 11. Dezember 2014 12:15
An: <[log in to unmask]>
Betreff: [FSL] TBSS - FOV angulation
Dear all,
Does anybody know if the DTIfit tool corrects the gradient direction table when I use an angulated FOV? Does it matter for TBSS?
I was talking to some researches that I know and they all used a non angulated FOV, but they were not sure if in the TBSS processing (or preprocessing steps, like DTIfit) the algorithm would correct the gradient table for this angulation.
Thank you very much,Raphael
--
Raphael F. CassebMedical Physicist, Ph.D. Student
Medical Physics Lab - State University of CampinasContact: +55 19 3521-8246
--
Raphael F. CassebMedical Physicist, Ph.D. Student
Medical Physics Lab - State University of CampinasContact: +55 19 3521-8246
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.
--
Raphael F. CassebMedical Physicist, Ph.D. Student
Medical Physics Lab - State University of CampinasContact: +55 19 3521-8246
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.
--
Raphael F. CassebMedical Physicist, Ph.D. Student
Medical Physics Lab - State University of CampinasContact: +55 19 3521-8246
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.