fsl_mrs tagshttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags2024-02-07T14:20:01+00:00https://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.192.1.19<h2 data-sourcepos="1:1-3:75" dir="auto">
<a id="user-content-2119-wednesday-7th-february-2024" class="anchor" href="#2119-wednesday-7th-february-2024" aria-hidden="true"></a>2.1.19 (Wednesday 7th February 2024)</h2>
<ul data-sourcepos="3:1-5:72" dir="auto">
<li data-sourcepos="3:1-3:75">Multiple metabolites can now be specified as the water scaling metabolite</li>
<li data-sourcepos="4:1-4:101">Default water scaling metabolite is now PCr+Cr to add robustness to one of PCr or Cr not being fit.</li>
<li data-sourcepos="5:1-5:72">Improved error logging in <code data-sourcepos="5:30-5:37">fsl_mrsi</code> when parallel processing enabled.</li>
</ul>2024-02-07T14:20:01+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.182.1.18<h2 data-sourcepos="1:1-3:119" dir="auto">
<a id="user-content-2118-thursday-7th-december-2023" class="anchor" href="#2118-thursday-7th-december-2023" aria-hidden="true"></a>2.1.18 (Thursday 7th December 2023)</h2>
<ul data-sourcepos="3:1-4:65" dir="auto">
<li data-sourcepos="3:1-3:119">Fixed bug in <code data-sourcepos="3:17-3:33">fsl_mrs_summarise</code> that resulted in hang if single level of listed directories weren't distinguishable.</li>
<li data-sourcepos="4:1-4:65">NIfTI-MRS tools v1.1.1 required. Fixes some visualisation bugs.</li>
</ul>2023-12-07T20:43:12+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.172.1.17<h2 data-sourcepos="1:1-3:55" dir="auto">
<a id="user-content-2117-tuesday-5th-december-2023" class="anchor" href="#2117-tuesday-5th-december-2023" aria-hidden="true"></a>2.1.17 (Tuesday 5th December 2023)</h2>
<ul data-sourcepos="3:1-3:55" dir="auto">
<li data-sourcepos="3:1-3:55">Fixed bug in windowed averaging introduced in v2.1.16</li>
</ul>2023-12-06T07:09:33+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.162.1.16<h2 data-sourcepos="1:1-3:50" dir="auto">
<a id="user-content-2116-saturday-25th-november-2023" class="anchor" href="#2116-saturday-25th-november-2023" aria-hidden="true"></a>2.1.16 (Saturday 25th November 2023)</h2>
<ul data-sourcepos="3:1-4:152" dir="auto">
<li data-sourcepos="3:1-3:50">Better visualisation of dynamic fitting results.</li>
<li data-sourcepos="4:1-4:152">Added experimental windowed averaging to phase and frequency alignment. Improves results for low SNR data or that corrupted by phase cycled artefacts.</li>
</ul>2023-11-26T14:37:55+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.152.1.15<h2 data-sourcepos="1:1-3:65" dir="auto">
<a id="user-content-2115-thursday-9th-november-2023" class="anchor" href="#2115-thursday-9th-november-2023" aria-hidden="true"></a>2.1.15 (Thursday 9th November 2023)</h2>
<ul data-sourcepos="3:1-5:42" dir="auto">
<li data-sourcepos="3:1-3:65">No changes to FSL-MRS functionality, only under-the-hood fixes.</li>
<li data-sourcepos="4:1-4:110">Further (to <code data-sourcepos="4:16-4:21">2.1.14</code>) changes to Docker CI images. Added build files and instructions to FSL-MRS repository.</li>
<li data-sourcepos="5:1-5:42">Fixes to version (versioneer) tracking.</li>
</ul>2023-11-09T17:13:32+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.142.1.14<h2 data-sourcepos="1:1-3:50" dir="auto">
<a id="user-content-2114-wednesday-8th-november-2023" class="anchor" href="#2114-wednesday-8th-november-2023" aria-hidden="true"></a>2.1.14 (Wednesday 8th November 2023)</h2>
<ul data-sourcepos="3:1-3:50" dir="auto">
<li data-sourcepos="3:1-3:50">Under-the-hood fixes to CI and testing pipeline.</li>
</ul>2023-11-08T20:53:52+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.132.1.132.1.13<h2 data-sourcepos="1:1-3:100" dir="auto">
<a id="user-content-2113-tuesday-5th-august-2023" class="anchor" href="#2113-tuesday-5th-august-2023" aria-hidden="true"></a>2.1.13 (Tuesday 5th August 2023)</h2>
<ul data-sourcepos="3:1-4:153" dir="auto">
<li data-sourcepos="3:1-3:100">Add group level f-tests to the <code data-sourcepos="3:35-3:44">fmrs_stats</code> tool. First level f-contrasts are not yet implemented.</li>
<li data-sourcepos="4:1-4:153">Removed / retained indices after <code data-sourcepos="4:37-4:55">fsl_mrs_proc unlike</code> (and related functions) are now listed in the NIfTI-MRS headers under the key "DIM_DYN Indices".</li>
</ul>2023-09-06T14:15:53+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.122.1.12v2.1.12<h2 data-sourcepos="1:1-3:54" dir="auto">
<a id="user-content-2112-thursday-10th-august-2023" class="anchor" href="#2112-thursday-10th-august-2023" aria-hidden="true"></a>2.1.12 (Thursday 10th August 2023)</h2>
<ul data-sourcepos="3:1-5:65" dir="auto">
<li data-sourcepos="3:1-3:54">Implemented more testing of <code data-sourcepos="3:32-3:43">fsl_mrs_proc</code> routines.</li>
<li data-sourcepos="4:1-4:46">Fixed further bugs in <code data-sourcepos="4:26-4:44">fsl_mrs_proc unlike</code>.</li>
<li data-sourcepos="5:1-5:65">Fixed issues in the example notebooks distributed with FSL-MRS.</li>
</ul>2023-08-10T15:16:43+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.112.1.11v2.1.11<h2 data-sourcepos="1:1-3:37" dir="auto">
<a id="user-content-2111-tuesday-8th-august-2023" class="anchor" href="#2111-tuesday-8th-august-2023" aria-hidden="true"></a>2.1.11 (Tuesday 8th August 2023)</h2>
<ul data-sourcepos="3:1-3:37" dir="auto">
<li data-sourcepos="3:1-3:37">Fixed bug in <code data-sourcepos="3:17-3:35">fsl_mrs_proc unlike</code>.</li>
</ul>2023-08-08T17:39:41+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.102.1.10v2.1.10<h2 data-sourcepos="1:1-3:109" dir="auto">
<a id="user-content-2110-tuesday-1st-august-2023" class="anchor" href="#2110-tuesday-1st-august-2023" aria-hidden="true"></a>2.1.10 (Tuesday 1st August 2023)</h2>
<ul data-sourcepos="3:1-4:84" dir="auto">
<li data-sourcepos="3:1-3:109">Coil covariance estimation is now common across all inputs to <code data-sourcepos="3:66-3:80">fsl_mrs_preproc</code> and <code data-sourcepos="3:88-3:107">fsl_mrs_preproc_edit</code>.</li>
<li data-sourcepos="4:1-4:84">Fallback option to disable coil pre-whitening when it isn't possible to calculate.</li>
</ul>2023-08-01T20:05:46+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.92.1.9v2.1.9<h2 data-sourcepos="1:1-3:94" dir="auto">
<a id="user-content-219-friday-28th-july-2023" class="anchor" href="#219-friday-28th-july-2023" aria-hidden="true"></a>2.1.9 (Friday 28th July 2023)</h2>
<ul data-sourcepos="3:1-3:94" dir="auto">
<li data-sourcepos="3:1-3:94">Coil covariance estimation can now use multiple spectra held in higher NIfTI-MRS dimensions.</li>
</ul>2023-07-28T14:29:34+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.82.1.8v2.1.8<h2 data-sourcepos="1:1-3:103" dir="auto">
<a id="user-content-218-tuesday-25th-july-2023" class="anchor" href="#218-tuesday-25th-july-2023" aria-hidden="true"></a>2.1.8 (Tuesday 25th July 2023)</h2>
<ul data-sourcepos="3:1-4:92" dir="auto">
<li data-sourcepos="3:1-3:103">
<code data-sourcepos="3:4-3:13">fsl_dynmrs</code> can now handle MRSI data. This requires the use of <code data-sourcepos="3:68-3:74">fsl_sub</code>, which is now a dependency.</li>
<li data-sourcepos="4:1-4:92">Custom initialisation functions can now be defined in dynamic fitting configuration files.</li>
</ul>2023-07-25T13:09:22+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.72.1.7v2.1.7<h2 data-sourcepos="1:1-3:120" dir="auto">
<a id="user-content-217-friday-7th-july-2023" class="anchor" href="#217-friday-7th-july-2023" aria-hidden="true"></a>2.1.7 (Friday 7th July 2023)</h2>
<ul data-sourcepos="3:1-11:30" dir="auto">
<li data-sourcepos="3:1-3:120">Added <code data-sourcepos="3:10-3:32">fsl_mrs_proc mrsi-align</code> which can perform frequency and phase alignment across voxels using cross correlation.</li>
<li data-sourcepos="4:1-4:109">Added <code data-sourcepos="4:10-4:32">fsl_mrs_proc mrsi-lipid</code> which can perform lipid removal using Bilgic et al's L2-regularised method.</li>
<li data-sourcepos="5:1-5:131">
<code data-sourcepos="5:4-5:22">fsl_mrs_proc fshift</code> can now take NIfTI images of matched shape witht he <code data-sourcepos="5:78-5:86">--shifthz</code> anf <code data-sourcepos="5:94-5:103">--shiftppm</code> to apply per-voxel shifts.</li>
<li data-sourcepos="6:1-6:79">Fixed bug with incorrectly calculated zero order phase when given in degrees.</li>
<li data-sourcepos="7:1-7:74">Improved interface and options for dynamic fitting driven preprocessing.</li>
<li data-sourcepos="8:1-8:40">Fixed minor bug in <code data-sourcepos="8:23-8:39">fsl_mrs_summarise</code>
</li>
<li data-sourcepos="9:1-9:96">Fixed bug where quantification information wasn't generated if no tissue fractions were given.</li>
<li data-sourcepos="10:1-10:74">Added warnings when quantification reference or water has zero integral.</li>
<li data-sourcepos="11:1-11:30">Moved to nifti-mrs 1.0.0 API</li>
</ul>2023-07-07T20:40:54+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.62.1.6v2.1.6<h2 data-sourcepos="1:1-3:51" dir="auto">
<a id="user-content-216-friday-5th-may-2023" class="anchor" href="#216-friday-5th-may-2023" aria-hidden="true"></a>2.1.6 (Friday 5th May 2023)</h2>
<ul data-sourcepos="3:1-7:53" dir="auto">
<li data-sourcepos="3:1-3:51">Add model performance outputs to dynamic fitting.</li>
<li data-sourcepos="4:1-4:257">Refined parameter-derived linewidth estimates of (default) voigt model. Previously the width of the Gaussian component was overestimated (by 50%), this did not affect per-metabolite QC measurement of FWHM reported in the main HTML remport and results CSV.</li>
<li data-sourcepos="5:1-5:198">fMRS contrasts formed from individual betas (e.g. using <code data-sourcepos="5:60-5:69">fmrs_stats</code>) now operate over all parameter classes, not just concentrations (i.e. sigma, gamma, eps, baseline, phase, and concentrations).</li>
<li data-sourcepos="6:1-6:156">
<code data-sourcepos="6:4-6:13">fmrs_stats</code> can now be used to express metabolite concentrations as ratios to another contrast (e.g. for scaling to another metabolite, for example tCr).</li>
<li data-sourcepos="7:1-7:53">Added better help and error text for <code data-sourcepos="7:41-7:51">fsl_dyn_mrs</code>.</li>
</ul>2023-05-05T06:20:16+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.52.1.5v2.1.5<h2 data-sourcepos="1:1-3:45" dir="auto">
<a id="user-content-215-wednesday-26th-april-2023" class="anchor" href="#215-wednesday-26th-april-2023" aria-hidden="true"></a>2.1.5 (Wednesday 26th April 2023)</h2>
<ul data-sourcepos="3:1-6:61" dir="auto">
<li data-sourcepos="3:1-3:45">Improved speed of coil combination for MRSI</li>
<li data-sourcepos="4:1-4:152">Noise or covariance matrix may be supplied directly for pre-whitening in coil combination (<code data-sourcepos="4:95-4:106">fsl_mrs_proc</code>, <code data-sourcepos="4:111-4:125">fsl_mrs_preproc</code>, <code data-sourcepos="4:130-4:149">fsl_mrs_preproc_edit</code>).</li>
<li data-sourcepos="5:1-5:41">More robust tests for coil combination.</li>
<li data-sourcepos="6:1-6:61">Fix 1D projection method for simulation of edited sequences</li>
</ul>2023-04-26T11:00:46+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.42.1.4v2.1.4<h2 data-sourcepos="1:1-3:63" dir="auto">
<a id="user-content-214-thursday-30th-march-2023" class="anchor" href="#214-thursday-30th-march-2023" aria-hidden="true"></a>2.1.4 (Thursday 30th March 2023)</h2>
<ul data-sourcepos="3:1-4:37" dir="auto">
<li data-sourcepos="3:1-3:63">Improved <code data-sourcepos="3:13-3:29">fsl_mrs_summarise</code> identification of dataset names.</li>
<li data-sourcepos="4:1-4:37">Fixed bug in <code data-sourcepos="4:17-4:36">fsl_mrs_proc apodize</code>
</li>
</ul>2023-03-30T12:10:33+01:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.32.1.3v2.1.3<h2 data-sourcepos="1:1-3:55" dir="auto">
<a id="user-content-213-wednesday-22nd-march-2023" class="anchor" href="#213-wednesday-22nd-march-2023" aria-hidden="true"></a>2.1.3 (Wednesday 22nd March 2023)</h2>
<ul data-sourcepos="3:1-4:55" dir="auto">
<li data-sourcepos="3:1-3:55">Improved noise baseline de-trending in QC estimation.</li>
<li data-sourcepos="4:1-4:55">Resolved dash/flask dependency issues for python 3.7.</li>
</ul>2023-03-22T16:26:02+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.22.1.2V2.1.2<h2 data-sourcepos="1:1-3:70" dir="auto">
<a id="user-content-212-tuesday-21st-march-2023" class="anchor" href="#212-tuesday-21st-march-2023" aria-hidden="true"></a>2.1.2 (Tuesday 21st March 2023)</h2>
<ul data-sourcepos="3:1-5:77" dir="auto">
<li data-sourcepos="3:1-3:70">Fixed bug in <code data-sourcepos="3:17-3:33">fsl_mrs_summarise</code> showing some fits inverted along x.</li>
<li data-sourcepos="4:1-4:36">Updated installation instructions.</li>
<li data-sourcepos="5:1-5:77">Updated <code data-sourcepos="5:12-5:18">fsl_mrs</code> report to include basis spectra (removed real/imag view).</li>
</ul>2023-03-21T20:19:29+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.12.1.1V2.1.1<h2 data-sourcepos="1:1-3:85" dir="auto">
<a id="user-content-211-monday-20th-march-2023" class="anchor" href="#211-monday-20th-march-2023" aria-hidden="true"></a>2.1.1 (Monday 20th March 2023)</h2>
<ul data-sourcepos="3:1-6:70" dir="auto">
<li data-sourcepos="3:1-3:85">Better handling of x-nuclei, including specific constants, ppm ranges, offsets etc.</li>
<li data-sourcepos="4:1-4:39">More appropriate xlabels for x-nuclei</li>
<li data-sourcepos="5:1-5:104">Fix issues around resolving symlinks, <code data-sourcepos="5:42-5:48">fsl_mrs</code> results generate symlinks with appropriate extensions.</li>
<li data-sourcepos="6:1-6:70">Fixed plotting bug (depreciation of grid_b parameter in matplotlib).</li>
</ul>2023-03-20T14:48:28+00:00William Clarkehttps://git.fmrib.ox.ac.uk/fsl/fsl_mrs/-/tags/2.1.02.1.0V2.1.0<h2 data-sourcepos="1:1-3:106" dir="auto">
<a id="user-content-210-thursday-19th-january-2023" class="anchor" href="#210-thursday-19th-january-2023" aria-hidden="true"></a>2.1.0 (Thursday 19th January 2023)</h2>
<ul data-sourcepos="3:1-5:87" dir="auto">
<li data-sourcepos="3:1-3:106">FSL-MRS now uses the nifti-mrs tools python package. <code data-sourcepos="3:57-3:65">mrs_tools</code> superseded by nifti-mrs implementation.</li>
<li data-sourcepos="4:1-4:64">Fixed bug in <code data-sourcepos="4:17-4:26">fmrs_stats</code> design/contrast matrix specification</li>
<li data-sourcepos="5:1-5:87">Fixed bug in fmrs statistics module for metabolites with an underscore in their name.</li>
</ul>2023-01-19T16:48:26+00:00William Clarke