[Freesurfer] hypothalamic nuclei question
External Email - Use Caution I am trying to run the hypothalamic subunits segmentation but I am getting an error message (see below). I have FS7.2 installed on Ubuntu 18.04 (hippocampal and thalamic nuclei work fine). This error occurs even after changing the voxel size to 1x1x1 as per the instructions (because this is HCP data with 0.7mm). Thanks for your help Niels --- nielsj@vein:/ImageData/DataSets/HCP/3T/100206/T1w$ mri_segment_hypothalamic_subunits --i T1w_acpc_dc_restore_1mm.nii.gz --o test using 1 thread processing 1/1 Traceback (most recent call last): File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 1463, in main() File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 90, in main threads=args.threads File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 164, in predict net = build_model(path_model, model_input_shape, len(label_list)) File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 577, in build_model input_model=None) File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 750, in unet input_model=enc_model) File "/usr/local/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", line 948, in conv_dec last_tensor = keras.layers.concatenate([cat_tensor, last_tensor], axis=ndims + 1, name=name) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py", line 931, in concatenate return Concatenate(axis=axis, **kwargs)(inputs) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 952, in __call__ input_list) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 1091, in _functional_construction_call inputs, input_masks, args, kwargs) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 822, in _keras_tensor_symbolic_call return self._infer_output_signature(inputs, args, kwargs, input_masks) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 862, in _infer_output_signature self._maybe_build(inputs) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/engine/base_layer.py", line 2710, in _maybe_build self.build(input_shapes) # pylint:disable=not-callable File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/utils/tf_utils.py", line 272, in wrapper output_shape = fn(instance, input_shape) File "/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/keras/layers/merge.py", line 519, in build raise ValueError(err_msg) ValueError: A `Concatenate` layer requires inputs with matching shapes except for the concat axis. Got inputs shapes: [(None, 176, 184, 176, 24), (None, 48, 184, 176, 480)] -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://secure-web.cisco.com/1k8Xn2D4J0byFyRwIbmBKVyMDjJThmhtuWNmuBVgygLkSVhxxPebqS7fYo4B7MWMirKuq5EEUt1IbYcelrWvGTKP0ZSVQ13IzPa6F-bBFGyDEVco097MGKGNKimELqErooVe13creAe1LKe_UOvX3wUVBkQ4wW7ehVp5SyN9tNsrJx4hmqUrlCRdvBGMaTpXov2G4O0n_6wIHKxDc1DGbEjq6X4kwYm8jVenxYxX29kYRjlAtOqrWGTfei3bbznPzC3Gb7y4onNieR0gmEMKSe9iBy5f5AQAw2DtWTFwU-_pEAcUaHXGgRxd-9Z4L7Cv1/https%3A%2F%2Fsites.google.com%2Fview%2Fnielsjanssen%2F ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
[Freesurfer] mri_vol2surf projections for subcortical structures
External Email - Use Caution Dear list I am working on a project in which we want to extract hippocampal surfaces using mri_tessellate and then overlay these surfaces with fmri activations from nifti files using mri_vol2surf. However, I am unclear whether mri_vol2surf can be used for surfaces derived from subcortical structures like the hippocampus. Crucially, these structures are unlike the cortex in that they have a closed shape and therefore the projection of activation to a surface may be more complex than in the case of cortex (which surface normal should one take?). So I guess my question is whether mri_vol2surf works for these kinds of surfaces or whether some other approach should be used. Thanks! Niels -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] make_average_subject error
External Email - Use Caution Dear all, I have seen this error mentioned several times on the list but I have never seen a solution posted. It is claimed that there is a patch and a README that explains the patch at: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ In this folder there are a bunch of files but there is no README so I am not sure what exactly I need to do. I tried replacing the files in my /usr/local/freesurfer/bin with those in this patch folder but the error remains. This error appears with all my data sets that I have tried. So it doesnt seem to be something specific to my data. Loading aseg from /media/fMRI_21/studyname/freesurfer/avgsub3/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: --- -1.0 0.0 0.0 128.0; 0.0 0.0 1.0 -128.0; 0.0 -1.0 0.0 128.0; 0.0 0.0 0.0 1.0; mghRead(mri/norm.mgz, -1): could not open file - Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault (core dumped) Linux nielsj-XXXYYY 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s avgsub3 exited with ERRORS at mié jul 31 12:05:20 WEST 2019 -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] brainstem-structures different versions?
External Email - Use Caution Hi I see on the website of brainstem substructures that the '-brainstem-structures' option in freesurfer 6.0 stable release produces brainstem segmentations that are labeled v10 whereas the script 'segmentBS.sh' available in beta versions of freesurfer produces v11 or v12 segmentations. What is the difference between these versions of the brainstem segmentation? Under what circumstances is the latest version recommended? Thank you for any clarification. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] hippocampal subfields downsampling question
In the mri output folder, I noticed that both the 0.33 mm and 1 mm (voxelspace) maps have subfields that do not overlap in space, meaning that each subfield occupies a unique location in space that does not overlap with other subfields (i.e., 12 subfields and 12 unique voxel intensities). I am wondering how this is achieved for both resolutions simultaneously. Do you 'fit' the subfields first to the 0.33 mm data and then transform the data to the 1mm space, or do you fit to both spaces separately? I would like to transform the subfields to 1.5 mm data and are able to do so accurately, but I run into problems with subfield overlap because of the down sampling. I am wondering how to best deal with this issue, and from seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there must be someway to deal with this issue. -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Ubuntu 16.04 solution?
This issue has been resolved. The problem was not Ubuntu 16.04. For some bizarre reason I received the wrong license file contents. When using my institutional email on the freesurfer website registration form I receive this file: The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Which is not the contents of the license file. However, when I put in my gmail email address on the registration form I receive an email with the correct license file. I hope the freesurfer support team can look into this issue. Thanks again. On Thu, Oct 20, 2016 at 4:57 PM, NIELS JANSSEN . wrote: > Hi Burkhard, > > Thanks for the message but this does not solve my problem. I untarred as > root in /usr/local, and as myself in /home. I also requested a new license > file (which appears the same btw), and it does not matter. For all options > I am still getting the same error saying my license is invalid (ERROR: > Invalid FreeSurfer license key found in license file). Note that when I > installed version 5.3 the license file worked fine (but I got the > nu_correct) problem. > > I am lost here as to what is causing this. I feel like going back to 14.04 > may be the only way forward. > > Thanks again. > > > > > > >> Hi Niels, I also downloaded the development version recently. After >> untarring all files >> are mine (my uid & gid). Did you unpack the tar file as root? >> Then, I had to request a new license from the freesurfer team. Freesurfer >> did >> not accept the old license anymore. But that was it - now it runs again. >> And I >> did not see this mri_nu_correct error anymore. >> all the best, >> Burkhard -- >> Dr. Burkhard Maess >> Max Planck Institute for Human Cognitive and Brain Sciences >> Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig >> Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess >> 'at' >> cbs.mpg.de, http://www.cbs.mpg.de > > > > > -- > Niels Janssen > Cognitive Neuroscience Laboratory > Institute of Biomedical Technologies > Center for Biomedical Research of the Canary Islands > University of La Laguna > Tenerife, Spain > http://www.neurocog.ull.es/en > -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Ubuntu 16.04 solution?
Hi Burkhard, Thanks for the message but this does not solve my problem. I untarred as root in /usr/local, and as myself in /home. I also requested a new license file (which appears the same btw), and it does not matter. For all options I am still getting the same error saying my license is invalid (ERROR: Invalid FreeSurfer license key found in license file). Note that when I installed version 5.3 the license file worked fine (but I got the nu_correct) problem. I am lost here as to what is causing this. I feel like going back to 14.04 may be the only way forward. Thanks again. > Hi Niels, I also downloaded the development version recently. After > untarring all files > are mine (my uid & gid). Did you unpack the tar file as root? > Then, I had to request a new license from the freesurfer team. Freesurfer > did > not accept the old license anymore. But that was it - now it runs again. > And I > did not see this mri_nu_correct error anymore. > all the best, > Burkhard -- > Dr. Burkhard Maess > Max Planck Institute for Human Cognitive and Brain Sciences > Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig > Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess > 'at' > cbs.mpg.de, http://www.cbs.mpg.de -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Ubuntu 16.04 solution?
Dear users, I have Ubuntu 16.04 (64bit) and I would like to use freesurfer. I first installed version 5.3 but got the well-known 'nu_correct' error: nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) Some searching revealed that this error is also described here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47050.html In this thread it was recommended to either downgrade perl to some earlier version (not which one), or to download the development version. I downloaded two development versions: freesurfer-Linux-centos6_x86_64-dev (on oct 10) and freesurfer-Linux-centos6_x86_64-stable-v6-beta-20161019-e582155 (on oct 19) But for both versions I get the same error when trying to test if the installation was correct: nielsj@nielsj--D2H-USB3:/usr/local/freesurfer/subjects$ mri_convert sample-001.mgz ~/sample-001.nii.gz mri_convert.bin sample-001.mgz /home/nielsj/sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... -- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -- I copied the same license.txt file as for the 5.3 version, where it worked, so I know the license.txt file is OK. One observation: after untarring the user:group properties of the files in /usr/local/freesurfer look weird and are 8481:1590 for all files, except the license.txt which is root. Is this normal? Can I install freesurfer on my machine or should I revert to Ubuntu 14.04? Thank you. -- Niels Janssen Cognitive Neuroscience Laboratory Institute of Biomedical Technologies Center for Biomedical Research of the Canary Islands University of La Laguna Tenerife, Spain http://www.neurocog.ull.es/en ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
