From markiewicz at stanford.edu  Mon Jun  6 10:30:50 2022
From: markiewicz at stanford.edu (Christopher Markiewicz)
Date: Mon, 6 Jun 2022 14:30:50 +0000
Subject: [Neuroimaging] ANN: NiBabel 4.0.0 release candidate
Message-ID: <DM8PR02MB81405FBA2914B4DF4CB0129AA9A29@DM8PR02MB8140.namprd02.prod.outlook.com>

Hi all,

Just a quick announcement that I've pushed a release candidate for NiBabel 4.0 to PyPI, with a final release aiming for next week. This window is intended to allow downstream projects a chance to find breakage and report bugs before they start affecting many users, so please make sure to run tests with `pip install --pre nibabel` if you are not already.

Please see the release notes here: https://github.com/nipy/nibabel/releases/tag/4.0.0rc0

These will also be updated in the docs shortly.

Best,

Chris Markiewicz
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From bdeck8317 at gmail.com  Tue Jun  7 10:28:28 2022
From: bdeck8317 at gmail.com (Benjamin Deck)
Date: Tue, 7 Jun 2022 10:28:28 -0400
Subject: [Neuroimaging] write_annotation issue in Nibabel
Message-ID: <CADkvNwhGj_tUK-qaxQGZ6VxBhu-VOoShkqmr_YGRdyAYBddyow@mail.gmail.com>

Hi there,

I am having an issue with writing an annotation file:

```
import numpy as np
from nibabel import freesurfer
from glob import glob

lh_labels= glob('*lh*.label')

# initialize variables
lh_vertices = []
# initialize names list starting with 'unknown'
names=['background']

for ii in lh_labels:
    lh_vertices.append(freesurfer.read_labels(ii))
    names.append(os.path.basename(ii.split('.',1)[0]))


lh_labels_array=np.concatente(lh_vertices)

# load in long version of li 2016 parcellation including all 116 ROIs
ctab_long=np.loadtxt(path_to_rgb, dtype='int')

# create ctab with the appropriate length
names_len=len(names)

ctab=np.delete(ctab_long, slice(names_len,116),0)

print('writing LH annotation file')
freesurfer.write_annot(outpath + 'lh.li2019_parc.annot',
labels=lh_labels_array, ctab=ctab, names=names)
```

However, I get the same error as @danjgale.

```
IndexError                                Traceback (most recent call last)
<ipython-input-31-dab2f8c108c2> in <module>
----> 1 freesurfer.write_annot('lh.li2019_parc.annot',
labels=lh_labels_array, ctab=ctab, names=names)
c:\programdata\miniconda3\lib\site-packages\nibabel\freesurfer\io.py in
write_annot(filepath, labels, ctab, names, fill_ctab)
    542
    543         # convert labels into coded CLUT values
--> 544         clut_labels = ctab[:, -1][labels]
    545         clut_labels[np.where(labels == -1)] = 0
    546

IndexError: index 8505 is out of bounds for axis 0 with size 51

```


If I print the variables and their shapes I get the following:


```
In [35]: len(names)
Out[35]: 51

In [27]: names
Out[27]:
['background',
 'Net_10_ROIs_1_lh_native_dil2',
 'Net_11_ROIs_1_lh_native_dil2',
 'Net_12_ROIs_1_lh_native_dil2',
 'Net_12_ROIs_2_lh_native_dil2',
 'Net_13_ROIs_1_lh_native_dil2',
 .....


In [36]: ctab.shape
Out[36]: (51, 4)

In [32]: ctab
Out[32]:
array([[255, 255, 255,   0],
       [ 25,   5,  25, 255],
       [ 25, 100,  40, 255],
       [ 70, 130, 180, 255],
       ....
```
Would really appreciate any advice or help.
-- 
*Benjamin L. Deck*
*Doctoral Student*
*Applied Cognitive and Brain Sciences*
*Department of Psychological and Brain Sciences*
*Drexel University*

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From samuel.debray at ens-paris-saclay.fr  Tue Jun 28 12:04:18 2022
From: samuel.debray at ens-paris-saclay.fr (=?UTF-8?Q?=E2=80=AAsamuel=2Edebray=40ens-paris-saclay=2Efr=E2=80=AC?=)
Date: Tue, 28 Jun 2022 18:04:18 +0200
Subject: [Neuroimaging] Z-map NiLearn compute_contrast
Message-ID: <-yqp0ekownzbe-8xx8z7-2c2kgb-brc28e-63vz94-ibg3wlwvmfdp-r9y7ua-ykj4xf-n31fccnij3lv-gqq11s-r0hke6-tiv4sg-za1sea-541kwj-gpovhz3umcdj68thwz-aioght-fpak0pbfnhv-xvwshr.1656432258077@email.android.com>

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