External Email - Use Caution        

If the brain scans went through successfully already, in an older dev version, do they need to be reprocessed? 

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: Thursday, July 28, 2022 11:28 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] Problem with hypothalamus subunits?
 
Thanks for reporting this bug, Victor. I just fixed it. The fix will be propagated to the development version in the next couple of days but, if you want, you can keep using the version you’ve got by adding the flag --crop 1000  (where 1000 is a number bigger than your image size in any dimension). That will have the same effect as the fix.

Cheers,

Eugenio


On Jul 27, 2022, at 15:03, Zeng, Victor (BIDMC - Keshavan - Psychiatry) <vzeng@bidmc.harvard.edu> wrote:

        External Email - Use Caution        

Hi all,
I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with running subunits: 

mri_segment_hypothalamic_subunits --s 10893/
using 1 thread
/mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023: DeprecationWarning: get_data() is deprecated in favor of get_fdata(), which has a more predictable return type. To obtain get_data() behavior going forward, use numpy.asanyarray(img.dataobj).

* deprecated from version: 3.0
* Will raise <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 5.0
  volume = np.squeeze(x.get_data())
predicting 1/1

the following problem occured when preprocessing image /..../0893/mri/nu.mgz :
'NoneType' object is not subscriptable
resuming program execution


segmentation  saved in:    /..../10893/mri/hypothalamic_subunits_seg.v1.mgz
volumes saved in:          /..../10893/mri/hypothalamic_subunits_volumes.v1.csv
resampled images saved in: /..../10893/mri/hypothalamic_subunits_nu_resampled_1mm.v1.mgz

If you use this tool in a publication, please cite:
Automated segmentation of the hypothalamus and associated subunits in brain MRI
B. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. Iglesias
NeuroImage 2020



Is this a problem with tensorflow? It does not seem clear. No files are actually being written

Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
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