Hi Hao - This will also be fixed in the new version. For now, if you do not have them as dicoms, please do your testing without a field map.

Thanks,
a.y

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Hao wen [hao.freesurfer@hotmail.com]
Sent: Tuesday, December 20, 2016 1:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] trac-all error with .nii.gz images, mri_probedicom

Hello:

More information to give, I think the problem is from the format of the magnitude and phase image for the registration-based B0-inhomogeneity compensation, I tried to comment the registration-based B0-inhomogeneity compensation, and it seems to work, So:


In TRACULA, we can not define the magnitude and phase image to be nii.gz???


Thanks



De : Hao wen
Envoyé : mardi 20 décembre 2016 18:44
À : freesurfer@nmr.mgh.harvard.edu
Objet : RE: trac-all error with .nii.gz images, mri_probedicom
 

Sorry, the command is not

trac-all -path -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txtt,

it is :

trac-all -prep -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt


Thanks

Hao

De : Hao wen
Envoyé : mardi 20 décembre 2016 18:42
À : freesurfer@nmr.mgh.harvard.edu
Objet : trac-all error with .nii.gz images, mri_probedicom
 

Hello, FreeSurfer experts:

I know that we are going to have a new version of FS 6.0.0, but with the curent newest version of TRACULA(trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp ) for FS5.3.0, I am working on UBUNTU14.0.


To run tracula in parallel on my machine, here is my config file( for test, I have two subjects, and all are recon-alled, I stored all the image into .nii.gz(dwi.nii.gz, fmap_magnitude.nii.gz, fmap_phasediff.nii.gz),I use the magnitude and phase image to do the correction for the B0-inhomogeneity, the gradient table format are .bvec and .bval , Here is one of my config file:


### This is to define the CAPS version subjects_dir and subject_id for FreeSurfer
setenv SUBJECTS_DIR /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/Freesurfer/Reconall/reconall_GENFI/clinica_reconall_result/prevdemals_67subjs/analysis-series-default/subjects
set dtroot = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result
set subjlist = ( sub-PREVDEMALS0010001BE/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010001BE_ses-M0 )

### This is to point to the dwi original data
set dcmroot = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test
set dcmlist = ( sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.nii.gz)

### This is to define the dwi gradient table(bvel and bvec)
set bvecfile = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bvec
set bvalfile = /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010001BE/ses-M0/dwi/sub-PREVDEMALS0010001BE_ses-M0_dwi.bval

### This is to define the registration-based B0-inhomogeneity compensation with the magnitude and phase map images
set dob0 = 1
set b0mlist = (sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_magnitude1.nii.gz)
set b0plist = (sub-PREVDEMALS0010001BE/ses-M0/fmap/sub-PREVDEMALS0010001BE_ses-M0_phasediff.nii.gz)

# This is to define Echo spacing for field mapping sequence (from sequence printout), only used when doing registration-based B0-inhomogeneity compensation.
set echospacing = 0.7

Here is the command to run the preprocessing:

trac-all -path -c /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/config_file/sub-PREVDEMALS0010001BE_config.txt

But it gave me some errro from mri_probedicom:

mri_probedicom --i /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/dmri_data_test/sub-PREVDEMALS0010002VH/ses-M0/fmap/sub-PREVDEMALS0010002VH_ses-M0_phasediff.nii.gz > /aramis/dataARAMIS/users/junhao.wen/PhD/PREVDEMALS/dMRI/tracula/tracula_result/sub-PREVDEMALS0010002VH/ses-M0/t1/freesurfer-cross-sectional/sub-PREVDEMALS0010002VH_ses-M0/dmri/b0info.dat
Linux DELLEED1 4.2.0-42-generic #49~14.04.1-Ubuntu SMP Wed Jun 29 20:22:11 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

trac-preproc exited with ERRORS at Tue Dec 20 18:22:04 CET 2016

The error is obvious, because the image here is not a dicom file, but I suppose tracula can deal with any format for mri_convert?

In case you need the trac-all.log, I atttached one of them here.

Really need your help, thanks in advance

Hao