[Freesurfer] Tracula B0 correction/movement parameters

2015-05-28 Thread Baur Volker
Dear experts, First: We want to use B0 field map correction (unwarping) within the trac-all -prep stream. However, as in http://fsl.fmrib.ox.ac.uk/fsl/fsl-4.1.9/fugue/feat_fieldmap.html, we have one magnitude and one real field map image, NOT one magnitude and one phase image. Can Tracula handl

[Freesurfer] Interpreting QA Tools Output -- Tal Normalization error?

2015-05-07 Thread Baur Volker
Dear colleagues and experts, we would greatly appreciate any help in interpreting the results of the QA Tools. Please look at our attachments containing snapshots of the results html file after running QA Tools. http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150505/b929e6cd/a

[Freesurfer] QA-Tools installation problem

2015-04-30 Thread Baur Volker
Dear experts, we have a problem with installation of QA-Tools. It seems that it is not because of ImageMagick and Gawk not being properly installed, but rather there seems to be some problems with environmental variables. For example, when changing into QA-Tools directory in the terminal and sta