You can try something like mri_convert lesionmap.mgz -at samseg.m3z lesionmap.mni152.mgz
On 2/3/2021 12:53 PM, XY XY wrote:
External Email - Use CautionDear Freesurfers,
I’m working on generating a heat map of white matter lesions in a disease group. I have the lesion probability maps for each individual generated in SAMSEG and I was wondering what the best method would be to place the maps of each individual in standard space to generate a population-wise probability map. Any recommendation?
Any input is appreciated!
Best,
David Kamson
On Feb 3, 2021, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: Hypothalamus segmentation - Freesurfer 7.1 (Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience)
- Re: Hypothalamus segmentation - Freesurfer 7.1 (Hoopes, Andrew)
- Re: White matter parcellation (Graterol)
- define freeview colormap from command line (Simone Cauzzo)
- FIR Analysis and task regressor (Doll, Laura)
- Re: define freeview colormap from command line (Wang, Ruopeng)
- Re: FIR Analysis and task regressor (Douglas N. Greve)
- Issue with the hypothalamic segmentation (Langan, Mackenzie)
- Re: Issue with the hypothalamic segmentation (Hoopes, Andrew)
- Re: white matter volume (Douglas N. Greve)
- Re: Issue with the hypothalamic segmentation (Langan, Mackenzie)
Message: 1 Date: Tue, 2 Feb 2021 13:07:50 -0500 From: "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" ladn@email.gwu.edu Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CACE7MB++y95_6mkUOwsJo1dexN=Ww7X9-Ve4g_mkG_nTsjgesw@mail.gmail.com Content-Type: text/plain; charset="utf-8"
External Email - Use CautionThank you for your help!
I have tested the hypothalamus segmentation on the development version of FS, and this was the error output that I got (see below). How should I proceed to fix this?
:~/Documents$ mri_segment_hypothalamic_subunits --s UCL55003_srs2
Using 1 thread
2021-02-02 12:19:04.878273: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 2021-02-02 12:19:04.899000: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2999995000 Hz 2021-02-02 12:19:04.899178: I tensorflow/compiler/xla/service/service.cc:150] XLA service 0x20b88f0 executing computations on platform Host. Devices: 2021-02-02 12:19:04.899215: I tensorflow/compiler/xla/service/service.cc:158] StreamExecutor device (0): <undefined>, <undefined> processing 1/1 Traceback (most recent call last): File "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 1464, in <module> main() File "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 91, in main threads=args.threads File "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 165, in predict net = build_model(path_model, model_input_shape, len(label_list)) File "/home/ladn/Documents/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 579, in build_model net.load_weights(model_file, by_name=True) File "/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/network.py", line 1514, in load_weights saving.load_weights_from_hdf5_group_by_name(f, self.layers) File "/home/ladn/Documents/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/saving.py", line 839, in load_weights_from_hdf5_group_by_name original_keras_version = f.attrs['keras_version'].decode('utf8') AttributeError: 'str' object has no attribute 'decode'
Also, what's the best way for me to run a second version of Freesurfer on the same computer? I used a virtualbox, but is there a way to run it outside of that?
Thank you so much for the help and stay safe, Alex
On Sat, Jan 30, 2021 at 1:25 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
It is not in version 7. You'll have to download a development version of FS to run it.
On 1/29/2021 9:26 PM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote:
External Email - Use CautionDear Freesurfer experts,
I am having some trouble getting the hypothalamus segmentation recognized on the command line for FreeSurfer 7.1.0. Is it even available for this version? If not, will it work on the 6.0 or the 7.1.1 version?
Thanks and stay safe!
All the best, Alex
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