Realignment error

Submitted by jLee on Fri, 07/27/2018 - 07:11

Dear

I have a problem with realingment error that is driving me crazy.

The error that occurred is as follows.

Moving Head Motion Corrected Files:17101603 OKMoving Head Motion Corrected Files:17101304 OKMoving Head Motion Corrected Files:17091101 OKMoving Head Motion Corrected Files:17081004 OKMoving Head Motion Corrected Files:17080406 OKMoving Head Motion Corrected Files:17072101 OKMoving Head Motion Corrected Files:17070306 OKMoving Head Motion Corrected Files:17051102 OKMoving Head Motion Corrected Files:17030704 OKMoving Head Motion Corrected Files:17021703 OKMoving Head Motion Corrected Files:16122605 OKMoving Head Motion Corrected Files:16120103 OKMoving Head Motion Corrected Files:16102803 OKMoving Head Motion Corrected Files:16090903 OKMoving Head Motion Corrected Files:16082602 OKMoving Head Motion Corrected Files:16081904 OKMoving Head Motion Corrected Files:16032502 OKMoving Head Motion Corrected Files:16031704 OKMoving Head Motion Corrected Files:15111904 OKMoving Head Motion Corrected Files:15110503 OKMoving Head Motion Corrected Files:15082003 OKMoving Head Motion Corrected Files:15073001 OKMoving Head Motion Corrected Files:15031705 OKMoving Head Motion Corrected Files:15012302 OKMoving Head Motion Corrected Files:15012102 OKMoving Head Motion Corrected Files:15011603 OKMoving Head Motion Corrected Files:14122401 OKMoving Head Motion Corrected Files:14101911 OKMoving Head Motion Corrected Files:14101801 OKMoving Head Motion Corrected Files:14092806 OKMoving Head Motion Corrected Files:14082309 OKMoving Head Motion Corrected Files:14071201 OKMoving Head Motion Corrected Files:14062210 OKMoving Head Motion Corrected Files:14062105 OKMoving Head Motion Corrected Files:14050407 OK
    'Error in Realign, time point number doesn't match: 14050407'
    'Error in Realign, time point number doesn't match: 14062105'
    'Error in Realign, time point number doesn't match: 14062210'
    'Error in Realign, time point number doesn't match: 14071201'
    'Error in Realign, time point number doesn't match: 14082309'
    'Error in Realign, time point number doesn't match: 14092806'
    'Error in Realign, time point number doesn't match: 14101801'
    'Error in Realign, time point number doesn't match: 14101911'
    'Error in Realign, time point number doesn't match: 14122401'
    'Error in Realign, time point number doesn't match: 15011603'
    'Error in Realign, time point number doesn't match: 15012102'
    'Error in Realign, time point number doesn't match: 15012302'
    'Error in Realign, time point number doesn't match: 15031705'
    'Error in Realign, time point number doesn't match: 15073001'
    'Error in Realign, time point number doesn't match: 15082003'
    'Error in Realign, time point number doesn't match: 15110503'
    'Error in Realign, time point number doesn't match: 15111904'
    'Error in Realign, time point number doesn't match: 16031704'
    'Error in Realign, time point number doesn't match: 16032502'
    'Error in Realign, time point number doesn't match: 16081904'
    'Error in Realign, time point number doesn't match: 16082602'
    'Error in Realign, time point number doesn't match: 16090903'
    'Error in Realign, time point number doesn't match: 16102803'
    'Error in Realign, time point number doesn't match: 16120103'
    'Error in Realign, time point number doesn't match: 16122605'
    'Error in Realign, time point number doesn't match: 17021703'
    'Error in Realign, time point number doesn't match: 17030704'
    'Error in Realign, time point number doesn't match: 17051102'
    'Error in Realign, time point number doesn't match: 17070306'
    'Error in Realign, time point number doesn't match: 17072101'
    'Error in Realign, time point number doesn't match: 17080406'
    'Error in Realign, time point number doesn't match: 17081004'
    'Error in Realign, time point number doesn't match: 17091101'
    'Error in Realign, time point number doesn't match: 17101304'
    'Error in Realign, time point number doesn't match: 17101603'
 
I checked, but the time point was correct.
What is this error. what should I do to reslove this error?
 
My working environment: DPABI v3.0, MATLAB R2018a, Linux
 
 Thank you ​in advance ​for​ your​ help.

Forums:

YAN Chao-Gan

Wed, 08/01/2018 - 04:41

Please report here how many time points do you have for these subjects in FunImgAR, and what your presetting is.

jLee

Wed, 08/01/2018 - 05:33

Thank you for your reply.

The time points are 90.

The presetting is following:

time point: 90

TR:3

slice number: 35, slice order: interleaved 

realign, bet, new segment DARTER, normalize, filter: 0.01 ~ 0.1, voxel size: 2mm

smooth by DARTEL, FWGM= 4

Default mask

Best regard,

jLee

jLee

Wed, 08/01/2018 - 05:33

Thank you for your reply.

The time points are 90.

The presetting is following:

time point: 90

TR:3

slice number: 35, slice order: interleaved 

realign, bet, new segment DARTER, normalize, filter: 0.01 ~ 0.1, voxel size: 2mm

smooth by DARTEL, FWGM= 4

Default mask

Best regard,

jLee

YAN Chao-Gan

Fri, 08/03/2018 - 08:15

How did you check the number of time points of you imaging data?

jLee

Fri, 08/03/2018 - 09:29

I checked it using load_nii for Matlab, nibabel for python, and freeview for freesurfer. The results were all equal to 90-time points.

YAN Chao-Gan

Sat, 08/04/2018 - 00:14

Then I am not sure what the problem is.

jLee

Tue, 08/28/2018 - 02:06

Should the number of lines in the realignment parameter (FD_Jenkinson_xxx.txt) file be the same as the time point? 

And I found that it was preprocessed normally when I rename the file. Was there a case like this? 

veeus18

Sat, 08/04/2018 - 13:21

If you set TR to 0 and num of volumes to 0 in DPARSFA, and run the process, it will generate a TRinfo.csv file, wherein it will list the voxel resolution, num volumes, TR, num slices. This is a nice way to check if any of your images are different from the others.