External Email - Use Caution
Hello,
I am trying out the development dmri-bids-config script https://secure-web.cisco.com/1w--1vLn2hIhDzN_sQmBI1_PGZkHehc5IsuQS_9ZRqntOosEohjdkyIFCVKGApczWeVr9OI3T4SCrGz69YaLoLGHAMvVm4IR5AcEKAObvLLu31o982_GqN642-HWAmJJOiMJEwfEgspYOdlGbIGoUjEF6p0LUNHZsS8078o-ZKttsF21celYWQb9xQtiilQ30aASxohOLgfShtHnDD4V4jOSusTBWE9Tz9Z-oXbEQbIWe8uCK9mv6XzRusE80TZTO5XHnPiZJyiUeVLZH-R8bjuTfofQRLHfovd6ZrU45DHf1bARkrJd6Y3pKRBGgeq0ukCS8J8kVrMD7gIDYPl-Buw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmri_bids_config to set up my BIDS-formatted data for TRACULA. It runs fine without error, but I have some concerns about the automatically generated protocol variables.
1) For “echospacing”, should we be using the echo spacing as found in the scanner protocol, or effective echo spacing (as parsed from the BIDS json sidecar)? These values are fairly different from each other. It is also not clear what units the config file expects (I assume “ms” based on some of the examples and protocols I have looked at). 2) “epifactor” seems to be generated by a mathematical operation on the total readout time as parsed from the BIDS json file. The value I get from this operation is off by a few orders of magnitude. In my case, the predicted value from the BIDS json file is 127001, while the protocol epifactor is 128. What I imagine is happening here is that the script assumes the TotalReadoutTime is in different units, because it does some division by (0.001) and then adds 1 to the result. So if the units matched mine, then I would have ended up with 127+1 = 128 (which matches the protocol).
In either case, I am happy to see this being configured for BIDS and am excited to see it deployed in 7.3!
Best, Steven
Hi Steven - Indeed you are right that the values from your scanner protocol are the ones to use. In this case it sounds like what it finds in the json files does not agree with the scanner protocol, and this is good to know. I will look into this. Glad to hear it worked well otherwise!
Anastasia. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Steven Meisler smeisler@g.harvard.edu Sent: Thursday, July 7, 2022 12:03 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [TRACULA] Auto-BIDS Config Variables Question
External Email - Use Caution
Hello,
I am trying out the development dmri-bids-config scripthttps://secure-web.cisco.com/1w--1vLn2hIhDzN_sQmBI1_PGZkHehc5IsuQS_9ZRqntOosEohjdkyIFCVKGApczWeVr9OI3T4SCrGz69YaLoLGHAMvVm4IR5AcEKAObvLLu31o982_GqN642-HWAmJJOiMJEwfEgspYOdlGbIGoUjEF6p0LUNHZsS8078o-ZKttsF21celYWQb9xQtiilQ30aASxohOLgfShtHnDD4V4jOSusTBWE9Tz9Z-oXbEQbIWe8uCK9mv6XzRusE80TZTO5XHnPiZJyiUeVLZH-R8bjuTfofQRLHfovd6ZrU45DHf1bARkrJd6Y3pKRBGgeq0ukCS8J8kVrMD7gIDYPl-Buw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmri_bids_config to set up my BIDS-formatted data for TRACULA. It runs fine without error, but I have some concerns about the automatically generated protocol variables.
1) For “echospacing”, should we be using the echo spacing as found in the scanner protocol, or effective echo spacing (as parsed from the BIDS json sidecar)? These values are fairly different from each other. It is also not clear what units the config file expects (I assume “ms” based on some of the examples and protocols I have looked at). 2) “epifactor” seems to be generated by a mathematical operation on the total readout time as parsed from the BIDS json file. The value I get from this operation is off by a few orders of magnitude. In my case, the predicted value from the BIDS json file is 127001, while the protocol epifactor is 128. What I imagine is happening here is that the script assumes the TotalReadoutTime is in different units, because it does some division by (0.001) and then adds 1 to the result. So if the units matched mine, then I would have ended up with 127+1 = 128 (which matches the protocol).
In either case, I am happy to see this being configured for BIDS and am excited to see it deployed in 7.3!
Best, Steven
freesurfer@nmr.mgh.harvard.edu
-
Steven Meisler -
Yendiki, Anastasia