How to measure metabolites in occipito-temporal cortex?

briefly speaking we are struggling to get reasonable data from a so-called Visual Word Form Area (see figure below). We’ve tried a field mapping approach default for our Siemens Trio and Fieldmap from CMRR. Both methods would make the initial shim even worse i.e. FASTMAP sets some shims to the limits all the time.
I wonder if there are some good tricks for such a difficult region? We’ve already tried with a twice time bigger and smaller voxels. The best we can do is to manually adjust linear shims instead of the automatic procedures.
Looking forward to hearing from You!
Bartosz Kossowski

Hi Bartosz,

I’m tagging @uzayemir and @Dinesh here - I’m consistently amazed by the quality of the spectra I see in their publications, and I wouldn’t be surprised if they had a few tricks up their sleeves regarding shimming on Siemens systems.


Hi Bartosz,
How many iterations are you using for FASTESTMAP?
You need to run 4 iterations as mentioned in Improved localization, spectral quality and repeatability with advanced MRS methodology in the clinical setting. Note that the last step is crucial to correct the linear terms for any 2nd order shims maxing out.

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Thank You for the response, Dinesh!

Yes, I usually follow Your instructions from a CMRR data sheet - Linear 6 proj., Full x 3 and Linear 6 proj. again. Recently, with @noeskera we have also tried similar procedure with the FAMASITO on a GE scanner. In 6 out of 7 subjects (on Siemens Trio) we run out of current at the very first “Full” iteration. Each subsequent iteration would not make it better anymore. It is even worse with FAMASITO, when (most often) an additional total shim current limit is applied.

Do You have the same with the GRE SHIM method, @uzayemir? I’ve seen in Your papers that You frequently use it?

Best regards,

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If the shims are maxed out after the first full-6, I would suggest to run the lin-3 or lin-6 afterwards to compensate this. Then full-6 again.

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I am providing the same recipe I had provided for the fMRS.

I think I told this to @noeskera when we were developing the semi-laser sequence for the GE, too. I would suggest not to use the FASTMAP for second-order shims. FASTMAP should provide the best linewidths but does not necessarily result in the best/practical spectral quality. Start with GRESHIM and then update the first order shims with FASTMAP’s first-order procedure. I have also started to read that other studies are also following this procedure for difficult ROIs.

" B0 shimming was performed first on the whole brain volume with the standard “GRE Brain” option implemented in the scanner (Siemens) and then by manually adjusting the shim currents to a water linewidth below 30 Hz in magnitude mode. Next, the adjustment volume was changed to that of the VOI, and interactive shimming of the linear shim currents was performed to achieve a water linewidth below 20 Hz in magnitude mode. This sequential shimming volume approach (whole head, followed by VOI) allowed for satisfactory B0 homogeneity in the hippocampus and prevented the generation of spurious echoes from insufficient water suppression. A similar approach was used for hippocampal MRS at 7 T.

However, This is not the end of the story, your ROI is problematic for the default CMRR semi-laser RF pulse order. I would suggest you run the semi-laser with an orientation of coronal. The default CMRR semi-laser configuration is not working for this type of ROI. Again read my hints from the fMRS thread.

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I appreciate Your comments very much!

@uzayemir, I’d rather use GRESHIM than FASTMAP, because I trust You. But, the old MAPSHIM implementation (available by default on the Trio) is really bad. According to this very comprehensive paper of M. Gajdosik, the GRESHIM on Prisma was also not doing great in the difficult region. Anyway, does anybody know if there is any update (WIP) available for the VB17 platform?

Eventually I see two options:

  1. Iterative FASTMAP - 2nd and Linear interleaved to prevent problems with current limits.
  2. GRESHIM (the whole-brain perhaps) with a linear FASTMAP tune-up.

I can try both on the Siemens scanner on a few subjects and will let You know. What do You think about combining global and local shimming? Finally, I don’t know how to deal with a GE scanner with a limited access to 2nd order shims. Or maybe there is no need to go into 2nd order shimming in a tiny voxel? In Gajdosik’s paper they’ve finally reached ~8.3Hz with a full global adjustment and a fine tuning of linear shims within the voxel.


I’ve done a few tests today. FWHM are copied from Adjustments window (magnitude). Voxel measuring 15x15x15 has been placed as usual in the occipito-temporal cortex; a few mm above cerebellum and sinuses.

  1. Iterative FASTMAP procedure
    Default shims (Tune Up)
    Linear 3 proj. - 45 Hz
    Full (1st & 2nd) - 71 Hz (limits reached)
    Linear 6 proj. - 28 Hz
    Full - 99 Hz (limits)
    Linear 6 proj. 28.7 Hz
    Full - 99 Hz

  2. 3D Shim procedure adapted from M. Gajdosik, 2021
    3D Shim, Standard, VOI 120x120x60 covering most of the brain, repeated 3 times
    VOI changed to the voxel size to measure FWHM - 34.4 Hz.
    Linear 6 proj. - 46 Hz
    Full - 84.8 Hz
    Linear 6 proj. - 28.8 Hz
    Full - 100 Hz

  3. Again 3D Shim fieldmapping
    3D Shim, Standard, VOI 100x100x50 covering most of the brain, repeated 3 times
    VOI changed to the voxel size to measure FWHM ~30 Hz
    Then I’ve decided to check how water peak looks like after (1) another one “Linear 6 proj.” and (2) Manual fine tuning. In the adjustment window I’ve managed to go down to 23Hz clicking manually linear and z2 terms, compared to 43 Hz after linear FASTMAP. However, haven’t noticed such a big difference in acquired water reference peaks - 13 and 15 Hz (real), respectively.

It’s not a big surprise to me that my initial 3D Shim results are worse than 3D Shim with a “brain” mode on a Pisma (M. Gajdosik). Nevertheless, I’m still confused using the FASTMAP. Is there anything more I can try, @Dinesh?


Hi Bartosz,
Since you mention VB17, are you using the FASTMAP WIP or the one from CMRR webpage?
I know that some of the parameters in the WIP are not correctly set such that FM will not work well!
Also for the lin-6proj are you using non-EPI mode with longer tau, e.g. 10ms or 20ms?

Thank You for the quick reply,
I’ve installed the one provided on Your (CMRR) website - ver. 2014-09. I didn’t change the default mode - EPI on and Tau=5ms. Would You recommend changing those values for Linear-6 only or all the modes?

Just for the last iteration of lin-6: epi off and tau=10ms