diff --git a/_images/index_51_0.png b/_images/index_51_0.png deleted file mode 100644 index 3d46be8..0000000 Binary files a/_images/index_51_0.png and /dev/null differ diff --git a/index.html b/index.html index b1fd555..baf1b21 100644 --- a/index.html +++ b/index.html @@ -687,40 +687,6 @@

5     |     Process anat/T2starw (GRE) -
                 Anova
-=======================================
-          F Value Num DF  Den DF Pr > F
----------------------------------------
-Shim_Mode  9.0936 6.0000 24.0000 0.0000
-=======================================
-
-Paired t-tests:
-                 Pair   P-Value  Adjusted P-Value
-0       (CP, patient)  0.005972          0.025083
-1        (CP, volume)  0.075373          0.131902
-2         (CP, phase)  0.011296          0.033889
-3           (CP, CoV)  0.000156          0.003279
-4        (CP, target)  0.030643          0.080437
-5        (CP, SAReff)  0.197466          0.276452
-6   (patient, volume)  0.205065          0.269148
-7    (patient, phase)  0.296440          0.366191
-8      (patient, CoV)  0.001437          0.010061
-9   (patient, target)  0.154750          0.232125
-10  (patient, SAReff)  0.031202          0.072804
-11    (volume, phase)  0.413730          0.457281
-12      (volume, CoV)  0.404085          0.471432
-13   (volume, target)  0.552388          0.552388
-14   (volume, SAReff)  0.075590          0.122108
-15       (phase, CoV)  0.009898          0.034641
-16    (phase, target)  0.496343          0.521160
-17    (phase, SAReff)  0.005612          0.029461
-18      (CoV, target)  0.043267          0.082600
-19      (CoV, SAReff)  0.001394          0.014638
-20   (target, SAReff)  0.036743          0.077159
-
-
-
@@ -990,40 +956,6 @@

6     |     Process fmap/TFL (flip angle maps)

-
-
                 Anova
-=======================================
-          F Value Num DF  Den DF Pr > F
----------------------------------------
-Shim_Mode 14.0743 6.0000 24.0000 0.0000
-=======================================
-
-Paired t-tests:
-                 Pair   P-Value  Adjusted P-Value
-0       (CP, patient)  0.007728          0.040570
-1        (CP, volume)  0.009006          0.037825
-2         (CP, phase)  0.079896          0.104863
-3           (CP, CoV)  0.318010          0.371012
-4        (CP, target)  0.010284          0.030853
-5        (CP, SAReff)  0.563249          0.622539
-6   (patient, volume)  0.821572          0.862651
-7    (patient, phase)  0.005550          0.116560
-8      (patient, CoV)  0.036644          0.059195
-9   (patient, target)  0.006302          0.066176
-10  (patient, SAReff)  0.010083          0.035289
-11    (volume, phase)  0.006565          0.045958
-12      (volume, CoV)  0.032112          0.056197
-13   (volume, target)  0.027717          0.052915
-14   (volume, SAReff)  0.012891          0.030078
-15       (phase, CoV)  0.989088          0.989088
-16    (phase, target)  0.011515          0.030226
-17    (phase, SAReff)  0.070778          0.099089
-18      (CoV, target)  0.236842          0.292570
-19      (CoV, SAReff)  0.061149          0.091724
-20   (target, SAReff)  0.018986          0.039871
-
-
-
@@ -1152,9 +1084,6 @@

7     |     Paper figures

-
-_images/index_51_0.png -

Figure 2. B1+ efficiency for one participant (sub-05) across all seven RF shimming conditions. The top left panel shows the tfl_b1map magnitude image with an overlay of the mask that was used to perform RF shimming. Text inserts show the mean (in nT/V) and CoV (in %) of B1+ efficiency along the spinal cord between C3 and T2.

@@ -1434,21 +1363,6 @@

7     |     Paper figures

-
-
- - -
-
- -

Figure 3. B1+ efficiency (A) and CSF/Cord signal ratio from the GRE scan (B) across subjects and across different RF shimming conditions. Data were measured in the spinal cord from C3 to T2 vertebral levels. To match the x-ticks across subjects, the C2-C3 and the T2-T3 intervertebral discs of each subject were aligned with that of the PAM50 template [De Leener et al., 2018], and the curves were linearly scaled.

diff --git a/reports/index.log b/reports/index.log new file mode 100644 index 0000000..59aab92 --- /dev/null +++ b/reports/index.log @@ -0,0 +1,64 @@ +Traceback (most recent call last): + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution + executenb( + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 1204, in execute + return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute() + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/util.py", line 84, in wrapped + return just_run(coro(*args, **kwargs)) + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/util.py", line 62, in just_run + return loop.run_until_complete(coro) + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete + return future.result() + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 663, in async_execute + await self.async_execute_cell( + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 965, in async_execute_cell + await self._check_raise_for_error(cell, cell_index, exec_reply) + File "/opt/hostedtoolcache/Python/3.8.18/x64/lib/python3.8/site-packages/nbclient/client.py", line 862, in _check_raise_for_error + raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content) +nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell: +------------------ +# Download data and define path variables + +# Google Colab-Only +if notebook=='colab': + !datalad install https://github.com/OpenNeuroDatasets/ds004906.git + os.chdir("ds004906") + !datalad get . # uncomment for production + # !datalad get sub-01/ # debugging + # Get derivatives containing manual labels + !datalad get derivatives + +if notebook!='colab': + os.chdir("../data/rf-shimming-7t/ds004906") + if notebook=='neurolibre-clean': + flist = open('cleanup.txt', 'r') + for f in flist: + fname = f.rstrip('\n') + fname = Path(os.getcwd()) / Path(fname) + + # or, if you get rid of os.chdir(path) above, + # fname = os.path.join(path, f.rstrip()) + if os.path.isfile(fname): # this makes the code more robust + print('Removing file: ' + str(fname)) + os.remove(fname) + elif os.path.isdir(fname): + print('Removing directory: ' + str(fname)) + rmtree(fname) + + # also, don't forget to close the text file: + flist.close() + +------------------ + +--------------------------------------------------------------------------- +FileNotFoundError Traceback (most recent call last) +Cell In[5], line 13 + 10 get_ipython().system('datalad get derivatives') + 12 if notebook!='colab': +---> 13 os.chdir("../data/rf-shimming-7t/ds004906") + 14 if notebook=='neurolibre-clean': + 15 flist = open('cleanup.txt', 'r') + +FileNotFoundError: [Errno 2] No such file or directory: '../data/rf-shimming-7t/ds004906' +FileNotFoundError: [Errno 2] No such file or directory: '../data/rf-shimming-7t/ds004906' +