Added creation of bvec and bval files when creating NIfTI files #335

cmadjar · 2018-08-13T21:57:16Z

For DWI files, the binary mnc2nii is not creating the .bvec and .bval files necessary to obtain the direction informations. Added support in the imaging pipeline so that those files can be created automatically within the function make_nii of the MRI.pm file.

Behaviour of the script:

if there are values in the MINC header acquisition:bvalues then create the .bval file using these values
if there are values in the MINC headers acquisition:direction_x, acquisition:direction_y and acquisition:direction_z then create the .bvec file using these values

Notes for existing projects

A script has been created in the tools directory to create the missing bval/bvec files for projects that have the 'create_nii' configuration set to 'Yes'. This script is called create_nifti_bval_bvec.pl.

Notes for people that want to create those files from a different script

Simply run mnc2nii, then call the MRI.pm functions create_dwi_nifti_bval_file and create_dwi_nifti_bvec_file to create the .bval and .bvec files. Args to the function are:

file hash ref (after loading the file via the File.pm library
full path to the .bval or .bvec file

…WI files (when bvalue and direction are found in the MINC header)

cmadjar · 2018-08-13T21:58:22Z

@MounaSafiHarab As I created the PR, I just thought I should probably create a tool script to back populate the .bvec and .bval files for projects that have NIfTI creation turned on. What do you think?

cmadjar · 2018-08-15T14:06:12Z

@MounaSafiHarab @nicolasbrossard this should be ready for review :)

nicolasbrossard · 2018-08-28T17:56:42Z

tools/create_nifti_bval_bvec.pl

+my $sth = $dbh->prepare($query);
+$sth->execute('acquisition:bvalues');
+
+my @file_ids;


my @file_ids = map { $_->{'FileID'} } @{ $sth->fetchall_arrayref( {} ) };

...but if you think it is too cryptic, leave the current code as is.

done. Thanks for the suggestion!

nicolasbrossard · 2018-08-28T17:59:44Z

tools/create_nifti_bval_bvec.pl

+
+    # determine paths for bval/bvec files
+    my $minc = $file->getFileDatum('File');
+    my ($bval_file, $bvec_file) = map { $minc }(0 .. 1);


Since you are creating an array of identical elements, use the repetiton (x) operator:

my ($bval_file, $bvec_file) = ($minc) x 2;

A lot simpler. Thanks!

nicolasbrossard · 2018-08-28T18:01:40Z

tools/create_nifti_bval_bvec.pl

+
+    # determine paths for bval/bvec files
+    my $minc = $file->getFileDatum('File');
+    my ($bval_file, $bvec_file) = map { $minc }(0 .. 1);


Since you are matching the end of the file name, the g pattern match modifier is not needed.

right. Removed the g pattern match modifier

nicolasbrossard · 2018-08-28T18:03:16Z

tools/create_nifti_bval_bvec.pl

+    $bvec_file =~ s/mnc$/bvec/g;
+
+    # create complementary nifti files for DWI acquisitions
+    my $bval_success = NeuroDB::MRI::create_dwi_nifti_bval_file(


I like "$data_dir/$bval_file" better than $data_dir . '/' . $bval_file

nicolasbrossard · 2018-08-28T18:03:23Z

tools/create_nifti_bval_bvec.pl

+    my $bval_success = NeuroDB::MRI::create_dwi_nifti_bval_file(
+        \$file, $data_dir . '/' . $bval_file
+    );
+    my $bvec_success = NeuroDB::MRI::create_dwi_nifti_bvec_file(


I like "$data_dir/$bvec_file" better than $data_dir . '/' . $bvec_file

nicolasbrossard · 2018-08-28T18:11:45Z

uploadNeuroDB/NeuroDB/MRI.pm

+
+    # clean up the bvals string
+    $bvals =~ s/\.\,//g; # remove all '.,' from the string
+    $bvals =~ s/\.$//g;  # remove the last trailing '.' from the string


Unnecessary g.

nicolasbrossard · 2018-08-28T18:13:01Z

uploadNeuroDB/NeuroDB/MRI.pm

+    # print bvals into bval_file
+    write_to_file($bval_file, $bvals, '>');
+
+    return 1 if (-e $bval_file);


You could also do

return -e $bval_file;

did not think of that. Nice!

nicolasbrossard · 2018-08-28T18:13:59Z

uploadNeuroDB/NeuroDB/MRI.pm

+        $mode = '>>'; # set to 0 to append to the file the other rows
+    }
+
+    return 1 if (-e $bvec_file);


return -e $bvec_file;

nicolasbrossard · 2018-08-28T18:55:55Z

uploadNeuroDB/NeuroDB/MRI.pm

+
+    return undef unless @bvecs;
+
+    # loop through all bvecs, clean them up and print them into the bvec file


I think opening the file, writing to it and then closing it on each iteration is not a good idea. I wouldn't even define a function to print to a file

s/^\"+|\"$//g for @bvec; open(OUT, '>', $bvec_file) or die "Cannot write to file $bvec_file: $!\n"; print OUT map { "$_\n" } @bvec; close(OUT);

uploadNeuroDB/NeuroDB/MRI.pm

nicolasbrossard · 2018-08-28T19:33:53Z

uploadNeuroDB/NeuroDB/MRI.pm

+        $file->getParameter('acquisition:direction_y'),
+        $file->getParameter('acquisition:direction_z')
+    );
+


I think @bvecs will always contain 3 elements and so will always evaluate to true. return undef unless @bvecs is unnecessary IMHO. Have you ever come across such a case?

Actually, for T1W acquisitions for example, those 3 elements are not there and it will return undef, skipping the bval/bvec creation since there are no fields to create them. This avoids having to add another config setting to specify the scan type for which to create bval/bvec files (which would be a config setting a bit obscure). So if those headers are present, continue in this function to create the bvec file, if they are not present, then return from the function and don't create bvec file. Does that make more sense?

cmadjar

@nicolasbrossard Thank you for your feedback!! They should all have been taken care of. Please re-review.

cmadjar · 2018-08-29T13:02:15Z

tools/create_nifti_bval_bvec.pl

+my $sth = $dbh->prepare($query);
+$sth->execute('acquisition:bvalues');
+
+my @file_ids;


done. Thanks for the suggestion!

cmadjar · 2018-08-29T13:02:59Z

tools/create_nifti_bval_bvec.pl

+
+    # determine paths for bval/bvec files
+    my $minc = $file->getFileDatum('File');
+    my ($bval_file, $bvec_file) = map { $minc }(0 .. 1);


A lot simpler. Thanks!

cmadjar · 2018-08-29T13:03:38Z

tools/create_nifti_bval_bvec.pl

+
+    # determine paths for bval/bvec files
+    my $minc = $file->getFileDatum('File');
+    my ($bval_file, $bvec_file) = map { $minc }(0 .. 1);


right. Removed the g pattern match modifier

cmadjar · 2018-08-29T13:04:14Z

tools/create_nifti_bval_bvec.pl

+    $bvec_file =~ s/mnc$/bvec/g;
+
+    # create complementary nifti files for DWI acquisitions
+    my $bval_success = NeuroDB::MRI::create_dwi_nifti_bval_file(


cmadjar · 2018-08-29T13:04:22Z

tools/create_nifti_bval_bvec.pl

+    my $bval_success = NeuroDB::MRI::create_dwi_nifti_bval_file(
+        \$file, $data_dir . '/' . $bval_file
+    );
+    my $bvec_success = NeuroDB::MRI::create_dwi_nifti_bvec_file(


cmadjar · 2018-08-29T13:09:49Z

uploadNeuroDB/NeuroDB/MRI.pm

-    my $nifti = $minc;
-    $nifti    =~ s/mnc$/nii/g;
+    my ($nifti, $bval_file, $bvec_file) = map { $minc }(0 .. 2);
+    $nifti     =~ s/mnc$/nii/g;


done. As well as the ($minc) x 2 instead of map { $minc }(0 .. 2)

cmadjar · 2018-08-29T13:10:38Z

uploadNeuroDB/NeuroDB/MRI.pm


    #  mnc2nii command
    my $m2n_cmd = "mnc2nii -nii -quiet " .
                    $data_dir . "/" . $minc . " " .
                    $data_dir . "/" . $nifti;
    system($m2n_cmd);

+    # create complementary nifti files for DWI acquisitions


indeed. A lot clearer. I also did that for the command four lines before and it all fits in one line :)

cmadjar · 2018-08-29T13:13:05Z

uploadNeuroDB/NeuroDB/MRI.pm

+
+    # clean up the bvals string
+    $bvals =~ s/\.\,//g; # remove all '.,' from the string
+    $bvals =~ s/\.$//g;  # remove the last trailing '.' from the string


cmadjar · 2018-08-29T13:13:59Z

uploadNeuroDB/NeuroDB/MRI.pm

+    # print bvals into bval_file
+    write_to_file($bval_file, $bvals, '>');
+
+    return 1 if (-e $bval_file);


did not think of that. Nice!

cmadjar · 2018-08-29T13:18:48Z

uploadNeuroDB/NeuroDB/MRI.pm

+        $file->getParameter('acquisition:direction_y'),
+        $file->getParameter('acquisition:direction_z')
+    );
+


Actually, for T1W acquisitions for example, those 3 elements are not there and it will return undef, skipping the bval/bvec creation since there are no fields to create them. This avoids having to add another config setting to specify the scan type for which to create bval/bvec files (which would be a config setting a bit obscure). So if those headers are present, continue in this function to create the bvec file, if they are not present, then return from the function and don't create bvec file. Does that make more sense?

nicolasbrossard · 2018-09-11T20:35:54Z

uploadNeuroDB/NeuroDB/MRI.pm

+    $bvals =~ s/\.$//;   # remove the last trailing '.' from the string
+
+    # print bvals into bval_file
+    open(FILE, '>', $bval_file) or die "Could not open file $bval_file $!";


Missing semi-colon in error message (see corresponding message in create_dwi_nifti_bvec_file).

done in the next commit!

cmadjar · 2018-09-13T16:22:27Z

@nicolasbrossard Fixed the missing colon. Thank you! Ready for review again :)

added creation of bvec and bval files when creating NIfTI files for D…

27141d8

…WI files (when bvalue and direction are found in the MINC header)

cmadjar added Bug Add to release notes [branch] minor labels Aug 13, 2018

cmadjar added this to the 20.1 milestone Aug 13, 2018

cmadjar requested review from nicolasbrossard, MounaSafiHarab and sruthymathew123 August 13, 2018 21:57

script to back populate bval/bvec files

7cce1e5

cmadjar added the Caveat for Existing Projects label Aug 15, 2018

Corrected a typo

c5d2e41

nicolasbrossard requested changes Aug 28, 2018

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nicolasbrossard reviewed Aug 28, 2018

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Nicolas' feedback

a926eb8

cmadjar commented Aug 29, 2018

View reviewed changes

MounaSafiHarab mentioned this pull request Aug 30, 2018

Create .nii and make BIDS compliant output file structure #198

Merged

cmadjar changed the base branch from minor to 20.1-dev September 11, 2018 19:06

nicolasbrossard requested changes Sep 13, 2018

View reviewed changes

nicolasbrossard removed the request for review from MounaSafiHarab September 13, 2018 15:34

harmonization of the 'die' statement

f849c42

nicolasbrossard approved these changes Sep 13, 2018

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cmadjar merged commit a8972fc into aces:20.1-dev Sep 13, 2018

cmadjar deleted the creation_bvec_bval_after_mnc2nii_conversion branch September 13, 2018 18:40

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Added creation of bvec and bval files when creating NIfTI files #335

Added creation of bvec and bval files when creating NIfTI files #335

cmadjar commented Aug 13, 2018 •

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cmadjar commented Sep 13, 2018


		return undef unless @bvecs;

		# loop through all bvecs, clean them up and print them into the bvec file

Added creation of bvec and bval files when creating NIfTI files #335

Added creation of bvec and bval files when creating NIfTI files #335

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cmadjar commented Aug 13, 2018 • edited Loading

Behaviour of the script:

Notes for existing projects

Notes for people that want to create those files from a different script

cmadjar commented Aug 13, 2018

cmadjar commented Aug 15, 2018

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cmadjar commented Sep 13, 2018

cmadjar commented Aug 13, 2018 •

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