ERROR (nifti_image_read): failed to find header file

[Cibu Thomas]

Hello
I have some data preprocessed using TORTOISE, which allows me to
output files according to the DTI-TK specs.
Since Nifit is the preferred format, I converted the analyze file to
nifti using freesurfer’s mri_convert and ran all the DTI-TK
preprocessing step (eg: outlier and SPD checks).
All this worked fine.
But when I did the bootstrapping, only one data set was processed
while the rest were rejected because of
** ERROR (nifti_image_read): failed to find header file for '
Please see below for a log.
I would greatly appreciate your help with this.

Cheers
Cibu Thomas

dti_template_bootstrap ixi_aging_template.nii.gz GT_09_subjs.txt
dti_rigid_sn iteration 1
registering AB_09b_Only_R1_tensor.nii.gz ...
Rigid Registration of AB_09b_Only_R1_tensor.nii.gz to ixi_aging_template.nii.gz
Similarity Measure : EDS
Reorient Option : FS
Reading ixi_aging_template.nii.gz ... Done in 0.1s
sampling step size = [2, 2, 2]
Gaussian smoothing: sigma = [0.873, 0.873, 0.624] ... Done in 0.34s
Reading AB_09b_Only_R1_tensor.nii.gz ... Done in 0.09s
Gaussian smoothing: sigma = [0.736, 0.738, 0.736] ... Done in 0.25s
Initial Difference = 3.42e+06
initial estimate provided by center of mass alignment
cgm optimizer ftol = 0.01
both iteration 0 : 1.51e+06
both iteration 1 : 1.32e+06
both iteration 2 : 1.3e+06
both iteration 3 : 1.3e+06
cpu time consumed in seconds: 2.25
Final Registration Parameters = -16.9 20.7 8.63 0.121 -0.0221 0.000405
Final Difference = 1.3e+06
Total Difference Computation = 36
Total Gradient Computation = 4
Output the rigid transformation as AB_09b_Only_R1_tensor.aff
inFile = AB_09b_Only_R1_tensor.nii.gz
outFile = AB_09b_Only_R1_tensor_aff.nii.gz
interpolation option is LEI
reorientOption = PPD
Reading AB_09b_Only_R1_tensor.nii.gz ... Done in 0.08s
trans (inverse) applied = [-15.653, 13.007, 20.084]
[ 1.000, 0.003, -0.022; -0.000, 0.993, 0.120; 0.022, -0.120, 0.992]
reading output volume specification from ixi_aging_template.nii.gz
backward resampling ...time consumed = 0.510
Writing AB_09b_Only_R1_tensor_aff.nii.gz ... Done in 0.510s
done

AP_09a_Only_R1_tensor.nii.gz ...
AP_09a_Only_R1_tensor.nii.gz to ixi_aging_template.nii.gz
Similarity Measure : EDS
Reorient Option : FS
Reading ixi_aging_template.nii.gz ... Done in 0.09s
sampling step size = [2, 2, 2]
Gaussian smoothing: sigma = [0.873, 0.873, 0.624] ... Done in 0.33s
AP_09a_Only_R1_tensor.nii.gz'... ** ERROR (nifti_image_read): failed
to find header file for '
Done in 0s
AP_09a_Only_R1_tensor.nii.gz
AP_09a_Only_R1_tensor.nii.gz
AP_09a_Only_R1_tensor_aff.nii.gz
interpolation option is LEI
reorientOption = PPD
AP_09a_Only_R1_tensor.nii.gz'... ** ERROR (nifti_image_read): failed
to find header file for '
Done in 0s
AP_09a_Only_R1_tensor.nii.gz
done

[Hui Zhang]

Hi Cibu,

Thanks for trying DTI-TK.  I think something may not be right with your subject list file.  It is worth checking the example file here, if you haven't

http://dti-tk.sourceforge.net/pmwiki/uploads/Documentation/subjs.txt

You can also try to include two copies of AB_09b_Only_R1_tensor.nii.gz in your subject list file.  If that does not work, the only thing I can think of is with the subject list file formatting.

Gary

[Cibu Thomas]

Thanks Gary
Looks like the problem was some blank spaces after carriage returns
Working fine now.
cheers
Cibu

[Hui Zhang]

Great.  I should fix that fragility though.

Gary

[mitz]

Hi Thomas,

 

I'm a begginer user of the TORTOISE and the DTITK. After completing the processings on DTITK, I exported the resulting tensor image for input to DTITK. I have not known how to to convert the output image to the NifTI format for the processings on DTITK. Would you recommend use freesurfer for converting? Or can I use Interoperability tools in DTITK? In the latter case, which command should I use? Please give me your suggestions.

 

Thanks,

 

Mitsu

[Hui Zhang]

Hi Mitsu,

I know the TORTOISE developers use DTI-TK themselves.  So there must be a straightforward way to convert TORTOISE processed data into the NIfTI format that DTI-TK uses.  I've cc'ed Mustafa, one of the TORTOISE developer that I know well.  Hopefully, he will point you in the right direction.

Best regards,

Gary

====================================

Gary Hui Zhang, Ph.D.

Assistant Professor

Microstructure Imaging Group

Centre for Medical Image Computing

UCL Department of Computer Science

[mitz]

Hi Gary,

 

Thank you for your kindness! I'm looking forward to seeing suggestions from the TORTOISE developers.

 

Thanks,

 

Mitsu
2012年7月2日月曜日 21時56分52秒 UTC+9 Gary:

[M. Okan Irfanoglu]

Hello everyone,

After you process your data in TORTOISE and compute the tensors in DIFF_CALC, you can click "Export Images" in DIFF_CALC and select "DTITK Tensor" option.

This will create another folder in your proc folder named "xxx_DMC_N1_SAVE_DTITK"   if you processed your data with  DIFFPREP and used non-linear fitting to compute the tensors. The tensor file in that folder is DTITK compatible and you can directly use it for registration if you want to.

However, I would like to point out that this tensor does not have to be positive definite (very few negative eigenvalues are expected though) so you might want to convert it to "spd" as described in DTITK pipeline.

Hope this helps.

[Hui Zhang]

Okan,

Thanks very much!

Gary