FieldMap Correction

Submitted by independentVar on Thu, 04/02/2020 - 09:00

Hi all,

I’m encountering a problem with the FieldMap Correction in DPARSF pointing to

DPARSFA_run (line 812): „Index exceeds matrix dimensions.“

 I have 2 phase dicoms and 2 magnitude dicoms per slice and as far as I can tell the nii look ok and are saved in the correct folder.

The settings I have used are

Cfg.FieldMap.IsNeedConvertDCM2IMG: 1

Cfg.FieldMap.IsCalculateVDM: 1

Cfg.FieldMap.EPIBasedFieldMap: 0

Cfg.FieldMap.IsFieldMapCorrectionUnwarpRealign: 1

Cfg.FieldMap.TE1: 0

Cfg.FieldMap.TE2: 0

Cfg.FieldMap.DataFormat: ‚TwoPhaseMagnitude‘

 

Does anybody have an idea how to find out what causes this error?

Thank you for your time! Best, Michael

Forums:

YAN Chao-Gan

Mon, 04/06/2020 - 02:30

Please list the file tree of your FieldMap directory.

independentVar

Mon, 04/06/2020 - 07:36

Thanks for answering my question so quickly.

I probably should have posted that "Check Data Organisation" returns:

"Congratulations, data organization checking passed!!! Now please go ahead to DPARSFA or DPABISurf! :)

ans = 1"

Here’s the filetree of the FieldMap directory anyway (excluding dcm names):

X:.

+---Magnitude1Img

|   \---SAD006

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_3_e1.json

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_3_e1.nii

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_3_e2.json

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_3_e2.nii

|          

+---Magnitude1Raw

|   \---SAD006

[84 dcm]

|          

+---PhaseDiffImg

|   \---SAD006

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_4_e1_ph.json

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_4_e1_ph.nii

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_4_e2_ph.json

|           SAD006_gre_adaptierteFieldMap_2pha2magn_20200313092958_4_e2_ph.nii

|          

\---PhaseDiffRaw

    \---SAD006

[84 dcm]          

YAN Chao-Gan

Mon, 04/06/2020 - 13:31

Could you revise Line 812 of DPARSFA_run.m

from

parfor i=1:AutoDataProcessParameter.SubjectNum

to

for i=1:AutoDataProcessParameter.SubjectNum

 

Thus, we can get the exact line of error?