question about setting up Dcm2Bids config file

[stephen...@gmail.com]

Hello,
I hope that this question is appropriate for this group (I apologize if this is not the case). I'm having some trouble setting up the config file to use with Dcm2Bids so that it properly handles the field map images in the data set. One of the magnitude fieldmap images only differs from the phase difference image in one field: ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] vs "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"]. I cannot seem to get the config file set up so that these are properly differentiated. I tried including statements such as "in": {"ImageType": "'\"P\""} for the former and "in": {"ImageType": "'\"M\""} for the latter in the config file with no luck. The tool is very new to me, so I am probably missing something obvious. Does anyone happen to know where I am going wrong? Apologies again if the group is not intended for questions such as this.
Best regards,
Steve wilson

 

[Chris Gorgolewski]

You should try opening an issue at https://github.com/cbedetti/Dcm2Bids/issues and/or trying the never and better maintained fork at https://github.com/jooh/Dcm2Bids

Best,

Chris

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[Stephen Wilson]

Thanks very much, Chris.

Best,

Steve

Stephen J. Wilson, Ph.D.
Associate Professor
Department of Psychology
The Pennsylvania State University
311 Moore Building
University Park, PA 16802
Telephone: 814-865-6219
Fax: 814-863-7002
wilsonlab.la.psu.edu

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[chare...@gmail.com]

Hi,

I don't know if this has been resolved or not, but I had exactly the same issue and here is how I solved it:

...

{

"dataType": "fmap",

"suffix": "magnitude1",

"criteria": {

"in": {"SeriesDescription": "CBU_FieldMapping"},

         "equal":{"ImageType":["ORIGINAL", "PRIMARY", "M", "ND"],"EchoTime":0.00519}

}

},

{

"dataType": "fmap",

"suffix": "magnitude2",

"criteria": {

"in": {"SeriesDescription": "CBU_FieldMapping"},

         "equal":{"ImageType":["ORIGINAL", "PRIMARY", "M", "ND"],"EchoTime":0.00765}

}

},

{

"dataType": "fmap",

"suffix": "phasediff",

"criteria": {

"in": {"SeriesDescription": "CBU_FieldMapping"},

         "equal":{"ImageType":["ORIGINAL", "PRIMARY", "P", "ND"]}

},

"customHeader": {

"EchoTime1":0.00519,

"EchoTime2":0.00765

}

  }

...

I hope this helps,

ian

On Sunday, October 8, 2017 at 4:29:38 AM UTC+1, Stephen Wilson wrote:

Thanks very much, Chris.

Best,

Steve

Stephen J. Wilson, Ph.D.
Associate Professor
Department of Psychology
The Pennsylvania State University
311 Moore Building
University Park, PA 16802
Telephone: 814-865-6219
Fax: 814-863-7002
wilsonlab.la.psu.edu

On Sat, Oct 7, 2017 at 11:28 PM, Chris Gorgolewski <krzysztof....@gmail.com> wrote:

You should try opening an issue at https://github.com/cbedetti/Dcm2Bids/issues and/or trying the never and better maintained fork at https://github.com/jooh/Dcm2Bids

Best,

Chris

On Oct 7, 2017 8:12 PM, <stephen...@gmail.com> wrote:

Hello,
I hope that this question is appropriate for this group (I apologize if this is not the case). I'm having some trouble setting up the config file to use with Dcm2Bids so that it properly handles the field map images in the data set. One of the magnitude fieldmap images only differs from the phase difference image in one field: ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] vs "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"]. I cannot seem to get the config file set up so that these are properly differentiated. I tried including statements such as "in": {"ImageType": "'\"P\""} for the former and "in": {"ImageType": "'\"M\""} for the latter in the config file with no luck. The tool is very new to me, so I am probably missing something obvious. Does anyone happen to know where I am going wrong? Apologies again if the group is not intended for questions such as this.
Best regards,
Steve wilson

 

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