Closed Boltzmachine closed 1 week ago
Yes, “ncsnr.nii.gz” are the original files, we renamed them. These files are provided in original NSD dataset.
So it is the same for all subjects? I see there is only one such file in the original NSD dataset.
There are multiple ncsnr.nii.gz files, one for every subject, in the original NSD dataset. They have the same filename but are in different folders, which is why we renamed them.
e.g.,
See the NSD Data Manual for more information: https://cvnlab.slite.page/p/channel/CPyFRAyDYpxdkPK6YbB5R1/notes/M3ZvPmfgU3
Thank you. Just need to confirm one more thing I saw the code in the script
betas = nsda.read_betas(subject=subject,
session_index=sess,
trial_index=[], # empty list as index means get all for this session
data_type='betas_fithrf', # GLMSingle beta2
data_format='func1pt8mm')
but the ncsnr.nii.gz
is read from the betas_fithrf_GLMdenoise_RR
or the betas_fithrf
folder?
betas_fithrf_GLMdenoise_RR folder, this code is not exactly the same as the one used for the paper
I see. Do you have any suggestions if I want to reproduce the preprocessing procedure in the paper?
It should be the same if you do proper z-scoring (z-score using training set only and apply it to the train & test set) and use the func1pt8mm betas_fithrf_GLMdenoise_RR betas
I see. I changed the corresponding parameters but got an assertion error
AssertionError Traceback (most recent call last)
Cell In[6], line 343
322 behavior = {
323 "cocoidx": coco73, #0
324 "subject": sub+1, #1
(...)
339 "shared1000": shared1000[int(behav.iloc[jj]['73KID'])-1], #16
340 }
342 assert (int(behav.iloc[jj]['SESSION'])-1)*750 + jj >= 0
--> 343 assert (int(behav.iloc[jj]['SESSION'])-1)*750 + jj < 27750
345 olds_behav_matrix[jjj] = np.array(list(behavior.values()))
347 behav = globals()[f'behav_ses{sess}']
AssertionError:
you can comment that out or replace it with 30000
27750 refers to the max possible number of trials before an additional 3 sessions of data were released after the Algonauts challenge ended, we used the full data for MindEye2
In
dataset_creation.ipynb
, I got an errorBut I did not find where to get the file (I only found
ncsnr.nii.gz
in NSD dataset)