Summary of what happened:
Hello, I downloaded the Two-sample ALE meta-analysis in Nimare Examples and got an error when doing the Subtraction analysis using Jupyter notebook. What should I do?
Command used:
from nimare.meta.cbma import ALESubtraction
from nimare.reports.base import run_reports
from nimare.workflows import PairwiseCBMAWorkflow
workflow = PairwiseCBMAWorkflow(
estimator=ALESubtraction(n_iters=10, n_cores=1),
corrector="fdr",
diagnostics=FocusCounter(voxel_thresh=0.01, display_second_group=True),
)
res_sub = workflow.fit(knowledge_dset, related_dset)
Feedback
PermissionError Traceback (most recent call last)
Cell In[9], line 10
3 from nimare.workflows import PairwiseCBMAWorkflow
5 workflow = PairwiseCBMAWorkflow(
6 estimator=ALESubtraction(n_iters=10, n_cores=1),
7 corrector="fdr",
8 diagnostics=FocusCounter(voxel_thresh=0.01, display_second_group=True),
9 )
---> 10 res_sub = workflow.fit(knowledge_dset, related_dset)
File ~\.conda\envs\nimare_env\lib\site-packages\nimare\workflows\cbma.py:162, in PairwiseCBMAWorkflow.fit(self, dataset1, dataset2, drop_invalid)
159 dataset2 = _check_type(dataset2, Dataset)
161 LGR.info("Performing meta-analysis...")
--> 162 results = self.estimator.fit(dataset1, dataset2, drop_invalid=drop_invalid)
164 return self._transform(results)
File ~\.conda\envs\nimare_env\lib\site-packages\nimare\meta\cbma\base.py:906, in PairwiseCBMAEstimator.fit(self, dataset1, dataset2, drop_invalid)
903 self.inputs_["coordinates2"] = self.inputs_.pop("coordinates")
905 # Now run the Estimator-specific _fit() method.
--> 906 maps, tables, description = self._fit(dataset1, dataset2)
908 if hasattr(self, "masker") and self.masker is not None:
909 masker = self.masker
File ~\.conda\envs\nimare_env\lib\site-packages\nimare\utils.py:703, in use_memmap.<locals>.inner_function.<locals>.memmap_context(self, *args, **kwargs)
701 if os.path.isfile(filename):
702 logger.debug(f"Removing temporary file: {filename}")
--> 703 os.remove(filename)
704 else:
705 logger.debug(f"Temporary file DNE: {filename}")
PermissionError: [WinError 32] The process cannot access this file because it is being used by another program.: 'C:\\Users\\Lenovo\\AppData\\Local\\Temp\\ALESubtraction6o_ka2vf20240111T133815'
Version:
nimare=0.2.0
python=3.10
Environment (custom installation):
conda create -n nimare_env python=3.10
conda activate nimare_env
pip install ipykernel
ipython kernel install --user --name=nimare_env
pip install nimare
Example download from:
( NiMARE: Neuroimaging Meta-Analysis Research Environment — NiMARE 0.2.0+0.g720c5c6.dirty documentation)
Extra questions
Display in the example:
“Typically, one would use at least 10000 iterations for a subtraction analysis. However, we have reduced this to 100 iterations for this example. Similarly here we use a voxel-level z-threshold of 0.01, but in practice one would use a more stringent threshold (e.g., 1.65).“
The code:
estimator=ALESubtraction(n_iters=10, n_cores=1),
Questions1: n_iters=10 means 100 iterations or just a writing errors？
Questions2: if chage iterations=10000, voxel_thresh=1.65, can the laptop support smooth operation?
laptop:
11th Gen Intel(R) Core™ i5-11260H @ 2.60GHz 2.61 GHz
RAM 16.0 GB (15.7 GB available)
Questions3: In addition, whether the functional decoding analysis can be carried out smoothly?
Questions4: If the laptop cannot support the operation, the minimum configuration recommended for renting cloud computing services?
Thank you for taking the time to read my letter of appeal. I look forward to your response and hope that you can provide any possible assistance or advice.
Sincerely,
Thea