External Email - Use Caution Dear 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-requ...@nmr.mgh.harvard.edu wrote: > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: Hypothalamus segmentation - Freesurfer 7.1 > (Lab of Autism and Developmental Neuroscience, Lab of Autism and > Developmental Neuroscience) > 2. Re: Hypothalamus segmentation - Freesurfer 7.1 (Hoopes, Andrew) > 3. Re: White matter parcellation (Graterol) > 4. define freeview colormap from command line (Simone Cauzzo) > 5. FIR Analysis and task regressor (Doll, Laura) > 6. Re: define freeview colormap from command line (Wang, Ruopeng) > 7. Re: FIR Analysis and task regressor (Douglas N. Greve) > 8. Issue with the hypothalamic segmentation (Langan, Mackenzie) > 9. Re: Issue with the hypothalamic segmentation (Hoopes, Andrew) > 10. Re: white matter volume (Douglas N. Greve) > 11. 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" <l...@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_ntsjg...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Thank 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 <dgr...@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 Caution >> Dear 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 >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/1FvwK2Q4o_omzwWs74PFlbrtdw14YNUieN1tko0x72qG2lFonMDOyPogsE9xKXjzdOhiiIvSZnywyuM4sb84PcVJxtB7o9Hz386ftng3F32Sr0Ng56HRXaaFUpr8XBElvjFj03gxMUtugMnAxC6ltPKMBtb5snr2idR98P1GpObEainrAdTZtbAUz7fBQ5bzS9ztPjMLpX9eKcc0ozLFjjC9iA9g5FTOCTbucNJ5U3dEBOawX2oM9Iq4kkFoC1X3RhXsYa_hVTXr_4lwgWXRoRw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1gqCfWet3dcFUo30svsPri6jQrY5OE-tJmMmJcQ878T-RSeoGRWH0JBElO7Qnyj3qAx-8us7ug0alzkgMuMnJce9EtsfesdgOiz7O3g07o8w12DDh93HpmBJhCMUI2ldTMXHJONVwwQSPaMAzT7dXMnyYy2wO5iGgEFES-0G19mosefLg6oizSNWNgELEIalnBU0gclmh3T6cn_Pdt8r0VL0fdXsriUIvjA2WS_CVzLMfH04WG2nSdiEc_JZM7deckesjti6rRdEhwI45vPwlXQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210202%2F0a22a0a2%2Fattachment-0001.html > > > ------------------------------ > > Message: 2 > Date: Tue, 2 Feb 2021 20:17:13 +0000 > From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <bl0pr04mb51543cb1d99a6d934a41f37bf9...@bl0pr04mb5154.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > Hi Alex, > > After sourcing the dev distribution, can you run: > > fspython -m pip install h5py==2.10.0 > > This is an unfortunate bug with older versions of keras and newer versions of > h5py, but we?ll be upgrading our internal scripts soon to deal with this. > Thanks for point this out - I?ll put a note in the dev TF-install > instructions. > > As for dealing with multiple FS versions, just install them in different > directories. Something like: > > /path/to/freesurfer/6.0.0 > /path/to/freesurfer/7.1.1 > /path/to/freesurfer/dev > etc? > > Best, > Andrew > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lab of Autism and > Developmental Neuroscience, Lab of Autism and Developmental Neuroscience > <l...@email.gwu.edu> > Date: Tuesday, February 2, 2021 at 1:08 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Hypothalamus segmentation - Freesurfer 7.1 > > External Email - Use Caution > Thank 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 > <dgr...@mgh.harvard.edu<mailto:dgr...@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 Caution > Dear 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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" > claiming to be > https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1FvwK2Q4o_omzwWs74PFlbrtdw14YNUieN1tko0x72qG2lFonMDOyPogsE9xKXjzdOhiiIvSZnywyuM4sb84PcVJxtB7o9Hz386ftng3F32Sr0Ng56HRXaaFUpr8XBElvjFj03gxMUtugMnAxC6ltPKMBtb5snr2idR98P1GpObEainrAdTZtbAUz7fBQ5bzS9ztPjMLpX9eKcc0ozLFjjC9iA9g5FTOCTbucNJ5U3dEBOawX2oM9Iq4kkFoC1X3RhXsYa_hVTXr_4lwgWXRoRw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" > claiming to be > https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<https://secure-web.cisco.com/1FvwK2Q4o_omzwWs74PFlbrtdw14YNUieN1tko0x72qG2lFonMDOyPogsE9xKXjzdOhiiIvSZnywyuM4sb84PcVJxtB7o9Hz386ftng3F32Sr0Ng56HRXaaFUpr8XBElvjFj03gxMUtugMnAxC6ltPKMBtb5snr2idR98P1GpObEainrAdTZtbAUz7fBQ5bzS9ztPjMLpX9eKcc0ozLFjjC9iA9g5FTOCTbucNJ5U3dEBOawX2oM9Iq4kkFoC1X3RhXsYa_hVTXr_4lwgWXRoRw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/188JVQyfUjDOBGyQaz38hHJZgEWxQNmukz-gckEnrx_u2_93ZReayaGcddhGUatVRCxfezvLNIRNtvdcO_UT4JdTyNsQGF6-qOxe9bp8vvcHHEKhMgGgeboEgeyPxEN5XqVgn1y1DCq7wSFFRqHkJXn9iKHQ5dXMeMSURb9sUSwoH_A6WuWUxxTPnio31i1lU1b3VeuK7YYoOskK_vNFBn_RnkiLwuERzzFWU3YJZCVQBvnkiN5k_L6woOuF6AjQuaSFBuDuh7oiBTVsXe4cfDQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210202%2F5fe61805%2Fattachment-0001.html > > > ------------------------------ > > Message: 3 > Date: Wed, 3 Feb 2021 08:15:25 +0000 > From: Graterol P?rez, Jos? Alberto <j.graterolpe...@uke.de> > Subject: Re: [Freesurfer] White matter parcellation > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <242467f39ae643d8af930a24b6dd9...@uke.de> > Content-Type: text/plain; charset="windows-1252" > > External Email - Use Caution > > Hey, Douglas. Thanks for the answer and the references. > > ________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve > <dgr...@mgh.harvard.edu> > Sent: Tuesday, February 2, 2021 5:57:33 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] White matter parcellation > > The subcortical GM structures are obtained from the whole brain segmentation > (Fischl, Neuron, 2002). The segmentation of the WM is performed by taking the > label of the closest point on cortex (Salat, Neuroimage, 2009) > > > > > On 2/1/2021 1:52 PM, Graterol P?rez, Jos? Alberto wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > I need help trying to understand how the white matter gets parcellated. I > have a clinical dataset, which means that the resolution is not as research > images, but it ran without a problem. I would like to measure the volume of > the basal ganglia and looking at wmparc.mgz I am not sure how Freesurfer > decides where a structure ends and the other one begins. I am attaching two > images to show what I mean. > > I would really appreciate some clarification. I am using FreeSurfer 7.1.1 > > Thanks in advance. > Jos? > > > ________________________________ > > Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; > Gerichtsstand: Hamburg | MailScanner has detected a possible fraud attempt > from "secure-web.cisco.com" claiming to be > http://secure-web.cisco.com/1YDQZYR7S2qJ4SG_NP8gFjH9ioGs9qVAJxK-GZmNW_gbT-5QUHxrPVTP5xn6UlBVqY2nW9sNQoU_345O7oDQRFm-dDi-dy9IzEObVr4RfJSSzHB0NV3vRHUgEX3Ya_v91P3TocbisuE1fxWi6ylHkc4Sxw3nITfA6n0Jg48C7r7piC4mWkEc_jKqDqkd6PlNgMUYrg0Abs4vKQu3d-jUm28pAgPgYc2Zv267P4xpxG1Mf-BshlKiS9l9uOywQVE0PzeF1FdHBzsmA7-yuSwey_g/http%3A%2F%2Fwww.uke.de<http://secure-web.cisco.com/1TNVlubeEY5RNf4oFHEY5w6gheVEoD4jo9r88zJkPdQ2aOlEQFLWA3ibkhLFQcnM5_K8aBICfUSAq-8vUUHSj-xx2Vssd8w4kXgyf1amgqCTReB780TWu7lTvgcJntfpA-NotaYQz5TDAwpgmUIokpu_mXWyeM1jlwQ5Mt4RYFFQLFUb_dEmXzRqtkPJp7ZaRkGuLZBW01AVPtbv2ULmyM2a6i7CmNrErvQm2kSdAYSiBlMnh2el8dO3zsqImHAkYAjLWT5S4-kKynzWM1352EQ/http%3A%2F%2Fwww.uke.de%2F> > Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Joachim Pr?l?, > Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel > > ________________________________ > > SAVE PAPER - THINK BEFORE PRINTING > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1zRhx4neXfxE6wjV2715n3qDQ0xa_CZIon5Iy-aK56jikSZh2JQJD8lhdUfOe5CEWNKo2-3Xg4lsIrHHQKcNDrpDPiJIEFBM06sBzYCoSo9BlKFLDVlXzbF-bXVWWWXNPOYpXnOj8SC779lmp0R_XuNzL8g3h_k0pmdtk1qf5WW1yBp4thc9zEyLQh_Yn78V0YgvzrVf3oyBNWYYutAbvlm9k56eO16k6T9S0nJ4QL8pkIdoPmOMlCLROER7xqsxBbgWVGnREEBrr1Q6gxnew_w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -- > > _____________________________________________________________________ > > Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; > Gerichtsstand: Hamburg | > http://secure-web.cisco.com/1YDQZYR7S2qJ4SG_NP8gFjH9ioGs9qVAJxK-GZmNW_gbT-5QUHxrPVTP5xn6UlBVqY2nW9sNQoU_345O7oDQRFm-dDi-dy9IzEObVr4RfJSSzHB0NV3vRHUgEX3Ya_v91P3TocbisuE1fxWi6ylHkc4Sxw3nITfA6n0Jg48C7r7piC4mWkEc_jKqDqkd6PlNgMUYrg0Abs4vKQu3d-jUm28pAgPgYc2Zv267P4xpxG1Mf-BshlKiS9l9uOywQVE0PzeF1FdHBzsmA7-yuSwey_g/http%3A%2F%2Fwww.uke.de > Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Joachim Pr?l?, > Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel > _____________________________________________________________________ > > SAVE PAPER - THINK BEFORE PRINTING > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1dpfaNelvVtfQqj0hWLeUiYxrpDYe9lDWuPZENukQWfA2oiKMZ6NygTZ8CNLoIdzbzAEJUXkpTd3k_OcV32M_awdlPwHrRloia-Sil2b_bep5hSGo0GqAA6qipuasrz5w63TrJ64hC5KxK8mqSapK_kcMUG4jwXKjTNxvUqjP2H2Trqdgr7xhlMi8ilGh8wNcBcRoeN_E6o1pDQVgWhDTpReio89xpDrpr8614LjlW5vBs-RUtyEWzxhWSOAbIg5l4mi1g1NEkXPT8HMiPiAAzQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2F793a8452%2Fattachment-0001.html > > > ------------------------------ > > Message: 4 > Date: Wed, 3 Feb 2021 12:38:28 +0100 > From: Simone Cauzzo <cauzzo.sim...@gmail.com> > Subject: [Freesurfer] define freeview colormap from command line > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <CABJ=6esnl2o2oedbupqdvtxastjtupwbpsnaezn3g27rse9...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear all, > Using your precious hints in a past thread, I'm now displaying several > surface analyses and taking a screenshot for each of them, everything from > command line using the command > freeview -f > ***/mni152.fnirt/surf/lh.inflated:overlay=***mni152.fnirt.lh.nii.gz:overlay_threshold=5,8 > -zoom 1.6 -ss ***.tif > Now, the colormap I'm using is thus by default "heat" with thresholds 5 and > 8. My images are very red. Opening the "configure overlay" menu in the GUI, > I noticed that the colormap is almost entirely red, and fades to yellow > only in the end. If I select "custom", the colormap appears more graded, as > I would like it to be. > Is there any way to specify the "custom" option in the "configure overlay" > menu from the command line? > > Thank you > Simone > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/11qkWDSqpk8N3fYIcGWIorunAAjVFQ0ur69RKWKL8hJLMU1IbFcA1mBvRlFtHvMsJXA0wiL--50N2fvB2d5Th5X3L1PqvL382V1I6UmT2ASpxzxwKrOwSpPG3oPN-t2aWnUBgQlOWaUmOrj2S8Tl6SlxyfcbAn4k4RFvZw8kpcRqJjqACRO6cW_eEyNHsKYQIwLdQRyOAqpk8VL8_CWboPCMOQS06sdCcZ-Kcws-snAfvqEkJU-DM2Mys83UwB_Wt3Te29FwLLi8GGUQcvCwcIA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2F3fbc625d%2Fattachment-0001.html > > > ------------------------------ > > Message: 5 > Date: Wed, 3 Feb 2021 13:32:21 +0000 > From: "Doll, Laura" <laura.d...@med.uni-heidelberg.de> > Subject: [Freesurfer] FIR Analysis and task regressor > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1612359214406.5...@med.uni-heidelberg.de> > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hi everyone, > > > Is it possible to do an FIR analysis using a task regressor instead of (or > additional to) a paradigm file? > > More precisely, we want to use pupil size as task regressor. It was recorded > during an auditory detection task (event related). > > This works when I use "-spmhrf" or other HRF options. > However, for FIR I cannot get the expected time course in the single subjects > data. > Tksurfer ends with an error because it cannot find the file h.nii.gz: > > > ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h > > > This file indeed does not exist, there is only one called "h-offset". > > The commands I used until that point are (here neglecting the original task, > but using -event-related etc instead of no task results in the same error): > > > mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask > -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1 > > selxavg3-sess -s S01_3 -analysis PupilFIR.lh > > tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer > > > Is there any solution for this? > Or any reason why it should not be done that way? > > > Best, > Laura > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/10S0ro1uuWjrqw09mzPNwymrcTdUTvqrAHo8AlwK0ywzn_mN5QLWkx0sA_uf0xa_YLUU8_8jFqEvEh-BhljSAOyd1ZNXAIpwXNdEJ5Tt_amDarD8mTSdBEjloMA335hb9K969q7AOBltdlxEvuVNHhK3oZK31WjDinBSvVid9k0fX-4OVprYuaI1eIS-YTrBSTNESt4Gq8x2BHuEAuW6LPwzMMMcKxwc6WpokAARmnhh_EwFKI8K9x1MLeuUkvyoOrqzC0WSJIJ169NOGpHe6yQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2Fa5a5a20a%2Fattachment-0001.html > > > ------------------------------ > > Message: 6 > Date: Wed, 3 Feb 2021 14:20:22 +0000 > From: "Wang, Ruopeng" <rwa...@mgh.harvard.edu> > Subject: Re: [Freesurfer] define freeview colormap from command line > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <6a61c7b7-e694-4536-abe2-e80e17bb6...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > You can specify custom colors like this: > > freeview -f lh.inlfated:overlay=xxx:overlay_custom=val,r,g,b,val2,r2,g2,b2 ... > > val is the value of the color point, r, g, b are RGB values in the range of 0 > to 255. > > You can find more details from ?freeview -h?. > > Best, > Ruopeng > >> On Feb 3, 2021, at 6:38 AM, Simone Cauzzo <cauzzo.sim...@gmail.com> wrote: >> >> External Email - Use Caution >> >> >> Dear all, >> Using your precious hints in a past thread, I'm now displaying several >> surface analyses and taking a screenshot for each of them, everything from >> command line using the command >> freeview -f >> ***/mni152.fnirt/surf/lh.inflated:overlay=***mni152.fnirt.lh.nii.gz:overlay_threshold=5,8 >> -zoom 1.6 -ss ***.tif >> Now, the colormap I'm using is thus by default "heat" with thresholds 5 and >> 8. My images are very red. Opening the "configure overlay" menu in the GUI, >> I noticed that the colormap is almost entirely red, and fades to yellow only >> in the end. If I select "custom", the colormap appears more graded, as I >> would like it to be. >> Is there any way to specify the "custom" option in the "configure overlay" >> menu from the command line? >> >> Thank you >> Simone >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > > ------------------------------ > > Message: 7 > Date: Wed, 3 Feb 2021 10:08:55 -0500 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] FIR Analysis and task regressor > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <63f7b1d7-df55-f02a-3f40-ffb5ad294...@mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Did you demean the task regressor? Is the problem that you cannot run > tksurfer-sess? Or are you reporting multiple problems? > > On 2/3/2021 8:32 AM, Doll, Laura wrote: >> >> ????????External Email - Use Caution >> >> Hi everyone, >> >> >> Is it possible to do an FIR analysis using a task regressor instead of >> (or additional to) a paradigm file? >> >> >> More precisely, we want to use pupil size as task regressor. It was >> recorded during an auditory detection task (event related). >> >> This works when I use "-spmhrf" or other HRF options. >> However, for FIR I cannot?get?the expected?time?course?in the single >> subjects data. >> Tksurfer ends with an error because it cannot find the file h.nii.gz: >> >> >> ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h >> >> >> This file indeed does not exist, there is only one called "h-offset". >> >> The commands I used until that point are (here neglecting the original >> task, but using -event-related etc instead of no task results in the >> same error): >> >> >> mkanalysis-sess?? -fsd bold -stc up? -surface fsaverage lh -fwhm 5 >> -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run >> -taskreg Pupil 1 >> >> selxavg3-sess -s?S01_3 -analysis PupilFIR.lh >> >> tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer >> >> >> Is there any solution for this? >> Or any reason why it should not be done that way? >> >> >> Best, >> Laura >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1ZhP7zXQt8RuTT5rhP7RzEsm3dbBXOd9ekeqBtVZxMr-HiHFnXdIsNqBgUyhdlH-GfEEHtvKJjWPkubthZGHwY84quODkHAIpHwNIPIBriZ2-rAzZ57yNdWm5OOWryhY8pV4anvYuXzRNpuJXe62VNtw7KJhD9tI-tml7Qy1_aS_02PFJDxUnAtQndq9MqL6Or1F5raTrnSDxHQrrC4Tdb8hENruNJL-0W0Ll2R_Ovye3Fl1qEr77QEFTKkvnGMq_rncscXPzRvO5Yy009OnatQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2Fe408e67b%2Fattachment-0001.html > > > ------------------------------ > > Message: 8 > Date: Wed, 3 Feb 2021 10:31:02 -0500 > From: "Langan, Mackenzie" <mackenzie.lan...@icahn.mssm.edu> > Subject: [Freesurfer] Issue with the hypothalamic segmentation > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <caho4oyal0jzhefex840s7-uzmprmdr_rm69+snmouwinjqp...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Good Morning, > > I have been trying to run the hypothalamic segmentation and get the > following error: > > *aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ > mri_segment_hypothalamic_subunits --s S05486* > > *Traceback (most recent call last):* > > * File > "/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", > line 10, in <module>* > > * import freesurfer as fs* > > * File > "/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", > line 8, in <module>* > > * from . import bindings* > > *ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not > found (required by > /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/* > *bindings.cpython-36m-x86_64-linux-gnu.so* > <http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F>*)* > > > > We installed the development version of freesurfer to see if that would > work to run this, but that didn't work. We then installed XCRYPT_2.0 but > still got the same error. We have two versions of python on our machine > which we amended to fix the problem, but still get the same error. I am at > a loss as to what I should try next to implement this. Any help would be > great. Thanks > > > > > Best, > > Mackenzie > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1dlzU9cNt3qf2lwLoMcb_DjCCM012_YczEiUFbw3eWX5N_rvXovIWm_BB48dJyKMZ3hGmKvxBatGTt-0w47n3i5c4aeMDrfzXoqJq3i5rer8SouXi_0ipzvl_-0G9I4BmhW8Oem49gI9EYe3Z7Rv3QPv89WqQ2HtcaMQ5nNlqfJElsWRmxDJLm54WwJJ3GWhHsmc-0-xgarY4pYoO824DtgeAuXhmVXh0gcpI2iCrlFcaKyfUiXKfHsZIjRBOs6-sv8cCpq9qRXoUtnSSih5ARQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2Fe916807f%2Fattachment-0001.html > > > ------------------------------ > > Message: 9 > Date: Wed, 3 Feb 2021 15:37:00 +0000 > From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > > <bl0pr04mb5154f030de2354fc3bc85c36f9...@bl0pr04mb5154.namprd04.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > Hi Mackenzie, > > Can you let us know what OS and version you?re running this on? > > Thanks, > Andrew > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Langan, Mackenzie > <mackenzie.lan...@icahn.mssm.edu> > Date: Wednesday, February 3, 2021 at 10:31 AM > To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] Issue with the hypothalamic segmentation > > External Email - Use Caution > Good Morning, > > I have been trying to run the hypothalamic segmentation and get the following > error: > > > aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ > mri_segment_hypothalamic_subunits --s S05486 > > Traceback (most recent call last): > > File > "/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", > line 10, in <module> > > import freesurfer as fs > > File > "/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", > line 8, in <module> > > from . import bindings > > ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' not > found (required by > /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/bindings.cpython-36m-x86_64-linux-gnu.so<http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F>) > > > > > > We installed the development version of freesurfer to see if that would work > to run this, but that didn't work. We then installed XCRYPT_2.0 but still got > the same error. We have two versions of python on our machine which we > amended to fix the problem, but still get the same error. I am at a loss as > to what I should try next to implement this. Any help would be great. Thanks > > > > > > > > Best, > > Mackenzie > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1sqFDIeaLL3F0MnnTdc8FfkBDJZaPTNyxO-2hkpb6TZtZyBmyVjww-UxtRipK_VpACqZi_JDZFbZlXVGQdG4Wymxhom7B7B-oJ8esI-rR3Yeub5Q8VjHZu8DBDcTMTUBT58-R8DTqlqtz5S8PWUEeV9BzCwMn_Bd3pZZDbqpB3Amw2vEGjb6GFDVz82druDZm6LU6SrFnv9BiQXA379IMwySrapTTrqT_xedtX2TEt8aNu8mLfEoPTMD9OWGCrDYcT6PNiZqgn4lCg_7q3-qvHQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2F0ba9ecbe%2Fattachment-0001.html > > > ------------------------------ > > Message: 10 > Date: Wed, 3 Feb 2021 11:31:58 -0500 > From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> > Subject: Re: [Freesurfer] white matter volume > To: <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <121dbf95-a986-dda4-e19d-483fcd000...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Not from a group analysis, but you can get it from running > asegstats2table. See our tutorial on ROIs > https://secure-web.cisco.com/1zq2UJ0mkCiIWSPVkPP5Ygbtu32ZBL_OwCoIZJpiSRFly544A-r23LFL09Bcnw-Ntna1Jdbup_4lN8EWtADGigGrZaDiS_KPpuD-LjPMHXHgApWctspO0cMSmRQj10QmrhnSoiBknrWrrrvJG8pR2JiPLy3x9JeBPqf3I1A8DN1yL2MuskdtxtdIVT2e8KvvKHkQnAJSQ-iL8FZ0VHhainHxwVIiV7Gh4jnrockoMlWeD55pqYnl4oyxFtLW46vVzLqc9Nmlxj6ahRgqu39caAA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FAnatomicalROI > > On 2/2/2021 11:44 AM, Sara Lyn wrote: >> >> ????????External Email - Use Caution >> >> If that's the correct way to do it then yes since I don't?know about >> this. If not, is the volume of white matter obtained from >> freesurfers?glmfit group analyses? >> >> On Tue, Feb 2, 2021 at 11:39 AM Douglas N. Greve >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >> >> sorry, still don't understand. do you want to get the volume of WM >> from DTI? >> >> On 2/2/2021 11:19 AM, Sara Lyn wrote: >>> >>> ????????External Email - Use Caution >>> >>> Hi Dr Greve, >>> >>> Instead of using DTI to get at the FA/MD etc measures is there a >>> way to get at the volume of the white matter? >>> >>> Best, >>> Sara >>> >>> On Tue, Feb 2, 2021 at 10:54 AM Douglas N. Greve >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>> Not sure what you mean >>> >>> On 2/1/2021 12:32 PM, Sara Lyn wrote: >>>> >>>> ????????External Email - Use Caution >>>> >>>> Hi, >>>> >>>> Is there a way to get at the white matter volume from a >>>> group analysis? >>>> >>>> Sara >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> >>>> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> >>>> <https://secure-web.cisco.com/1nxIWaZHNI7xNtv85vkNHiK2rzIYpWyRgsNK2sYLfcAoTWyH4nSJEVLRGcnHxr97Vi8Icr7uk_oFxUBPO0I8nlD9KwcNgX2mqq6yOIpJTVpx76geIQXuhPKliIL2KOV4b00z3LD_75LfkmM2ZREsai9hWUYqz1iSv77kQETpj-4XkQRPDdIIfi2W2jkOdvssNCWywGAF6e111YdqjKm0HtYMVI4CYBjFFvE8Tk_60tVQehASKha2zqOWVuQlCD2mdfUxbiuyc6UfRMC7wuRWH_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> >>> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <https://secure-web.cisco.com/1nxIWaZHNI7xNtv85vkNHiK2rzIYpWyRgsNK2sYLfcAoTWyH4nSJEVLRGcnHxr97Vi8Icr7uk_oFxUBPO0I8nlD9KwcNgX2mqq6yOIpJTVpx76geIQXuhPKliIL2KOV4b00z3LD_75LfkmM2ZREsai9hWUYqz1iSv77kQETpj-4XkQRPDdIIfi2W2jkOdvssNCWywGAF6e111YdqjKm0HtYMVI4CYBjFFvE8Tk_60tVQehASKha2zqOWVuQlCD2mdfUxbiuyc6UfRMC7wuRWH_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> >>> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> >>> <https://secure-web.cisco.com/1mFhEizu4Fx-vZ0Cn8uHzkNGSCaMMFACs4pDOVxupD9yud98dsA6MG_BtyxgPpvhWKsLySWrrAOreJMoBwyQ0UZ8MCbjCUz7d7XC-2X3i2xMCWyAcLAsTIC_P6qfQ8p24t5fK15SrlcU4kwXKumjpTBCrXUKmt-mhwarJF2Am7A4duXq0JS4hJXwKXHkOqIetSBhSApQLHh2ZjRQ6z80XBD1SyiQ51Ow9HNBu4D8ekgUix8j-Ik1ahcYhhe30r4pghx7Hm6FSeg27Vi0DBQ279g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> >> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/1mFhEizu4Fx-vZ0Cn8uHzkNGSCaMMFACs4pDOVxupD9yud98dsA6MG_BtyxgPpvhWKsLySWrrAOreJMoBwyQ0UZ8MCbjCUz7d7XC-2X3i2xMCWyAcLAsTIC_P6qfQ8p24t5fK15SrlcU4kwXKumjpTBCrXUKmt-mhwarJF2Am7A4duXq0JS4hJXwKXHkOqIetSBhSApQLHh2ZjRQ6z80XBD1SyiQ51Ow9HNBu4D8ekgUix8j-Ik1ahcYhhe30r4pghx7Hm6FSeg27Vi0DBQ279g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1331meVKiYUK0w8_mxif3OAyD0sDF9w4HlbzR_Ef-xcbn34yT1EwMvXpCTBVF26k6N8EWHCOGJ4cu2rjMxywyjZt3mMSpWcL6pg3DKdVSwnymIV2v3ypokimUOVkQmA0DuFEwCU5DatoXU4Ktfwq5jVraIAczl2-j-VbwAuMylAb2uMZG-HM8jkjvOQgmVK9zxnZBQo1Ve--D-F8NbQAK6fCh58MncuZhIeb9cXXQ_BBSyEQi0JZeBuRkh7QAqRKlgFDd9WMTEboXgxl-ba6UdQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2Feb6734b1%2Fattachment-0001.html > > > ------------------------------ > > Message: 11 > Date: Wed, 3 Feb 2021 11:45:08 -0500 > From: "Langan, Mackenzie" <mackenzie.lan...@icahn.mssm.edu> > Subject: Re: [Freesurfer] Issue with the hypothalamic segmentation > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAHO4oyYMO=z-aj-sp67mm5kdbd+_iwcnfqv0vhrsft48kpi...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi Andrew > We are running Ubuntu 19.10 on our computer and as for Freesurfer were we > tried to run this on freesurfer 7 and the development version but both > produced this error. (freesurfer 7: freesurfer-linux-centos7_ > x86_64-7.1.0-20200511-813297 Freesurfer DEV: freesurfer-linux-centos8_ > x86_64-dev-20201109-2e16dca) > > -Mackenzie > > On Wed, Feb 3, 2021 at 10:37 AM Hoopes, Andrew <ahoo...@mgh.harvard.edu> > wrote: > >> Hi Mackenzie, >> >> >> >> Can you let us know what OS and version you?re running this on? >> >> >> >> Thanks, >> >> Andrew >> >> >> >> *From: *freesurfer-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Langan, Mackenzie < >> mackenzie.lan...@icahn.mssm.edu> >> *Date: *Wednesday, February 3, 2021 at 10:31 AM >> *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *[Freesurfer] Issue with the hypothalamic segmentation >> >> * External Email - Use Caution * >> >> Good Morning, >> >> >> >> I have been trying to run the hypothalamic segmentation and get the >> following error: >> >> >> >> *aalqadi@athena:/zstore/data/aalqadi/aalqadi/mPFC/data$ >> mri_segment_hypothalamic_subunits --s S05486* >> >> *Traceback (most recent call last):* >> >> * File >> "/usr/local/freesurfer_dev/freesurfer/python/scripts/mri_segment_hypothalamic_subunits", >> line 10, in <module>* >> >> * import freesurfer as fs* >> >> * File >> "/usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/__init__.py", >> line 8, in <module>* >> >> * from . import bindings* >> >> *ImportError: /lib/x86_64-linux-gnu/libcrypt.so.1: version `XCRYPT_2.0' >> not found (required by >> /usr/local/freesurfer_dev/freesurfer/python/packages/freesurfer/* >> *bindings.cpython-36m-x86_64-linux-gnu.so* >> <http://secure-web.cisco.com/1hzKok6ieorAQWILbwXrHm4nWv5aGVWrgLXUjICNL0HcYQDptT0fNHU6AOnJE3qXzhl9NRtNMMllRlwPcgtVISVPA9DsJir2pbwpc4pB0rKgOo_wc0yoGtFyiaXPXPRResPg1pGzrgr4u8Ao1pz7izacK37z0ZG3aoldmpUuq7kUqK3wyc40aHRkJp7A41zrUm-ikFytp9N0shHTbuPDQfnmsIvxVlN5ohXYytZXde24kCCukWp5zEZbAtWoVD6A8g0X2TtrYVzai92-jQmruSg/http%3A%2F%2Fbindings.cpython-36m-x86_64-linux-gnu.so%2F> >> *)* >> >> >> >> >> >> We installed the development version of freesurfer to see if that would >> work to run this, but that didn't work. We then installed XCRYPT_2.0 but >> still got the same error. We have two versions of python on our machine >> which we amended to fix the problem, but still get the same error. I am at >> a loss as to what I should try next to implement this. Any help would be >> great. Thanks >> >> >> >> >> >> >> >> Best, >> >> Mackenzie >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://secure-web.cisco.com/19hlZ_7axUn8AdTxkDXxN0gm31q3caM72TmC2x6KVSreK-IU6x0CTaOcPOjHGpRK_JUcrqFsZGtksu7KzoHZ3M7IvU1I-PSoW3mwZfZPlkMfDr0w8PJi7iG-cJo6tQqplQqxsbReSDnnh2mp4SNSiqiGQqmGCDKIxLnGe30CHCQdxzwkM0ocR9hPP2z_PxjAv8na_c98JEJWleGzbUKkm1-DqCpOuLGoVxtk7hQ8HE9PMiSIybL2JDnJVlsg00XtK9BthcjsWGYHwS6Z-c4UQxA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1_gssMb6BqiOvp7v6qbU78gOqAcAPspjJ__BkRPAFG2tAgG6qoVuVT3IOzTsBUciBx5pxj8rh97G1dQmHEiHo98-r6jHyNlFSj1gDwvZFPc_NlXCQhCkOdc_h0ENmDXEw-Osd1vbzTUPXsYIL2gBEmyLUTLCfeAnn9Tre2iQ6R281_-pJmBYoWURzATKKM1BneUsrx8glL21E7rCwap4At-giPLNopiPXmcc3T6ZCL1JP6XeViOvpIpfa9s5rj5tkzT4_MForItqU0KLHo2BuEg/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210203%2F9d701747%2Fattachment-0001.html > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/14lrtjNnm3PEC-7QaJQn7C68uWUGABowPO95pcu1Ff1UbD34jeJ4RaxMQa8M9ZNeMiY_RbCgul_iStme9dV-lIVa7XHE-OPnRlL16m5cxbGIdL1zqQ9vvuqY6TxjlwijWKhrZskEWx58epUhTextw-zPufCHTrfojLvwTMNgy9Yp-3mFq47yvr91w9eRszgzT0t8_24nE00wnSuXcYl8LZ_Ta103UhYJz0-Od7yAvqvI0dCmRfybN-ouSM_TTl9YDxZ8J-bgk1mrwQ3NJ0jCp3Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > End of Freesurfer Digest, Vol 204, Issue 4 > ****************************************** _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
