GE File Not Being Read by Tarquin

researc...@gmail.com

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Nov 17, 2017, 10:31:52 PM11/17/17

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Hello Everyone!

I have been put in charge of maintaining our processing of raw MRS, and I haven't been able to get the files from one of our sites inputted into Tarquin.

This is the output I get when running the terminal version:

"

tarquin --input P58368.7 --format ge --output_pdf ex.pdf

2017-Nov-17 19:01:15 INFO : TARQUIN 4.3.7 Started

2017-Nov-17 19:01:15 INFO : Loading data file : P58368.7

2017-Nov-17 19:01:15 INFO : Rdb reader rev : 26.002001

2017-Nov-17 19:01:15 INFO : P-file offset : 0

2017-Nov-17 19:01:15 INFO : Frame size : -57344

2017-Nov-17 19:01:15 INFO : Offset to data : -57344

2017-Nov-17 19:01:15 INFO : Nechoes : 0

2017-Nov-17 19:01:15 INFO : Water ref frames : 1.000000

error loading FID: Unrealistic number of reference frames, check data type.

2017-Nov-17 19:01:15 INFO : TARQUIN Finished

"

I created a small video showing what happens when I try through the GUI, though, admittedly, it's not very informative. Both GE files that I opened in the video came from the same machine, a GE Sigma 750W, except both acquisitions were separated by a few months. I get the same error output when I try to run through any of the new acquisitions.

Any thoughts on possible solutions? I am new to processing MRS through Tarquin, so any guidance at all would be greatly appreciated!

Thank you so much for your time,

Best

John Duncan

Matt Lyon

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Jan 11, 2018, 5:13:33 AM1/11/18

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Hi Duncan,

The problem is due to the header of the GE P-file being changed in DV26.
The line below refers to which version.

2017-Nov-17 19:01:15 INFO : Rdb reader rev : 26.002001

Unfortunately I am experiencing this exact issue, and have not found a way to fix this. At the moment I am trying to find a way to edit the header of the P-file to a version that was working with TARQUIN such as DV24.

Will update when I have found a fix

Regards

Matt

Martin

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Jan 14, 2018, 10:31:01 AM1/14/18

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Hi both,

I can confirm GE have changed the format of their p-files. I haven't been able to figure out the winning combination of new offsets yet - it looks like a more significant change than usual...

Martin

Nicole V

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Feb 8, 2018, 7:48:36 PM2/8/18

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Hi Martin,

Do you have any updates on this issue? I have been trying to process p-files from a GE Discovery MR750 3T system with no luck.

Thank you!

Nicole

Martin Wilson

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Feb 9, 2018, 4:22:53 AM2/9/18

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Hi Nicole,

I'm about 90% sure this is fixed in the source code, but no release yet. Are you using the Linux binary version of TARQUIN?

Martin

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Nicole V

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Feb 9, 2018, 10:42:18 AM2/9/18

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Hi Martin,

Thanks for your quick reply. Yes, I am using the Linux binary version!

Thank you,

Nicole

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Martin Wilson

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Feb 12, 2018, 8:20:03 AM2/12/18

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Hi Nicole,

Try this download and let me know if your problem is resolved:

https://www.dropbox.com/s/fbumo3oy5vewlpj/TARQUIN_Linux_4.3.11_RC.tar.gz?dl=0

Martin

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Nicole V

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Feb 13, 2018, 9:35:49 AM2/13/18

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Hi Martin,

Everything seems to be working! Do you by chance have an updated Mac version as well?

Thank you!

Nicole

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researc...@gmail.com

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Feb 14, 2018, 9:55:10 PM2/14/18

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Hi Martin,

Just wanted to say thank you for working on this!

My group uses the Mac version currently, though we're hoping to move to the linux version relatively soon. Any chance there's an updated Mac Version as well?

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Martin Wilson

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Feb 15, 2018, 2:58:11 AM2/15/18

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Yes, I’ll do a proper release now I know the GE issue is resolved.

Martin

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Martin Wilson

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Feb 21, 2018, 5:51:54 AM2/21/18

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Mac version now available from here:

https://sourceforge.net/projects/tarquin/files/TARQUIN_4.3.11/

Martin

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researc...@gmail.com

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Feb 26, 2018, 2:25:46 PM2/26/18

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Hey Martin,

sorry to bring bad news, but I'm still getting an error.

Here is the output:

`

2018-Feb-26 11:22:46 INFO : TARQUIN 4.3.11 Started

2018-Feb-26 11:22:46 INFO : Loading data file : P33792.7

2018-Feb-26 11:22:46 INFO : Rdb reader rev : 26.002001

2018-Feb-26 11:22:46 INFO : P-file offset : 213684

2018-Feb-26 11:22:46 INFO : Frame size : 32768

2018-Feb-26 11:22:46 INFO : Offset to data : 246452

2018-Feb-26 11:22:46 INFO : Nechoes : 1

2018-Feb-26 11:22:46 INFO : Water ref frames : 2.000000

2018-Feb-26 11:22:46 INFO : Water sup frames : 8.000000

2018-Feb-26 11:22:46 INFO : Number of coils : 12

2018-Feb-26 11:22:46 INFO : x dim : 1

2018-Feb-26 11:22:46 INFO : y dim : 1

2018-Feb-26 11:22:46 INFO : z dim : 1

2018-Feb-26 11:22:46 INFO : nStart = 50

2018-Feb-26 11:22:46 INFO : nEnd = 2048

2018-Feb-26 11:22:46 INFO : Averaging metabolite FIDs

2018-Feb-26 11:22:46 INFO : Averaging across 8 of 8 FIDs

TARQUIN Version 4.3.11

**** TARQUIN is a research tool and is NOT for clinical use. ****

2018-Feb-26 11:22:46 INFO : Rdb reader rev : 26.002001

2018-Feb-26 11:22:46 INFO : P-file offset : 213684

2018-Feb-26 11:22:46 INFO : Frame size : 32768

2018-Feb-26 11:22:46 INFO : Offset to data : 246452

2018-Feb-26 11:22:46 INFO : Nechoes : 1

2018-Feb-26 11:22:46 INFO : Water ref frames : 2.000000

2018-Feb-26 11:22:46 INFO : Water sup frames : 8.000000

2018-Feb-26 11:22:46 INFO : Number of coils : 12

2018-Feb-26 11:22:46 INFO : x dim : 1

2018-Feb-26 11:22:46 INFO : y dim : 1

2018-Feb-26 11:22:46 INFO : z dim : 1

2018-Feb-26 11:22:46 INFO : Averaging water ref FIDs

2018-Feb-26 11:22:46 INFO : Number of W fids does not match WS fids.

2018-Feb-26 11:22:46 INFO : Averaging accross 2 water reference fids.

Parameters Before Preprocessing

-------------------------------

Input file: P33792.7

Water reference file: P33792.7

Data points: 4096

Rows: 1

Columns: 1

Slices: 1

Echo time: 1606.39 s

Sampling frequency: 5000 Hz

Transmitter frequency: 1.27828e+08 Hz

Starting sample: 50

Ending sample: 2048

Removing signals in: [-45,+45] Hz

Autophasing yes/no?: yes

Water eddy correction?: no

Autoreferencing yes/no?: yes

Reference: 4.65 ppm

2018-Feb-26 11:22:46 INFO : Starting 'Preprocessing'

2018-Feb-26 11:22:46 INFO : Preprocessing fid 1 of 1

2018-Feb-26 11:22:46 INFO : Starting 'autophasing mag method water'

2018-Feb-26 11:22:46 INFO : Finished 'autophasing mag method water'

2018-Feb-26 11:22:46 INFO : Ref start = 4.650000 ppm

2018-Feb-26 11:22:46 INFO : Ref new = 4.651194 ppm

2018-Feb-26 11:22:46 INFO : Residual water freq. (Hz) : 0.152588

2018-Feb-26 11:22:46 INFO : Starting 'building Hankel LP matrix'

2018-Feb-26 11:22:46 INFO : Finished 'building Hankel LP matrix'

2018-Feb-26 11:22:46 INFO : Starting 'SVD of LP matrix'

2018-Feb-26 11:22:47 INFO : Finished 'SVD of LP matrix'

2018-Feb-26 11:22:47 INFO : Starting 'estimating LP parameters'

2018-Feb-26 11:22:47 INFO : Finished 'estimating LP parameters'

2018-Feb-26 11:22:47 INFO : Starting 'estimating LP amplitudes'

2018-Feb-26 11:22:47 INFO : Finished 'estimating LP amplitudes'

2018-Feb-26 11:22:47 INFO : Starting 'autophasing (new)'

2018-Feb-26 11:22:47 INFO : Finished 'autophasing (new)'

2018-Feb-26 11:22:47 DEBUG : Max Phi0 : 0.00

2018-Feb-26 11:22:47 INFO : Ref start = 4.650000 ppm

2018-Feb-26 11:22:47 INFO : Ref new = 4.679842 ppm

2018-Feb-26 11:22:47 DEBUG : Width pts : 60.41

2018-Feb-26 11:22:47 DEBUG : Width Hz est : 6.15

2018-Feb-26 11:22:47 DEBUG : Init beta est : 94.24

2018-Feb-26 11:22:47 INFO : Ymax = 8111561.067328

2018-Feb-26 11:22:47 INFO : sdev noise = 204130.557947

2018-Feb-26 11:22:47 INFO : SNR guess = 19.8686

2018-Feb-26 11:22:47 INFO : Finished 'Preprocessing'

Parameters After Preprocessing

------------------------------

Input file: P33792.7

Water reference file: P33792.7

Data points: 4096

Rows: 1

Columns: 1

Slices: 1

Echo time: 1606.39 s

Sampling frequency: 5000 Hz

Transmitter frequency: 1.27828e+08 Hz

Starting sample: 50

Ending sample: 2048

Removing signals in: [-45,+45] Hz

Autophasing yes/no?: yes

Water eddy correction?: no

Autoreferencing yes/no?: yes

Reference: 4.67984 ppm

2018-Feb-26 11:22:47 INFO : Simulating using 12 threads.

2018-Feb-26 11:22:48 INFO : All simulation threads stopped.

2018-Feb-26 11:22:48 ERROR : incorrect echo time (1606.39 in FID does not match 0.00 in basis)

2018-Feb-26 11:22:48 INFO : TARQUIN Finished

ERROR: Basis set and fid parameter mismatch, please resimulate

`

And this is for both the Mac and Linux versions.

John

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Martin Wilson

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Mar 2, 2018, 7:49:58 AM3/2/18

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Hi,

Thanks for the info. Can you work around it by manually setting the echo time (this is the real problem I think)?

Also, please send me the data if you're able.

Martin

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Dave Lythgoe

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Mar 2, 2018, 1:35:31 PM3/2/18

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Hi Martin,

I've just tried this with some DV25 data, which previously worked with the last version of Tarquin. It incorrectly reads the TE at 1.6 s, where it should have been 0.035 s. As you suggested, manually typing in the TE works fine.

Cheers,

Dave

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Martin

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Mar 12, 2018, 11:00:19 AM3/12/18

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Hi,

Thanks for the bug report, I've just tested some other data RDB_26.002001 that finds the correct TE. Are you able to send me an example?

Martin

researc...@gmail.com

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Apr 19, 2018, 1:46:28 PM4/19/18

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Hi Martin!

Any update on reading GE p-files?

Best,

John Duncan

Martin Wilson

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Apr 24, 2018, 4:24:06 AM4/24/18

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Hi John,

The data you sent me (TE=35ms) works ok with the latest version of the source code, so I'm wondering if I made a mistake with the binary release. Have you found a problem with the latest release?

Martin

Martin

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researc...@gmail.com

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May 3, 2018, 10:06:21 PM5/3/18

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Yes, we are still having trouble reading it. Here is the output from command: tarquin --input P88064.7 --format ge --output_pdf test.pdf

'

2018-May-03 19:02:22 INFO : TARQUIN 4.3.11 Started

2018-May-03 19:02:22 INFO : Loading data file : P85504.7

2018-May-03 19:02:22 INFO : Rdb reader rev : 26.002001

2018-May-03 19:02:22 INFO : P-file offset : 213684

2018-May-03 19:02:22 INFO : Frame size : 32768

2018-May-03 19:02:22 INFO : Offset to data : 246452

2018-May-03 19:02:22 INFO : Nechoes : 1

2018-May-03 19:02:22 INFO : Water ref frames : 2.000000

2018-May-03 19:02:22 INFO : Water sup frames : 8.000000

2018-May-03 19:02:22 INFO : Number of coils : 12

2018-May-03 19:02:22 INFO : x dim : 1

2018-May-03 19:02:22 INFO : y dim : 1

2018-May-03 19:02:22 INFO : z dim : 1

2018-May-03 19:02:22 INFO : nStart = 50

2018-May-03 19:02:22 INFO : nEnd = 2048

2018-May-03 19:02:22 INFO : Averaging metabolite FIDs

2018-May-03 19:02:22 INFO : Averaging across 8 of 8 FIDs

TARQUIN Version 4.3.11

**** TARQUIN is a research tool and is NOT for clinical use. ****

2018-May-03 19:02:22 INFO : Rdb reader rev : 26.002001

2018-May-03 19:02:22 INFO : P-file offset : 213684

2018-May-03 19:02:22 INFO : Frame size : 32768

2018-May-03 19:02:22 INFO : Offset to data : 246452

2018-May-03 19:02:22 INFO : Nechoes : 1

2018-May-03 19:02:22 INFO : Water ref frames : 2.000000

2018-May-03 19:02:22 INFO : Water sup frames : 8.000000

2018-May-03 19:02:22 INFO : Number of coils : 12

2018-May-03 19:02:22 INFO : x dim : 1

2018-May-03 19:02:22 INFO : y dim : 1

2018-May-03 19:02:22 INFO : z dim : 1

2018-May-03 19:02:22 INFO : Averaging water ref FIDs

2018-May-03 19:02:22 INFO : Number of W fids does not match WS fids.

2018-May-03 19:02:22 INFO : Averaging accross 2 water reference fids.

Parameters Before Preprocessing

-------------------------------

Input file: P85504.7

Water reference file: P85504.7

Data points: 4096

Rows: 1

Columns: 1

Slices: 1

Echo time: 1606.39 s

Sampling frequency: 5000 Hz

Transmitter frequency: 1.27828e+08 Hz

Starting sample: 50

Ending sample: 2048

Removing signals in: [-45,+45] Hz

Autophasing yes/no?: yes

Water eddy correction?: no

Autoreferencing yes/no?: yes

Reference: 4.65 ppm

2018-May-03 19:02:22 INFO : Starting 'Preprocessing'

2018-May-03 19:02:22 INFO : Preprocessing fid 1 of 1

2018-May-03 19:02:22 INFO : Starting 'autophasing mag method water'

2018-May-03 19:02:22 INFO : Finished 'autophasing mag method water'

2018-May-03 19:02:22 INFO : Ref start = 4.650000 ppm

2018-May-03 19:02:22 INFO : Ref new = 4.664324 ppm

2018-May-03 19:02:22 INFO : Residual water freq. (Hz) : 1.831055

2018-May-03 19:02:22 INFO : Starting 'building Hankel LP matrix'

2018-May-03 19:02:22 INFO : Finished 'building Hankel LP matrix'

2018-May-03 19:02:22 INFO : Starting 'SVD of LP matrix'

2018-May-03 19:02:23 INFO : Finished 'SVD of LP matrix'

2018-May-03 19:02:23 INFO : Starting 'estimating LP parameters'

2018-May-03 19:02:23 INFO : Finished 'estimating LP parameters'

2018-May-03 19:02:23 INFO : Starting 'estimating LP amplitudes'

2018-May-03 19:02:23 INFO : Finished 'estimating LP amplitudes'

2018-May-03 19:02:23 INFO : Starting 'autophasing (new)'

2018-May-03 19:02:23 INFO : Finished 'autophasing (new)'

2018-May-03 19:02:23 DEBUG : Max Phi0 : 0.63

2018-May-03 19:02:23 INFO : Ref start = 4.650000 ppm

2018-May-03 19:02:23 INFO : Ref new = 4.639257 ppm

2018-May-03 19:02:23 DEBUG : Width pts : 23.83

2018-May-03 19:02:23 DEBUG : Width Hz est : 2.42

2018-May-03 19:02:23 DEBUG : Init beta est : 7.22

2018-May-03 19:02:23 INFO : Ymax = 33880319.383140

2018-May-03 19:02:23 INFO : sdev noise = 194853.587139

2018-May-03 19:02:23 INFO : SNR guess = 86.9379

2018-May-03 19:02:23 INFO : Finished 'Preprocessing'

Parameters After Preprocessing

------------------------------

Input file: P85504.7

Water reference file: P85504.7

Data points: 4096

Rows: 1

Columns: 1

Slices: 1

Echo time: 1606.39 s

Sampling frequency: 5000 Hz

Transmitter frequency: 1.27828e+08 Hz

Starting sample: 50

Ending sample: 2048

Removing signals in: [-45,+45] Hz

Autophasing yes/no?: yes

Water eddy correction?: no

Autoreferencing yes/no?: yes

Reference: 4.63926 ppm

2018-May-03 19:02:23 INFO : Simulating using 12 threads.

2018-May-03 19:02:23 INFO : All simulation threads stopped.

2018-May-03 19:02:23 ERROR : incorrect echo time (1606.39 in FID does not match 0.00 in basis)

2018-May-03 19:02:23 INFO : TARQUIN Finished

ERROR: Basis set and fid parameter mismatch, please resimulate

'

John

Martin

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Laura Garrison

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Oct 10, 2019, 10:21:27 AM10/10/19

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I am also still having trouble reading the new p-file format, using the Mac OS binary version. I appreciate any help in fixing this, it seems to work fine on a colleague's linux installation, so we're wondering if this is mac-specific...

Here is the output from running the p-file with the v26 header format:

2019-Oct-10 14:22:25 INFO : TARQUIN 4.3.11 Started

2019-Oct-10 14:22:25 INFO : Loading data file : data/spectra/005_PROBE-SV_35_ve_front/P29184.7

2019-Oct-10 14:22:25 INFO : Rdb reader rev : 26.002001

2019-Oct-10 14:22:25 INFO : P-file offset : 213684

2019-Oct-10 14:22:25 INFO : Frame size : 32768

2019-Oct-10 14:22:25 INFO : Offset to data : 246452

2019-Oct-10 14:22:25 INFO : Nechoes : 1

2019-Oct-10 14:22:25 INFO : Water ref frames : 2.000000

2019-Oct-10 14:22:25 INFO : Water sup frames : 16.000000

2019-Oct-10 14:22:25 INFO : Number of coils : 32

2019-Oct-10 14:22:25 INFO : x dim : 1

2019-Oct-10 14:22:25 INFO : y dim : 1

2019-Oct-10 14:22:25 INFO : z dim : 1

2019-Oct-10 14:22:25 INFO : nStart = 50

2019-Oct-10 14:22:25 INFO : nEnd = 2048

2019-Oct-10 14:22:25 INFO : Averaging metabolite FIDs

2019-Oct-10 14:22:25 INFO : Averaging across 16 of 16 FIDs

TARQUIN Version 4.3.11

**** TARQUIN is a research tool and is NOT for clinical use. ****

2019-Oct-10 14:22:25 INFO : Rdb reader rev : 26.002001

2019-Oct-10 14:22:25 INFO : P-file offset : 213684

2019-Oct-10 14:22:25 INFO : Frame size : 32768

2019-Oct-10 14:22:25 INFO : Offset to data : 246452

2019-Oct-10 14:22:25 INFO : Nechoes : 1

2019-Oct-10 14:22:25 INFO : Water ref frames : 2.000000

2019-Oct-10 14:22:25 INFO : Water sup frames : 16.000000

2019-Oct-10 14:22:25 INFO : Number of coils : 32

2019-Oct-10 14:22:25 INFO : x dim : 1

2019-Oct-10 14:22:25 INFO : y dim : 1

2019-Oct-10 14:22:25 INFO : z dim : 1

2019-Oct-10 14:22:26 INFO : Averaging water ref FIDs

2019-Oct-10 14:22:26 INFO : Number of W fids does not match WS fids.

2019-Oct-10 14:22:26 INFO : Averaging accross 2 water reference fids.

Parameters Before Preprocessing

-------------------------------

Input file: data/spectra/005_PROBE-SV_35_ve_front/P29184.7

Water reference file: data/spectra/005_PROBE-SV_35_ve_front/P29184.7

Data points: 4096

Rows: 1

Columns: 1

Slices: 1

Echo time: -272.66 s

Sampling frequency: 5000 Hz

Transmitter frequency: 1.27715e+08 Hz

Starting sample: 50

Ending sample: 2048

Removing signals in: [-45,+45] Hz

Autophasing yes/no?: yes

Water eddy correction?: no

Autoreferencing yes/no?: yes

Reference: 4.65 ppm

2019-Oct-10 14:22:26 INFO : Starting 'Preprocessing'

2019-Oct-10 14:22:26 INFO : Preprocessing fid 1 of 1

2019-Oct-10 14:22:26 INFO : Starting 'autophasing mag method water'

2019-Oct-10 14:22:26 INFO : Finished 'autophasing mag method water'

2019-Oct-10 14:22:26 INFO : Ref start = 4.650000 ppm

2019-Oct-10 14:22:26 INFO : Ref new = 4.666727 ppm

2019-Oct-10 14:22:26 INFO : Residual water freq. (Hz) : 2.136230

2019-Oct-10 14:22:26 INFO : Starting 'building Hankel LP matrix'

2019-Oct-10 14:22:26 INFO : Finished 'building Hankel LP matrix'

2019-Oct-10 14:22:26 INFO : Starting 'SVD of LP matrix'

2019-Oct-10 14:22:26 INFO : Finished 'SVD of LP matrix'

2019-Oct-10 14:22:27 INFO : Starting 'estimating LP parameters'

2019-Oct-10 14:22:27 INFO : Finished 'estimating LP parameters'

2019-Oct-10 14:22:27 INFO : Starting 'estimating LP amplitudes'

2019-Oct-10 14:22:27 INFO : Finished 'estimating LP amplitudes'

2019-Oct-10 14:22:27 INFO : Starting 'autophasing (new)'

2019-Oct-10 14:22:27 INFO : Finished 'autophasing (new)'

2019-Oct-10 14:22:27 DEBUG : Max Phi0 : -0.25

2019-Oct-10 14:22:27 INFO : Ref start = 4.650000 ppm

2019-Oct-10 14:22:27 INFO : Ref new = 4.671506 ppm

2019-Oct-10 14:22:27 DEBUG : Width pts : 31.64

2019-Oct-10 14:22:27 DEBUG : Width Hz est : 3.22

2019-Oct-10 14:22:27 DEBUG : Init beta est : 17.52

2019-Oct-10 14:22:27 INFO : Ymax = 3800616.626468

2019-Oct-10 14:22:27 INFO : sdev noise = 26112.421192

2019-Oct-10 14:22:27 INFO : SNR guess = 72.7741

2019-Oct-10 14:22:27 INFO : Finished 'Preprocessing'

Parameters After Preprocessing

------------------------------

Input file: data/spectra/005_PROBE-SV_35_ve_front/P29184.7

Water reference file: data/spectra/005_PROBE-SV_35_ve_front/P29184.7

Data points: 4096

Rows: 1

Columns: 1

Slices: 1

Echo time: -272.66 s

Sampling frequency: 5000 Hz

Transmitter frequency: 1.27715e+08 Hz

Starting sample: 50

Ending sample: 2048

Removing signals in: [-45,+45] Hz

Autophasing yes/no?: yes

Water eddy correction?: no

Autoreferencing yes/no?: yes

Reference: 4.67151 ppm

2019-Oct-10 14:22:27 INFO : Simulating using 8 threads.Warning, negative delay requsted!!Warning, negative delay requsted!!

Warning, negative delay requsted!!

2019-Oct-10 14:22:27 INFO : All simulation threads stopped.

2019-Oct-10 14:22:27 ERROR : incorrect echo time (-272.66 in FID does not match 0.00 in basis)

2019-Oct-10 14:22:27 INFO : TARQUIN Finished

Alex

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Oct 10, 2019, 10:52:58 AM10/10/19

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Hello Martin (and Laura, and group),

Per Laura's message, we've encountered an issue in the latest tarquin (4.3.11) reading certain recent versions of the GE P-file header inconsistently.

Quick fix, initialize te_int to 0 around lines 321 and 328 of common/fidio/CFIDReaderGE.cpp, ie:

int te_int=0;

On many contemporary architectures, the size of int is going to be 4 bytes rather than the assumed 2. The read statement is only filling the first two bytes of te_int, leaving the remaining bytes un-initialized. Often we're lucky enough that these are coincidentally zero and everything works beautifully, but there are various random cases where they're filled with junk, yielding bogus (often negative) TE values and causing everything to fail.

(I'll probably come back to you in some weeks/months with more GE header improvements, but this little fix would help greatly for now).

Best regards,
Alex.

Alex

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Oct 10, 2019, 11:31:27 AM10/10/19

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Sorry, this is an incomplete 'fix'. Thinking about it some more, the TE is of course actually stored as a 32-bit int (for all header revisions). A 16-bit int would overflow for longer TEs.

So, it's a mystery to me why the reader was going to the trouble of doing a 2-byte read into te_int at all, instead of a 4-byte read straight into TE as with other revisions? Maybe endian issues with some obscure ancient releases? The following seems just fine for recent data (also note: fwiw, the field shifted in 25.002, not 25.001)...

common/fidio/CFIDReaderGE.cpp

319     else if ( (rdb_header_rev > 11.0) && (rdb_header_rev <= 25.001) )
320     {
321         // int te_int=0; // ARC remove
322         file.seekg(4*303, std::ios_base::beg);
323         file.read((char*)&TE, 4);
324         // TE = te_int; // ARC remove
325     }
326     else if ( rdb_header_rev > 25.001 )
327     {
328         //int te_int; // ARC remove
329         file.seekg(4*303-64, std::ios_base::beg);
330         file.read((char*)&TE, 4);
331         // TE = te_int; // ARC remove
332     }

Alex

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Nov 27, 2019, 9:31:22 AM11/27/19

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Greetings,

For the benefit of anyone still experiencing this issue, here are some (unofficial and entirely unsupported) binaries for Linux and macOS, incorporating the fix for recent GE P-files.

For Linux: https://drive.google.com/open?id=1yQcJVcPHvgKsPhFySxCoQ0_w1lZMCOIc

For MacOS (10.14): https://drive.google.com/open?id=10MCZs40dkVJ8fGVqmwQT4VPNcpkQ2i1A

I'm afraid it's command-line only for MacOS, due to archaic Qwt5 and finite patience on my part.

Hope this is useful for someone.

- Alex.

thak...@gmail.com

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Oct 16, 2020, 10:33:58 AM10/16/20

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Dear all,

My apologies if i overlooked any response regarding similar questions. I used Tarquin for single-voxel data long ago and I think it is very user-friendly software. Recently, all data at our site is collected from MR750 3T scanners. I was trying to use GE p files as well as converted DCM files (single voxel as well as 2D CSI data) to analyze using this software. I do have issues reading the data. Looking for some help. Thank you

Sunitha

Nick Bolo

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Jun 7, 2021, 9:23:42 AM6/7/21

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Hi Alex,

Thanks for providing the fix (tarquin.redist.macos.10.14.tar.gz), which I've just downloaded for Mac (I've got OS version 10.15.7).

I haven't tried it yet, but I have a question for you before installing.

I've got single voxel presscsi on a GE MR750 DV26.0. In the supported version of Tarquin (V 4.3.11), the Tarquin GUI reads the TE (= 0.028 sec) correctly, but I get the same error message as in this e-mail train (incorrect echo time (-272.67 in FID does not match 0.00 in basis)) when I run in command line.

Also, manually entering the echo time (--echo 0.028) doesn't change the error message.

I have a lot of spectra, so I am really interested in getting the command line to work, but of course the GUI is great for quickly inspecting spectra, and it seems to work.

My question is, to install the fix, where should I place all the files (tarquin, simulate, libcvm.a, etc...) that are in the "redist" folder?

Are there separate versions of tarquin for the GUI and the command line?

(I guess that's actually 2 questions)

Thanks again.

Best,

Nick

On Wednesday, November 27, 2019 at 9:31:22 AM UTC-5 Alex wrote:

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