[Mristudio-users] Diffeomorph file format

Sat Oct 1 16:52:51 EDT 2016

I believe the conversion to byte is referring to reformatting the subject data from data types of, e.g., integer 16-bit or float 32-bit, to an 8-bit data type (byte) so that mapping can be computed from the 8-bit data format template. It could be confusing if folks are thinking data formats as in Analyze vs. NIFTI.

--Lei

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Lei Wang, Ph.D.
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From: mristudio-users [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Tuesday, September 27, 2016 8:09 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support <mristudio-users at mristudio.org>
Subject: Re: [Mristudio-users] Diffeomorph file format

Hi Mark,

In DiffeoMap, there is a button that can convert images to a byte format. I don't have DiffeoMap in my laptop (I'm out of my office), but it is one of those in the upper right column with a letter "B", I thought...

On Wed, Sep 21, 2016 at 5:46 PM, Mark Wagshul <Mark.Wagshul at einstein.yu.edu<mailto:Mark.Wagshul at einstein.yu.edu>> wrote:
Hi.  I am new to using Diffeomorph and am running into a file format problem.  When I try to run a single channel LDDMM using one of the supplied templates (JHU-MNI-SS-T1), it gives me an error saying that the template needs to be a byte image.  I thought this was supplied by the Diffeomorph software so would already be in the required format.

Anyone have an experience with this?

Thanks,

Mark

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Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

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From: mristudio-users [mailto:mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org>] On Behalf Of Ming Peng
Sent: Wednesday, July 13, 2016 11:52 AM
To: mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
Subject: [Mristudio-users] How to recalculate gradient table of Philips DICOM files with 'gradient overplus' on

Hi:
  I have a dataset of DICOM files (a directory contains lots of .dcm files), and these data are collected from Philips device with "gradient overplus" option on.
  After googling, I found that the gradient table of these data should be recalculated if the "gradient overplus" option is on for Philips devices. And I found several tools:
  1 - DTI_gradient_table_creator
    http://godzilla.kennedykrieger.org/~jfarrell/software_web.htm#DTI_gradient_table_creator<https://urldefense.proofpoint.com/v2/url?u=http-3A__godzilla.kennedykrieger.org_-7Ejfarrell_software-5Fweb.htm-23DTI-5Fgradient-5Ftable-5Fcreator&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=T3LTsygGGhu6owN1Pl2H1LXJhiO_q6jqSIoDGjOwCcI&m=gFJYZTSGCw1yFrD8Se-etG4obMROKCNoMhkLTW47vVE&s=fSc4zc2iPDOXZM3pYeKOK5VSatrV96goWForGsJHPRQ&e=>

     This tool can only parse data in PAR/REC format, however my data are thousands of separate .dcm files from a single patient.

  2 - DTI gradient table
      http://jp.mathworks.com/matlabcentral/fileexchange/41876-dti-gradient-table/content/dti_grad_table.m<https://urldefense.proofpoint.com/v2/url?u=http-3A__jp.mathworks.com_matlabcentral_fileexchange_41876-2Ddti-2Dgradient-2Dtable_content_dti-5Fgrad-5Ftable.m&d=CwMFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=T3LTsygGGhu6owN1Pl2H1LXJhiO_q6jqSIoDGjOwCcI&m=gFJYZTSGCw1yFrD8Se-etG4obMROKCNoMhkLTW47vVE&s=mcKGyZ_k9X1-hKXo4MIwvrMKxXCa9Sv5I04EFnxO52A&e=>

     It only works for a multi-frame dcm file.

   My questions is:
      a - How can i recalculate the gradient table from these .dcm files ?
      b - Is there any other tools suited for this situation ?

   Thanks

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