Re: [Freesurfer] Cohen´s D effect size
External Email - Use Caution Sorry, I wrote this previous email from a different adress because I did not receive emails from the freesurfer's support list Thank you! El sáb., 25 dic. 2021 17:01, Miguel Ángel Rivas Fernández < miguelrivasf...@gmail.com> escribió: > Dear Tim, > > > Thank you for your reply. I used these two commands and now it seems that > everything worked fine: > > > 1) cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh > > 2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 > --sum test.output > > > After using the second command, I can open the test.output file and see > the mean Cohen's D of each significant cluster. Is correct the second > command? > > mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 > --sum test.output > > Thank you very much. > > > Best regards, > > Steve. > > El sáb., 25 dic. 2021 15:57, Tim Schäfer escribió: > >> External Email - Use Caution >> >> Hi Steve, >> >> what exactly do you mean by unable to open? What happens if you try to >> load it as an overlay for fsaverage in FreeView? Is there any error message >> if you try to open it? >> >> Best, >> >> Tim >> >> >> -- >> Dr. Tim Schäfer >> Postdoc Computational Neuroimaging >> Department of Child and Adolescent Psychiatry, Psychosomatics and >> Psychotherapy >> University Hospital Frankfurt, Goethe University Frankfurt am Main, >> Germany >> >> > On 12/22/2021 5:02 PM Steve Petersen wrote: >> > >> > >> > External Email - Use Caution >> > >> > Dear Freesurfer experts, >> > >> > I would really appreciate it if anyone can give me some guidance about >> this >> > question that I posted a few days ago. I conducted a One-way ANOVA and >> now >> > I would to report the Cohen's D effect size for each pairwise comparison >> > (t-tests). For that purpose, I estimated the Cohen's D effect size of >> > significant clusters using the suggested command >> > < >> https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html >> >: >> > >> > >> > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh >> > >> > Now, I get the cohensd.mgh file but I am not able to open this file. How >> > can I see the particular effect size of each significant cluster >> included >> > in the sig.cluster.summary file?. >> > >> > Thank you very much in advance for your time! >> > >> > Best regards, >> > >> > Steve, >> > >> > El mié, 15 dic 2021 a las 19:14, Steve Petersen () >> > escribió: >> > >> > > Dear Freesurfer experts, >> > > >> > > I am attempting to estimate the Cohen's D effect size of significant >> > > clusters using the suggested command >> > > < >> https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html >> >: >> > > >> > > >> > > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh >> > > >> > > Now, I get the cohensd.mgh file but I am not able to open this file. >> How >> > > can I see the particular effect size of each significant cluster >> included >> > > in the sig.cluster.summary file?. >> > > >> > > Thank you very much for your help! >> > > >> > > Best regards, >> > > >> > > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > >> https://secure-web.cisco.com/1DzWVfD7aS3RdSncH3YwQ3Gj-hgoNwquNSuAofwpNP31cDynL2xd2pSKjoIWA3ul3pF2QUWS6xwforZUGNvOjq0gUlXCH6YrmQRhFgDbwqvGLGkgks3D45HwD1Po5jsnZ1OHc0htwaNGHlWqDQjBHeVHR7
Re: [Freesurfer] Cohen´s D effect size
External Email - Use Caution Dear Tim, Thank you for your reply. I used these two commands and now it seems that everything worked fine: 1) cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh 2) mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --sum test.output After using the second command, I can open the test.output file and see the mean Cohen's D of each significant cluster. Is correct the second command? mri_segstats --i cohensd.mgh --seg cluster.sig.ocn.mgh --exclude 0 --sum test.output Thank you very much. Best regards, Steve. El sáb., 25 dic. 2021 15:57, Tim Schäfer escribió: > External Email - Use Caution > > Hi Steve, > > what exactly do you mean by unable to open? What happens if you try to > load it as an overlay for fsaverage in FreeView? Is there any error message > if you try to open it? > > Best, > > Tim > > > -- > Dr. Tim Schäfer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > > On 12/22/2021 5:02 PM Steve Petersen wrote: > > > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > I would really appreciate it if anyone can give me some guidance about > this > > question that I posted a few days ago. I conducted a One-way ANOVA and > now > > I would to report the Cohen's D effect size for each pairwise comparison > > (t-tests). For that purpose, I estimated the Cohen's D effect size of > > significant clusters using the suggested command > > < > https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html > >: > > > > > > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh > > > > Now, I get the cohensd.mgh file but I am not able to open this file. How > > can I see the particular effect size of each significant cluster included > > in the sig.cluster.summary file?. > > > > Thank you very much in advance for your time! > > > > Best regards, > > > > Steve, > > > > El mié, 15 dic 2021 a las 19:14, Steve Petersen () > > escribió: > > > > > Dear Freesurfer experts, > > > > > > I am attempting to estimate the Cohen's D effect size of significant > > > clusters using the suggested command > > > < > https://secure-web.cisco.com/1X891GVe1oH7WnmTPBGAEzMHwOsWJmix391s9QJXxMfAcqdheP__HRM8V-6y8Ex3czwzr3E908fS7Hi6Ct_l2LZe2L1p8y8mZ4uVDvXEsKWHFo7SiNOAPFmJ4waZHuZCoE5cUimkRnnEHEc-Bd_uZj6YxAv1UwUF_tNXnGj3YzbePeOge7ccWlp2KlLFS0zYQRZFVrxzjd0jiYy1CIOKm4exZqpE_i1bujkCEzLsXOKy5c7ic5HlkskGnXqAV83lvx60-hNMS3ZrZsjq-eXBRQB1P-dp1KKrgIEBDGUMoItwgqz5YmOmWwE5fOWy-iI8BmK2hHfa1L01J_6bU-Z6ACw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg52144.html > >: > > > > > > > > > fscalc gamma.mgh div rstd.mgh -o cohensd.mgh > > > > > > Now, I get the cohensd.mgh file but I am not able to open this file. > How > > > can I see the particular effect size of each significant cluster > included > > > in the sig.cluster.summary file?. > > > > > > Thank you very much for your help! > > > > > > Best regards, > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > > https://secure-web.cisco.com/1DzWVfD7aS3RdSncH3YwQ3Gj-hgoNwquNSuAofwpNP31cDynL2xd2pSKjoIWA3ul3pF2QUWS6xwforZUGNvOjq0gUlXCH6YrmQRhFgDbwqvGLGkgks3D45HwD1Po5jsnZ1OHc0htwaNGHlWqDQjBHeVHR7zpgg_q9kZUMq2IfIpGOGpChoPxaP2lTUlFlS8fouQ8AxcY2OTE-EHQWovNIEEhrP1UZNN8ZEVIMdouf_bzoVo26YAp7GqmlDMniaa43UJSAaycNU-0ViAu1_MStJj5i17R-hj6bP9xQpxkw2zgZ2Xuepc0ZONsZrxf9TnTACRZ_KrPDHhrs769GH_cyKA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1NDcgEvrY7HMK1td_Qv2dzzeMNvx6MdxI2W8VRX_lwQfI1gv9lKVAYxK58nDQWhth_kh5zVHfgQO06YD6DyH5E4wrxYWmlx07vx-g7Rq_drgQpRqDqrCQHUc4Vg1bJWrOs-x2rNZyZ26tn6DxYuJ5CFyvYDlaiYF099OVNH-_-8b5j5DDH5drdiE7rVcTnxFLUi4mvzyRdDrvDlTh5eSdDPzWDgDDXRvhZ4BbHakcE2nHUb4_T9GfnkEm39yduBqkjWLLFXOx-ZrbNzPx1U4pN2VXoEpbYU-jQrJbfk_GOPq4IxMR3OPjYap5IkFRFe4c/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer: Re-run recon-all in older versions
External Email - Use Caution I am in the same situation as Steve. Is there a particular flag to rerun subjects in freesurfer 5.3. Best regards, El vie., 12 nov. 2021 16:45, Miguel Ángel Rivas Fernández < miguelrivasf...@gmail.com> escribió: > Hi Douglas, > > I would going from freesurfer 6 to freesurfer 5.3, not from FS 5.3 to FS 6. > > > Best, > > El vie., 12 nov. 2021 15:51, Douglas N. Greve > escribió: > >> If you are going from 5.3 to 6, you should just be able to run recon-all >> -all on the 5.3 folder and it should take into account your previous edits >> (make a copy first though:) >> >> On 11/12/2021 4:40 AM, Steve Petersen wrote: >> >> External Email - Use Caution >> Dear all, >> >> We conducted the recon-all and applied a quality control protocol in >> several subjects using the FSurfer 6 version. Now, we would like to run the >> recon-all again on an older version of FSurfer (5.3 v) but considering the >> edits we made on those previous recon-all. Is this possible?, and if so, >> what would be the command? >> >> Thank you very much in advance. >> >> Best regards, >> >> Steve. >> >> ___ >> 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/1ohY0i3u1vzc0x-JNwyqvnfBmvTJAz78Y59irTbOA2wXO9nbJQYKQDpzZpmIs_ruBFWcVtg7DFrg1E-fxzGnJIMvb0dXQyrFaaXvesxf5CXKvsDA4oCXcaAhffiO1kjL0fcjWJNG8WU2v6q_eR8liyjUCW8cwv1523Gr40E4V-P4A-u_ysBwJWVgAGms3m5uiOCHr7GlUahnPPBaattMfnIGRoH3SdLwkD_QGgEJf44NF0iJDxrvE2iu5k5r3u9PcRA2iSk7Dq2k4OnMLwGRNH_Er4mqziwVyPmqbRisRYaPuiW4Fmqcgi0q_BIuDbTjcBaFbsU1uUTd3Fhvcy7xBlg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> 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 >> http://secure-web.cisco.com/16TiIUV9VuvtDhCs_xopalyDIqaLe38n-FwaO0VBHRPGv7X5PmQFOObe7-riDF6bWQYV-6sa4Mabjgh_E2OcEDXMsEIPc5f0FPuSvjnktZamlW9o6u_ZtqKN372plkhiB0tqaMmK1Zs3tWayegNNLUDxfL2wm_hp7-6Ns9fg11_AsB1PDEcaNP7YiIVmnEKvHSqHKR4TGNJ8rCEED7BNMuj4OIta-xWDBBrYEokeNFRaVs_O6v2YVMmoUB40G71jGiZ6U41BylnW71NVF2K3ImjkiQ74pfCZnmumj8_HoTz0NcBy8bXb8LwilNUn6rVFAwv2gzldz2HPra6H8sqC7ow/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline >> . 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. >> 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer: Re-run recon-all in older versions
External Email - Use Caution Hi Douglas, I would going from freesurfer 6 to freesurfer 5.3, not from FS 5.3 to FS 6. Best, El vie., 12 nov. 2021 15:51, Douglas N. Greve escribió: > If you are going from 5.3 to 6, you should just be able to run recon-all > -all on the 5.3 folder and it should take into account your previous edits > (make a copy first though:) > > On 11/12/2021 4:40 AM, Steve Petersen wrote: > > External Email - Use Caution > Dear all, > > We conducted the recon-all and applied a quality control protocol in > several subjects using the FSurfer 6 version. Now, we would like to run the > recon-all again on an older version of FSurfer (5.3 v) but considering the > edits we made on those previous recon-all. Is this possible?, and if so, > what would be the command? > > Thank you very much in advance. > > Best regards, > > Steve. > > ___ > 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/1WPi6-EmssmI2iLG15xmYyxeYhSGoyNTDf4oPy_Qx9k1Tb0M9RQOv9WTJrUWgbNihGlui9uC-4BcxOAeFvHudYChKBzDDk6iFKNx5wnJlKr_89Uhd-gNki8YrcLYSNVq3CCcnEd07QpvU6lmcNSLDzV5jpjVS4GF3jUSGD8GebkagTIo57EROT7f57zVro5gguXVhd7JpIaOGhWe8VvBzuznrDTuJC-0ppt05Hss9i9nUmvYCpMkAYCUK3eCC8dSxgynAnJtNbZQpYHFOHPtp_T47zyCkMVqIbXGKgaQxp490B78f8MrKvK8nZ95Py3SX1VDkg_G-VngdrqZAszKO1w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 > http://secure-web.cisco.com/1fWn93lUWOA0uXuAi-LRAomJY4zMi6OfnzcFLbgFB0QFT47eHzSexc9UXZ_15h46iUmWrdrzLAP2gzS0i4sctofRUz9eg-d15Ox7O3gkuKRxTDP7TCBpoOgprdldE79lf2pdKeFvX1SR6GNVzpZOFm955tpEd3G1Z_Oa4mxpgp34KW0BjUoBI3xucqS836DUoQyeHpfLSMrkRhc5CJbvhO6xhFn2I3AEt6IrnyyA4nmorMTEjPHVEDeNPc8ZYR1C3N4U17jDlKOQohEmmQWdoR_ZeGThjIQU4QQQ7OZOzK-rnB5uDqB44sLchFUoXQjLub8I-GqmYEUZhP-h3-TqY6Q/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > . 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. > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer V6: aparcstats2table command python issues
External Email - Use Caution Dear Freesurfer experts, I am trying to use the aparcstats2table command (FSurfer V.6) in order to export the thickness measures but there should be an issue with my python version. This is the complete output: aparcstats2table --hemi lh --subjects 4166 --meas thickness --parc aparc.a2009s --tablefile thickness.txt Usage: python [options] python: error: no such option: --hemi Could you give me some suggestions to solve this problem? Thank you very much in advance. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Export stats: HCP Multi Modal parcellation
External Email - Use Caution Hello Glasser, In addition to freesurfer's asegstats2table, I would be interested in volume, cortical thickness and area of the HCP atlas (please, see attached .csv file). Other software (e.g CAT12 <http://secure-web.cisco.com/1COAdbRtDckHN6yiHBswwxyVsNqxiQs4J0BIS3hCQNJzehplVAuaKl0ugaaaCSeAfNzGdiJpsvU6rvCBU9qIhWpNEmuB5E_ojQBwSRyr9qaSyv5oU0ed91aiW7flrQXvoPLoIyDuKczkUZI6P9NtmVQQqy01bFfwg_qZ8BES-sVkfG4hnppkEYdZb_dXubwS-Xt-QLigkXU9P3ZcpEIZB1hUvLLXtw-RM99oapY7Dm8XYjdgD9PM7R654BuszY4iuqGBnbLgZEA4VGHPlQJsk9A/http%3A%2F%2Fwww.neuro.uni-jena.de%2Fcat12-html%2Fcat_methods_RBM.html%23FS_HCP>) allows exporting these measurements in HCP parcellation but I would like to know if it is possible with MRI data processed un FS.v6 Thank you in advance. Best regards, # El mié., 31 mar. 2021 15:28, Glasser, Matthew escribió: > External Email - Use Caution > > What stats are you looking for? > > Matt. > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Wednesday, March 31, 2021 at 4:36 AM > *To: *Freesurfer support list > *Subject: *[Freesurfer] Export stats: HCP Multi Modal parcellation > > > > *External Email - Use Caution* > > > > Dear Freesurfer experts, > > > > it is possible to export the stats of subjects reconstructed with > freesurfer v.6 using the HCP Multi Modal parcellation? (Glasser et al., > 2016). > > > > Thank you in advance. > > > > Best regards, > > > -- > > *Miguel Ángel Rivas Fernández* > > > > > -- > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1zrZ5NgwlmYyTyG0sGwBn4QgIqRsDKmXsWOeLE3T6NKGEKHoICs0g131f8SZqVQ9ipaWG2fl0iCv8_kq0zGE1aLTDbKq872D46BHHxMF91NDp6UksZOMoNeV1aAkCwsrjyKTDlnlqE2GeYcUDQDJFMf0qBKOkBGanibW1T4xs3c8yBL1Sj2W7ZCKUI5PQd-vUsf1mIQll5eyexTepf0DAnjkzMfhVdtRDNpW38Z8cpCNpspWzfNDFy6EA-GSXnwl3oBg_9YlXcN3Mw9iUJpZmKA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer lh_L_V1_ROI_thickness lh_L_MST_ROI_thickness lh_L_V6_ROI_thickness lh_L_V2_ROI_thickness lh_L_V3_ROI_thickness lh_L_V4_ROI_thickness lh_L_V8_ROI_thickness lh_L_4_ROI_thickness lh_L_3b_ROI_thickness lh_L_FEF_ROI_thickness lh_L_PEF_ROI_thickness lh_L_55b_ROI_thickness lh_L_V3A_ROI_thickness lh_L_RSC_ROI_thickness lh_L_POS2_ROI_thickness lh_L_V7_ROI_thickness lh_L_IPS1_ROI_thickness lh_L_FFC_ROI_thickness lh_L_V3B_ROI_thickness lh_L_LO1_ROI_thickness lh_L_LO2_ROI_thickness lh_L_PIT_ROI_thickness lh_L_MT_ROI_thickness lh_L_A1_ROI_thickness lh_L_PSL_ROI_thickness lh_L_SFL_ROI_thickness lh_L_PCV_ROI_thickness lh_L_STV_ROI_thickness lh_L_7Pm_ROI_thickness lh_L_7m_ROI_thickness lh_L_POS1_ROI_thickness lh_L_23d_ROI_thickness lh_L_v23ab_ROI_thickness lh_L_d23ab_ROI_thickness lh_L_31pv_ROI_thickness lh_L_5m_ROI_thickness lh_L_5mv_ROI_thickness lh_L_23c_ROI_thickness lh_L_5L_ROI_thickness lh_L_24dd_ROI_thickness lh_L_24dv_ROI_thickness lh_L_7AL_ROI_thickness lh_L_SCEF_ROI_thickness lh_L_6ma_ROI_thickness lh_L_7Am_ROI_thickness lh_L_7PL_ROI_thickness lh_L_7PC_ROI_thickness lh_L_LIPv_ROI_thickness lh_L_VIP_ROI_thickness lh_L_MIP_ROI_thickness lh_L_1_ROI_thickness lh_L_2_ROI_thickness lh_L_3a_ROI_thickness lh_L_6d_ROI_thickness lh_L_6mp_ROI_thickness lh_L_6v_ROI_thickness lh_L_p24pr_ROI_thickness lh_L_33pr_ROI_thickness lh_L_a24pr_ROI_thickness lh_L_p32pr_ROI_thickness lh_L_a24_ROI_thickness lh_L_d32_ROI_thickness lh_L_8BM_ROI_thickness lh_L_p32_ROI_thickness lh_L_10r_ROI_thickness lh_L_47m_ROI_thickness lh_L_8Av_ROI_thickness lh_L_8Ad_ROI_thickness lh_L_9m_ROI_thickness lh_L_8BL_ROI_thickness lh_L_9p_ROI_thickness lh_L_10d_ROI_thickness lh_L_8C_ROI_thickness lh_L_44_ROI_thickness lh_L_45_ROI_thickness lh_L_47l_ROI_thickness lh_L_a47r_ROI_thickness lh_L_6r_ROI_thickness lh_L_IFJa_ROI_thickness lh_L_IFJp_ROI_thickness lh_L_IFSp_ROI_thickness lh_L_IFSa_ROI_thickness lh_L_p9.46v_ROI_thickness lh_L_46_ROI_thickness lh_L_a9.46v_ROI_thickness lh_L_9.46d_ROI_thickness lh_L_9a_ROI_thickness lh_L_10v_ROI_thickness lh_L_a10p_ROI_thickness lh_L_10pp_ROI_thickness lh_L_11l_ROI_thickness lh_L_13l_ROI_thickness lh_L_OFC_ROI_thickness lh_L_47s_ROI_thickness lh_L_LIPd_ROI_thickness lh_L_6a_ROI_thickness lh_L_i6.8_ROI_thickness lh_L_s6.8_ROI_thickness lh_L_43
[Freesurfer] Export stats: HCP Multi Modal parcellation
External Email - Use Caution Dear Freesurfer experts, it is possible to export the stats of subjects reconstructed with freesurfer v.6 using the HCP Multi Modal parcellation? (Glasser et al., 2016). Thank you in advance. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness measure for external analysis.
External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis with thickness measurements of two brain regions. Can we use safely the metrics exported or by contrary a previous transformation is required before export the stats of each subject? Thanks for your time. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Flip left-right orientation command
External Email - Use Caution Dear Douglas, In these emails I asked to you how to flip the left-right orientation of an image in PIL orientation and you recommend to me this command mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii All have worked fine but now I am in the same situation with an image in RAS orientation. *Which command should I use to flip the left/right orientation of an image in RAS orientation?*. As I explained in my previous emails, the orientation is fine. The reason is that am using a software to detect brain lesions that only works in left hemisphere and my subject have the lesion in the right hemisphere. After the lesion estimation I need to flip the left-right orientation. Thank you very much for your time and attention. Best regards, El vie., 14 feb. 2020 a las 17:34, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > Yes, it works!. > > Thank you so much. > > El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve (< > dgr...@mgh.harvard.edu>) escribió: > >> You can try, >> mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii >> but I'm not promising anything >> >> On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote: >> >> External Email - Use Caution >> Dear Douglas, >> >> My image is in the correct orientation. The reason is that am using a >> software to detect brain lesions that only works in left hemisphere and my >> subject have the lesion in the right hemisphere. I tried it with the >> following command and it works >> >> mri_convert --in_orientation PIL t1.nii t1_flip.nii >> >> Now I would like to come back to the original orientation, which command >> should I use? >> >> Thanks in advance. >> >> Best regards, >> >> El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (< >> dgr...@mgh.harvard.edu>) escribió: >> >>> Is the image in the wrong orientation (ie, is it not truly in PIR) or do >>> you want to change the orientation? doing a left-right swap is more than >>> changing the orientation >>> >>> On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote: >>> >>> External Email - Use Caution >>> Dear Freesurfer experts, >>> >>> Which command should I use to flip the left-right orientation of a T1 >>> image?. Actually my image is in PIR orientation, I used the following >>> command >>> >>> mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii' >>> >>> *PIR* >>> >>> >>> Thanks in advance, >>> >>> Best regards, >>> >>> -- >>> *Miguel Ángel Rivas Fernández* >>> >>> ___ >>> Freesurfer mailing >>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> -- >> *Miguel Ángel Rivas Fernández* >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > *Miguel Ángel Rivas Fernández* > -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Group analysis with qdec: qcache change this?
External Email - Use Caution Dear freesurfer experts, Before running group analysis in qdec is necessary run the qcache command over all subjects but, does this command change some segmentation file (eg. rh/lh Pial or white surface) or other importants file? We would also like to perform external analysis using the output metrics obtained with the recon-all. This is why we want to know if we can safely use this command without affecting any segmentation measure. Thanks in advance Best regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Flip left-right orientation command
External Email - Use Caution Yes, it works!. Thank you so much. El vie., 14 feb. 2020 a las 17:22, Douglas N. Greve () escribió: > You can try, > mri_convert --in_orientation PIR t1_flip.nii t1_flip_flip.nii > but I'm not promising anything > > On 2/14/2020 11:03 AM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > Dear Douglas, > > My image is in the correct orientation. The reason is that am using a > software to detect brain lesions that only works in left hemisphere and my > subject have the lesion in the right hemisphere. I tried it with the > following command and it works > > mri_convert --in_orientation PIL t1.nii t1_flip.nii > > Now I would like to come back to the original orientation, which command > should I use? > > Thanks in advance. > > Best regards, > > El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve (< > dgr...@mgh.harvard.edu>) escribió: > >> Is the image in the wrong orientation (ie, is it not truly in PIR) or do >> you want to change the orientation? doing a left-right swap is more than >> changing the orientation >> >> On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote: >> >> External Email - Use Caution >> Dear Freesurfer experts, >> >> Which command should I use to flip the left-right orientation of a T1 >> image?. Actually my image is in PIR orientation, I used the following >> command >> >> mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii' >> >> *PIR* >> >> >> Thanks in advance, >> >> Best regards, >> >> -- >> *Miguel Ángel Rivas Fernández* >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > *Miguel Ángel Rivas Fernández* > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Flip left-right orientation command
External Email - Use Caution Dear Douglas, My image is in the correct orientation. The reason is that am using a software to detect brain lesions that only works in left hemisphere and my subject have the lesion in the right hemisphere. I tried it with the following command and it works mri_convert --in_orientation PIL t1.nii t1_flip.nii Now I would like to come back to the original orientation, which command should I use? Thanks in advance. Best regards, El vie., 14 feb. 2020 a las 16:01, Douglas N. Greve () escribió: > Is the image in the wrong orientation (ie, is it not truly in PIR) or do > you want to change the orientation? doing a left-right swap is more than > changing the orientation > > On 2/11/2020 4:06 PM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > Which command should I use to flip the left-right orientation of a T1 > image?. Actually my image is in PIR orientation, I used the following > command > > mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii' > > *PIR* > > > Thanks in advance, > > Best regards, > > -- > *Miguel Ángel Rivas Fernández* > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer error in matlab
External Email - Use Caution
Hi Andrew,
Yes, we are using FS 6.0 and I think that is correctly sourced in MATLAB
environment. I used the same commands that we are using in other Mac
workstation where all works fine. The commands used to source freesurfer in
Matlab were these:
bash_path=getenv ('PATH');
setenv(
'PATH',[bash_path,':/Applications/freesurfer',':/Applications/freesurfer/bin']);
setenv FREESURFER_HOME /Applications/freesurfer
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
How can I set the DYLD_LIBRARY_PATH?
Thanks in advance.
Best,
El mié., 12 feb. 2020 a las 1:15, Hoopes, Andrew ()
escribió:
> If I understand correctly, you're having trouble running freesurfer
> binaries from within matlab, right? Is freesurfer fully sourced in your
> MATLAB environment? I’m guessing this is an issue with your
> DYLD_LIBRARY_PATH not being set, but it's possible there are other issues
> going on. You should check to see if the DYLD_LIBRARY_PATH environment
> variable in your MATLAB shell matches what you see in the terminal after
> sourcing freesurfer. Also, are you using 6.0?
>
> Best,
> Andrew
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández
> Sent: Friday, February 7, 2020 6:17 AM
> To: Freesurfer support list
> Subject: [Freesurfer] freesurfer error in matlab
>
> External Email - Use Caution
>
> Dear Freesurfer devs,
>
> I am trying to run FreeSurfer in Matlab and I received the following error
> message
>
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
> Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
> Expected in: /usr/lib/libSystem.B.dylib
>
> I tried to fix this error disabling the SIP but this did not work. Maybe
> could be due to the gcc compiler?
>
> Any help would be appreciated
>
> Thanks in advance
>
> Best regards,
>
> --
> Miguel Ángel Rivas Fernández
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
--
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Flip left-right orientation command
External Email - Use Caution Dear Freesurfer experts, Which command should I use to flip the left-right orientation of a T1 image?. Actually my image is in PIR orientation, I used the following command mri_info --orientation '/home/rmn/Desktop/study/E03/3d/coanat_E03.nii' *PIR* Thanks in advance, Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer error in matlab
External Email - Use Caution Dear Freesurfer devs, I am trying to run FreeSurfer in Matlab and I received the following error message dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib I tried to fix this error disabling the SIP but this did not work. Maybe could be due to the gcc compiler? Any help would be appreciated Thanks in advance Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] TRACULA question: Preprocessing exited with ERRORS
External Email - Use Caution Dear Freesurfer experts, I am a beginner in the use of TRACULA. I tried to run the preprocessing step of the trac-all command and it seems that all have worked fine. However, at the end of the command TRACULA finished with an error. This is the final output tkregister2 --mov /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat_orig.nii.gz --targ /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anatorig2anat.mat --reg /Applications/freesurfer_dev/freesurfer/subjects/TUTORIAL_DATA/4220/4220/4220/dmri/xfms/anat2anatorig.dat tkregister2: Command not found. Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Mon Dec 9 22:00:14 CET 2019 You can find the configuration file and the trac-all.log file in attached. Best regards, -- *Miguel Ángel Rivas Fernández* trac-all.log Description: Binary data dmrirc.tutorial Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Thalamic nuclei segmentation
External Email - Use Caution Dear Freesurfer devs, I tried to run the thalamic nuclei segmentation (T1 and T2 as input) using the freesurfer dev version and the terminal gave to me the following error rmnlab1:~ neucoga$ segmentThalamicNuclei.sh 4001 /Applications/freesurfer_dev/freesurfer/subjects/4001/mri/orig/T2.nii THALAMUS BBREGISTER_MODE t2 Setting ITK threads to 1 # #@# Thalamic Nuclei processing domingo, 8 de diciembre de 2019, 20:55:24 CET -- Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer_dev/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer_dev/freesurfer/MCRv84//sys/os/maci64:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib:/Applications/freesurfer_dev/freesurfer/lib/gcc/lib Error using SegmentThalamicNuclei (line 138) Additional volume does not exist 255 Darwin rmnlab1.inv.usc.es 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64 Thalamic nuclei exited with ERRORS at domingo, 8 de diciembre de 2019, 20:55:31 CET For more details, see the log file /Applications/freesurfer_dev/freesurfer/subjects/4001/scripts/thalamic-nuclei-BBREGISTER_MODE.log Is the command right? I think that I have followed correctly the instructions of the website. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview error
External Email - Use Caution I tried in the command window where I started freeview but nothing happened. This is the output miguel@miguel-VirtualBox:~$ ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang () escribió: > Can you run the command in the command window that you start freeview? > > Ruopeng > > On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández < > miguelrivasf...@gmail.com> wrote: > > External Email - Use Caution > > Dear Ruopeng, > > I put that command in the freeview command console and this is the output > > [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz > This is not a shell. Only freeview commands are supported. Type '-h' for > all the available commands. > > > > Best regards, > > El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (< > rpw...@nmr.mgh.harvard.edu>) escribió: > >> If you run: >> >> ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz >> >> What does it show? >> >> Ruopeng >> On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote: >> >> External Email - Use Caution >> Dear Freesurfer devs, >> >> I tried to open the brainmask.mgz file in freeview but I obtained this >> error: >> >> >> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could >> not open file >> MRIread failed: Unable to read from >> /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz >> mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could >> not open file >> >> Any suggestion about what could be the problem?, maybe the write >> permissons of the freesurfer folder? >> >> I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >> version that is installed in a Ubuntu 18.04 virtual machine. It is very >> strange because few weeks ago everything it was working correctly. >> >> Thanks in advance. >> >> >> Best regards, >> -- >> *Miguel Ángel Rivas Fernández* >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > *Miguel Ángel Rivas Fernández* > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freeview error
External Email - Use Caution Dear Ruopeng, I put that command in the freeview command console and this is the output [FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz This is not a shell. Only freeview commands are supported. Type '-h' for all the available commands. Best regards, El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (< rpw...@nmr.mgh.harvard.edu>) escribió: > If you run: > > ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz > > What does it show? > > Ruopeng > On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > Dear Freesurfer devs, > > I tried to open the brainmask.mgz file in freeview but I obtained this > error: > > > mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could > not open file > MRIread failed: Unable to read from > /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz > mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could > not open file > > Any suggestion about what could be the problem?, maybe the write > permissons of the freesurfer folder? > > I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c > version that is installed in a Ubuntu 18.04 virtual machine. It is very > strange because few weeks ago everything it was working correctly. > > Thanks in advance. > > > Best regards, > -- > *Miguel Ángel Rivas Fernández* > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freeview error
External Email - Use Caution Dear Freesurfer devs, I tried to open the brainmask.mgz file in freeview but I obtained this error: mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder? I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly. Thanks in advance. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use Caution Dear Bram, Thanks for your help, yes I tried to fix this issue following Bruce´s suggestions and everything worked fine. I manually filled the brain lesions in the wm.mgz and now the recon-all did not stop in the correcting defect. Best regards, El lun., 8 jul. 2019 a las 17:17, Diamond, Bram Ryder (< brdiam...@mgh.harvard.edu>) escribió: > Hi Miguel! > > I'll be happy to help with your issue, but I'm having trouble finding your > subject's directory on our server. Could you please try and upload the data > via FTP, again? Also, have you tried either of Bruce's suggestions? > > Thanks, > Bram > > Bram R. Diamond, BSc > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas > Fernández > Sent: Wednesday, June 26, 2019 11:37 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error: Correcting defect > > External Email - Use Caution > > Hello Bruce, > > Ok, I have sent to you the subject via FileDrop if you want to take a > look. Thanks. > > Best regards, > > El mié., 26 jun. 2019 a las 17:04, Bruce Fischl (< > fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>) escribió: > Hi Miguel > > depending on the lesions it may not be fixable (since they may change the > topology of the cortex). If you upload the subject we will take a look, or > you can try manually filling in the lesion in the wm.mgz (or marking it as > lesion in the aseg.mgz) and seeing if that helps > > cheers > Bruce > On Wed, 26 Jun 2019, Miguel Ángel Rivas > Fernández wrote: > > > > > External Email - Use Caution > > > > > > I ran the recon-all in one subject and and this process was stopped in > the topology correction. In > > particular during the > > > > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". > > > > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview > and I noticed that the this > > error would be located in the lh.inflated.nofix file. I am not > completely sure but I suspect that > > this error may be due to the fact that there is a large amount of brain > lesion and this would > > difficult the topology correction. How can I fix this problem? > > > > Thanks in advance. > > > > Best regards, > > > > -- > > Miguel Ángel Rivas Fernández > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Miguel Ángel Rivas Fernández > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Change image orientation
External Email - Use Caution Dear Freesurfer devs, Is possible to change the image orientation of the t1.nii images? In that case, what command should be used?. I would like to change them from a LPI orientation to a RAI orientation. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all error: Correcting defect
External Email - Use Caution Hello Bruce, Ok, I have sent to you the subject via FileDrop if you want to take a look. Thanks. Best regards, El mié., 26 jun. 2019 a las 17:04, Bruce Fischl () escribió: > Hi Miguel > > depending on the lesions it may not be fixable (since they may change the > topology of the cortex). If you upload the subject we will take a look, or > you can try manually filling in the lesion in the wm.mgz (or marking it as > lesion in the aseg.mgz) and seeing if that helps > > cheers > Bruce > On Wed, 26 Jun 2019, Miguel Ángel Rivas > Fernández wrote: > > > > > External Email - Use Caution > > > > > > I ran the recon-all in one subject and and this process was stopped > in the topology correction. In > > particular during the > > > > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". > > > > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview > and I noticed that the this > > error would be located in the lh.inflated.nofix file. I am not > completely sure but I suspect that > > this error may be due to the fact that there is a large amount of brain > lesion and this would > > difficult the topology correction. How can I fix this problem? > > > > Thanks in advance. > > > > Best regards, > > > > -- > > Miguel Ángel Rivas Fernández > > > >_______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cerebellum and brainstem mask
External Email - Use Caution Dear Freesurfer devs, I would like to exclude from the T1 image those voxels that correspond to the cerebellum and brainstem. I tried to do this using the following commands although I am not completely sure if they are the right ones: 1. Extract cerebellum and brain stem labels from the aseg.mgz file mri_extract_labels aseg.mgz 45 46 47 6 7 8 16 cerebellum_brainstem.mgz 2. Binarize the mask mri_binarize --i cerebellum_brainstem.mgz --o cerebellum_brainstem_mask.mgz --min 0 --max 0 3. Convert the mask to native space mri_convert -rl orig/001.mgz -rt nearest cerebellum_brainstem_mask.mgz cerebellum_brainstem_mask.nii Any help would be appreciated. Thanks in advance. Best regards, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Matlab error in Freesurfer
External Email - Use Caution Could it be a solution to reinstall freesurfer? I tried to install a newer gcc version and now Matlab gave to me this error -- ERROR: FreeSurfer environment FREESURFER_HOME is not defined. If you are outside the NMR-Martinos Center, please set this variable to the location where you installed FreeSurfer. If you are inside the NMR-Martinos Center, please source the standard environment. If you need to install FreeSurfer, go to: http://surfer.nmr.mgh.harvard.edu -- Attempting to use /Applications/freesurfer directory. using /Applications/freesurfer/subjects/10018/mri/aseg.mgz aseg volume to correct midline setting seed for random number generator to 1234 mris_ca_label: SUBJECTS_DIR not defined in environment No such file or directory mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 10018 lh /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Signal 124 ans = 252 Best, El jue., 14 mar. 2019 a las 18:59, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > > Hello Douglas, > > Yes it works > > El jue., 14 mar. 2019 a las 18:51, Greve, Douglas N.,Ph.D. (< > dgr...@mgh.harvard.edu>) escribió: > >> It looks like the library is not set up properly. Does freesurfer work >> outside of matlab? >> >> On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote: >> > >> > External Email - Use Caution >> > >> > >> > Dear Freesurfer devs, >> > >> > >> > Have you had occasion to review this error?. Could it be due to the >> > gcc version? >> > >> > Thank you very much for your help. >> > >> > >> > Best regards, >> > >> > El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández >> > (mailto:miguelrivasf...@gmail.com>>) >> escribió: >> > >> > >> > Dear Freesurfer experts, >> > >> > I am trying to run Freesurfer commands (eg. mri_ca_label) using >> > Matlab in a Mac computer (macOS High Sierra 10.13.6 version) >> > and I'm receiving the following error that I suspect are due to >> > library incompatibilities: >> > >> > >> > dyld: lazy symbol binding failed: Symbol not found: >> > ___emutls_get_address >> > Referenced from: >> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >> > Expected in: /usr/lib/libSystem.B.dylib >> > >> > dyld: Symbol not found: ___emutls_get_address >> > Referenced from: >> > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib >> > Expected in: /usr/lib/libSystem.B.dylib >> > >> > mris_ca_label -aseg >> > /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 >> > 10018 lh >> > /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg >> > >> >> /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs >> > /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: >> Aborted >> > >> > ans = >> > >> >134 >> > >> > >> > >> > I realized that this error has been previously reported >> > < >> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html >> > >> > and, as Andrew said, one of the possible solutions could be to >> > disable the SIP (System Protection Integrity). I have disabled the >> > SIP following the instructions indicated here >> > < >> http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ >> > >> > but unfortunately Matlab continues giving the same error. >> > >> > >> > How could I solve this problem?. Any help would be appreciated. >> > >> > >> > Thanks in advance. >> > >> > Best, >> > >> > -- >> > *Miguel Ángel Rivas Fernández* >> > >> > >> > >> > -- >> > *Miguel Ángel Rivas Fernández* >> > >> > ___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > *Miguel Ángel Rivas Fernández* > -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Matlab error in Freesurfer
External Email - Use Caution Hello Douglas, Yes it works El jue., 14 mar. 2019 a las 18:51, Greve, Douglas N.,Ph.D. (< dgr...@mgh.harvard.edu>) escribió: > It looks like the library is not set up properly. Does freesurfer work > outside of matlab? > > On 3/14/19 1:46 PM, Miguel Ángel Rivas Fernández wrote: > > > > External Email - Use Caution > > > > > > Dear Freesurfer devs, > > > > > > Have you had occasion to review this error?. Could it be due to the > > gcc version? > > > > Thank you very much for your help. > > > > > > Best regards, > > > > El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández > > (mailto:miguelrivasf...@gmail.com>>) > escribió: > > > > > > Dear Freesurfer experts, > > > > I am trying to run Freesurfer commands (eg. mri_ca_label) using > > Matlab in a Mac computer (macOS High Sierra 10.13.6 version) > > and I'm receiving the following error that I suspect are due to > > library incompatibilities: > > > > > > dyld: lazy symbol binding failed: Symbol not found: > > ___emutls_get_address > > Referenced from: > > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > > dyld: Symbol not found: ___emutls_get_address > > Referenced from: > > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > > Expected in: /usr/lib/libSystem.B.dylib > > > > mris_ca_label -aseg > > /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 > > 10018 lh > > /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg > > > > /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs > > /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted > > > > ans = > > > >134 > > > > > > > > I realized that this error has been previously reported > > < > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html > > > > and, as Andrew said, one of the possible solutions could be to > > disable the SIP (System Protection Integrity). I have disabled the > > SIP following the instructions indicated here > > < > http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ > > > > but unfortunately Matlab continues giving the same error. > > > > > > How could I solve this problem?. Any help would be appreciated. > > > > > > Thanks in advance. > > > > Best, > > > > -- > > *Miguel Ángel Rivas Fernández* > > > > > > > > -- > > *Miguel Ángel Rivas Fernández* > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Matlab error in Freesurfer
External Email - Use Caution Dear Freesurfer devs, Have you had occasion to review this error?. Could it be due to the gcc version? Thank you very much for your help. Best regards, El mié., 13 mar. 2019 a las 16:09, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > > Dear Freesurfer experts, > > I am trying to run Freesurfer commands (eg. mri_ca_label) using Matlab in > a Mac computer (macOS High Sierra 10.13.6 version) and I'm receiving the > following error that I suspect are due to library incompatibilities: > > > dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > dyld: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz > -seed 1234 10018 lh > /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg > /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs > /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted > > ans = > >134 > > > > I realized that this error has been previously reported > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html> > and, as Andrew said, one of the possible solutions could be to disable the > SIP (System Protection Integrity). I have disabled the SIP following the > instructions indicated here > <http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/> > but unfortunately Matlab continues giving the same error. > > > How could I solve this problem?. Any help would be appreciated. > > > Thanks in advance. > > Best, > > -- > *Miguel Ángel Rivas Fernández* > -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Matlab error in Freesurfer
External Email - Use Caution Dear Freesurfer experts, I am trying to run Freesurfer commands (eg. mri_ca_label) using Matlab in a Mac computer (macOS High Sierra 10.13.6 version) and I'm receiving the following error that I suspect are due to library incompatibilities: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib mris_ca_label -aseg /Applications/freesurfer/subjects/10018/mri/aseg.mgz -seed 1234 10018 lh /Applications/freesurfer/subjects/10018/surf/lh.sphere.reg /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs /Applications/freesurfer/subjects/10018/label/lh.aparc.annot: Aborted ans = 134 I realized that this error has been previously reported <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-November/054961.html> and, as Andrew said, one of the possible solutions could be to disable the SIP (System Protection Integrity). I have disabled the SIP following the instructions indicated here <http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/> but unfortunately Matlab continues giving the same error. How could I solve this problem?. Any help would be appreciated. Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hypointensities in Freesurfer
External Email - Use Caution Hi Douglas, have you had occasion to review this matter? I was thinking that we also have FLAIR and T2 images... Thanks in advance for your help. Best, El vie., 8 feb. 2019 a las 18:36, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > Hi, > > Yes, I would like to know the x,y,z MNI coordinates of lesions for each > subject. > > > BEST, > > El vie., 8 feb. 2019 18:34, Greve, Douglas N.,Ph.D. < > dgr...@mgh.harvard.edu> escribió: > >> not sure what you want. MNI coords for each lesion? >> >> On 2/8/19 7:21 AM, Miguel Ángel Rivas Fernández wrote: >> >> External Email - Use Caution >> >> Hi Freesurfer devs, >> >> >> I saw that Freesurfer export measures of hypointensities. I was wondering >> if it´s possible to know where are located this brain lesions using as >> reference some neuroanatomical atlas. >> >> >> Best, >> >> -- >> *Miguel Ángel Rivas Fernández* >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hypointensities in Freesurfer
External Email - Use Caution Hi, Yes, I would like to know the x,y,z MNI coordinates of lesions for each subject. BEST, El vie., 8 feb. 2019 18:34, Greve, Douglas N.,Ph.D. escribió: > not sure what you want. MNI coords for each lesion? > > On 2/8/19 7:21 AM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > > Hi Freesurfer devs, > > > I saw that Freesurfer export measures of hypointensities. I was wondering > if it´s possible to know where are located this brain lesions using as > reference some neuroanatomical atlas. > > > Best, > > -- > *Miguel Ángel Rivas Fernández* > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hypointensities in Freesurfer
External Email - Use Caution Hi Freesurfer devs, I saw that Freesurfer export measures of hypointensities. I was wondering if it´s possible to know where are located this brain lesions using as reference some neuroanatomical atlas. Best, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Pial surface error
External Email - Use Caution Hi Bruce, Effectively, I was referring to the big chunck of gray matter that is missing from surfaces (I attached another image). I have decided to revise the pial and white matter segmentation again because in the study that I am carrying out I found an "unexpected" or perhaps not very frequent result in the literature. I have compared general (eg BrainSegVolNotVent) and specific (eg Middle temporal, fusiform) measures of volume, thickness and area (Desikan-Killiany atlas) between a control group of healthy adults and two experimental groups, (single and multiple domain Mild Cognitive Impairment adults) using an ANCOVA (age, sex, years of education and eTIV as covariates) in external analysis (SPSS software). Results showed that control group present a higher volume, area and thickness than the multiple-domain MCI group (a result consistent with previous studies). However, no significant differences were observed between the control and the single-domain MCI groups. Specifically, the single-domain MCI group showed an equal or even higher mean volume, thickness and area than the control group in sevaral ROI´s. Given this situation, we have decided to review the recon-all's output again in order to verify that there is no error that is influencing this last result. Could there be an error in the recon-all output that may be influencing these results? Could you suggest some procedure to check the output of the recon-all? I fixed skullstrip as well as pial and white matter surface errors when it was necessary. In the next few days I will analyze this data using QDEC. Any recommendation will be very appreciated. Thanks in advance, Cheers, El jue., 29 nov. 2018 a las 16:40, Bruce Fischl () escribió: > Hi Miguel, > > not sure exactly where you mean, but the big chunk of gray that is > missing from the surfaces is probably hippocampus (so not a problem, since > it is not neocortex) > > cheers > Bruce > > > On Thu, 29 Nov 2018, Miguel Ángel Rivas Fernández > wrote: > > > > > External Email - Use Caution > > > > Hi Freesurfer devs, > > > > I´m doing a visual quality control of my pial and white matter > segmentation using freeview and I > > noticed that several subjects could present an error in pial surface > segmentation. I have attached > > two images. > > > > Is this an pial surface error? in that case, How can I fix it? maybe > adding control points in order > > to extend the pial surface limit? > > > > > > Thanks > > > > Cheers, > > > > > > -- > > Miguel Ángel Rivas Fernández > > > >_______ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Volume, area and thickness external analysis
External Email - Use Caution Hi FreeSurfer devs, Is there any difference bet I ran the recon-all several participants (using the command recon-all -subjid -all) and I want to out an external analysis using the volume, area and thickness measures of the Destrieux and Desikan-Killiany atlas. *Do these measures suffer any change if I add the qcache flag to the command* (i.e recon-all -subjid -all -qcache) or by contrary this flag is only necessary when the analysis is made using QDEC? I have this doubt because I saw that when I used the -qcache flag, Freesurfer make a smoothing of the images using a FWHM filter of 5,10,12. Thanks in advance, Cheers, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Ventricles segmentation
External Email - Use Caution Hello Freesurfer devs, Is possible segment the brain ventricles using Freesurfer in terms of mm3 or ml? I would be interested in study the ventricular enlargement. Is possible with Freesurfer or other toolbox. Any help would be appreciated. Thanks in advance. Cheers, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Desikian-Killiany and Destrieux atlas
External Email - Use Caution Hello Freesurfer devs, Is there available any Desikian-Killiany and Destrieux atlas template or image downloadable with all brain labels of the atlas? I would to use this image to show my results in a lab meeting? I would need somethig similar that the lookup table used in the freeview. Cheers, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec table
External Email - Use Caution Hi Freesurfer devs, How can I create a qdec.table.dat file? I tried using a txt file but it doesn´t works. I attached the qdec.table.dat file that I have created. Sorry for this absurd question and thanks in advance. Cheers, -- *Miguel Ángel Rivas Fernández* qdec.table.dat Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Export stats
External Email - Use Caution Hi Bruce, No, I would want to export all measures in a xls or sav file in order todo perform external analysis. The question is if it's possible to export jointly the mean area, volume...measures in an unique file. I have tried It using the asegstats2table command but only works using separated commands, that is, one for mean area, other for mean volume, other for thickness, etc... Cheers, El jue., 1 nov. 2018 16:00, Bruce Fischl escribió: > Hi Miguel > > the stats are already stored in a text file in the stats dir. Do you need > something not in those files? > cheers > Bruce > On Thu, 1 Nov 2018, Miguel Ángel Rivas > Fernández wrote: > > > > > External Email - Use Caution > > > > > > Hi Freesurfer devs, > > > > Is there any way to export all the stats using an unique command? For > example, export the mean area, > > volume, thickness, thicknessstd, meancurv values of the > Desikian-Killiany atlas using an unique > > command or is only possible export it using separate commands? > > > > Thanks in advance, > > > > > > Cheers > > > > -- > > Miguel Ángel Rivas Fernández > > > >___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Export stats
External Email - Use Caution Hi Freesurfer devs, Is there any way to export all the stats using an unique command? For example, export the mean area, volume, thickness, thicknessstd, meancurv values of the Desikian-Killiany atlas using an unique command or is only possible export it using separate commands? Thanks in advance, Cheers -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] denoising and recon-all {Disarmed}
External Email - Use Caution
Dear Falk,
I tried to search your poster presentation in the 2018 ISMRM web but
unfortunately I did not find it. Can you attach the link? I would be
interested in this information and how to proceed.
Thanks in advance,
Best,
El vie., 12 oct. 2018 a las 13:59, Falk Lüsebrink ()
escribió:
> External Email - Use Caution
>
> Dear Lisa,
>
>
>
> what you potentially can do is to use the denoised surface (*h.white) as a
> starting point (instead of *h.orig) in the unfiltered stream. This should
> remove any bias introduced by the denoising, however, you should gain the
> advantages of denoised surfaces, e.g. less need for manual intervention,
> less topological defects, etc.
>
>
>
> I had a poster presentation for this method at last ISMRM.
>
>
>
> Best,
>
> Falk
>
>
>
> *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:
> freesurfer-boun...@nmr.mgh.harvard.edu] *Im Auftrag von *Lisa Crystal
> Krishnamurthy
> *Gesendet:* Donnerstag, 11. Oktober 2018 19:07
> *An:* Freesurfer support list
> *Betreff:* Re: [Freesurfer] denoising and recon-all {Disarmed}
>
>
>
> *External Email - Use Caution*
>
> The ONLM denoising algorithm in the following package: (*MailScanner has
> detected a possible fraud attempt from
> "na01.safelinks.protection.outlook.com" claiming to be*
> https://sites.google.com/site/pierrickcoupe/softwares/denoising-for-medical-imaging
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fpierrickcoupe%2Fsoftwares%2Fdenoising-for-medical-imaging=02%7C01%7Clkrishnamurthy%40gsu.edu%7Cadf6338b011843f3549d08d62f89e5d0%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C63674876225518=F0mfd%2B63mdYPHplRq4jcjz9FuSvE2nUxMxqDlFfIZB4%3D=0>
> )
>
>
>
> Best,
>
> -Lisa
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> mailto:freesurfer-boun...@nmr.mgh.harvard.edu
> ] *On Behalf Of *Glasser, Matthew
> *Sent:* Thursday, October 11, 2018 12:39 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] denoising and recon-all
>
>
>
> *External Email - Use Caution*
>
> What are you using for denoising?
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Lisa
> Crystal Krishnamurthy
> *Reply-To: *Freesurfer support list
> *Date: *Thursday, October 11, 2018 at 11:05 AM
> *To: *"freesurfer@nmr.mgh.harvard.edu"
> *Subject: *[Freesurfer] denoising and recon-all
>
>
>
> *External Email - Use Caution*
>
> Hi,
>
>
>
> I have found that denoising the MPRAGE prior to FS recon-all seems to
> improve the segmentation (see attached pdf). However, it is not clear if
> the denoising algorithm may cause some signal intensity changes (especially
> in voxels with partial voluming at the edge of the brain) that violate
> assumptions of recon-all. Could you help me understand what the assumptions
> of your algorithm are, and what I need to do to make sure my images conform
> to those assumptions?
>
>
>
> Your help is greatly appreciated.
>
> Best,
>
> -Lisa
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
*Miguel Ángel Rivas Fernández*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Hippocampal-Amygdala subfields error
External Email - Use Caution Hi everyone, Here a question and an answer of FreeSurfer experts that would be for interest. - Could there be any difference in accuracy when the recon-all is executed on two Mac computers that have a different processor? that is, it is preferable to execute the recon-all of all the subjects in the same computer?. Sorry for this absurd question but I would be sure about this. - *Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine. * Best -- Forwarded message - From: Iglesias Gonzalez, Eugenio Date: mié., 10 oct. 2018 a las 11:53 Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error To: Miguel Ángel Rivas Fernández Cc: Hoopes, Andrew Hi again, MA. I totally forgot to attach the binary. The thing is that I don’t have it on my hard drive, so I need to recompile it, but our MAC server seems to be down rrr Andrew: any ideas why breck is not responding? MA: sorry for the delay; we’ll definitely get to the bottom of this. Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *Miguel Ángel Rivas Fernández *Date: *Wednesday, 10 October 2018 at 09:39 *To: *"Iglesias Gonzalez, Eugenio" *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error Hi Eugenio, It´s possible that you have forgotten to attach the file in this email? because I don´t find anywhere. Another question, could there be any difference in accuracy when the recon-all is executed on two Mac computers that have a different processor? that is, it is preferable to execute the recon-all of all the subjects in the same computer?. Sorry for this absurd question but I would be sure about this. Best, El mié., 3 oct. 2018 a las 19:52, Iglesias Gonzalez, Eugenio (< e.igles...@ucl.ac.uk>) escribió: Allrighty, here are the instructions (depending on the location of FREESURFER_HOME, the following commands might need to be preceded by “sudo”) 1. Save the attached file to a directory of your choice. From the terminal, cd into that directory. 2. Decompress with: tar xvf segmentSubjectT2_autoEstimateAlveusML.tar.gz 3. Move existing version of the code:mv $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old 4. Replace with new version: mv ./segmentSubjectT2_autoEstimateAlveusML.app $FREESURFER_HOME/bin/ 5. Rerun the code If this doesn’t work, you can revert the changes with: 1. Delete new version with:rm –rf $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app 2. Restore previous version: mv $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app.old $FREESURFER_HOME/bin/segmentSubjectT2_autoEstimateAlveusML.app If it works: there’s no need to rerun the subjects that didn’t crash. Please let us know what happens! Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *Miguel Ángel Rivas Fernández *Date: *Wednesday, 3 October 2018 at 18:32 *To: *"Iglesias Gonzalez, Eugenio" *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error Hi Eugenio, I ran the command with the version *freesurfer-darwin-OSX-ElCapitan* (downloaded from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev) but anyway I can try with the updated executable. If the problem solved, it is necessary to run the command with this updated executable in the subjects in which before I had no problem? I guess it would not be necessary but I would like to be sure about this. Thanks Cheers, El mié., 3 oct. 2018 a las 19:17, Iglesias Gonzalez, Eugenio (< e.igles...@ucl.ac.uk>) escribió: Hi MA, I believe the FreeSurfer course is ongoing this week, which would be taking most of Andrew’s time. Our main hypothesis is that the binary with the bug fixed did not make it to the public distribution for some reason. If you want: I can send you the updated executable; you can then give it a shot, and if it solves the problem, we’ll know what the problem was. Let me know if you want to do this. Otherwise we can wait for Andrew to find time to take a look. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ *From: *Miguel Ángel Rivas Fernández *Date: *Wednesday, 3 Octob
Re: [Freesurfer] Re recon -all
External Email - Use Caution Hi Bruce, What an absurd mistake, sorry. However, I ran the command and I got the following error: pcpb3846:~ lab1-rmn$ recon-all -autorecon2-cp -autorecon3 -subjid 5054 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rwxr-xrwx 1 root wheel 508088 Sep 28 19:52 /Applications/freesurfer/subjects/5054/scripts/recon-all.log Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64 # #@# Intensity Normalization2 Fri Sep 28 23:13:36 CEST 2018 /Applications/freesurfer/subjects/5054/mri \n mri_normalize -f /Applications/freesurfer/subjects/5054/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz \n mghRead(/Applications/freesurfer/subjects/5054/mri/aseg.presurf.mgz, -1): could not open file using control points from file /Applications/freesurfer/subjects/5054/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz mri_normalize: could not read aseg from file aseg.presurf.mgz Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64 recon-all -s 5054 exited with ERRORS at Fri Sep 28 23:13:38 CEST 2018 For more details, see the log file /Applications/freesurfer/subjects/5054/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Why? Thanks for your help, Best, El vie., 28 sept. 2018 a las 19:38, Bruce Fischl (< fis...@nmr.mgh.harvard.edu>) escribió: > Looks like you have an incorrect space after the word recon > > On Sep 28, 2018, at 1:35 PM, Miguel Ángel Rivas Fernández < > miguelrivasf...@gmail.com> wrote: > > External Email - Use Caution > > > Hi Freesurfer devs, > > > I tried to re run the recon -all after put some control points in the > brainmask and I get the following error: > > > pcpb3846:~ lab1-rmn$ recon -all -autorecon2-cp -autorecon3 -4025 cp_before > > -bash: recon: command not found > > > > > What could be the problem? The Freesurfer version that I am using at this > moment is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c > > > > > Thanks in advance, > > > Best, > -- > *Miguel Ángel Rivas Fernández* > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re recon -all
External Email - Use Caution Hi Freesurfer devs, I tried to re run the recon -all after put some control points in the brainmask and I get the following error: pcpb3846:~ lab1-rmn$ recon -all -autorecon2-cp -autorecon3 -4025 cp_before -bash: recon: command not found What could be the problem? The Freesurfer version that I am using at this moment is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Thanks in advance, Best, -- *Miguel Ángel Rivas Fernández* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal-Amygdala subfields error
External Email - Use Caution Hi Eugenio, Did you have chance to review the error that I have reported some days ago when I ran the hippocampal and amygdala command? It was happened only in 17 subjects (sample size 295). I rerun the HippocampalSubfieldsandAmygdalaNuclei command and I got the same error: *Fitting mesh to image data mask took 683.6633 secondsTransforming pointsTransforming pointsWrote image to file image.mgzINFO: dst volume info differs from the one stored in lta. gets modified now.volume geometry:extent : (691, 691, 473)voxel : ( 0., 0., 0.)x_(ras) : ( 0., -1., 0.)y_(ras) : (-0.0047, 0., 1.)z_(ras) : ( 1., 0., 0.0047)c_(ras) : ( 4.2397, 13.6233, 12.2196)file: T2isotropic.mgzvolume geometry:extent : (640, 640, 225)voxel : ( 0.3594, 0.3594, 0.7000)x_(ras) : ( 0., -1., 0.)y_(ras) : (-0.0047, 0., 1.)z_(ras) : ( 1., 0., 0.0047)c_(ras) : ( 4.2397, 13.6234, 12.2196)file: /Applications/freesurfer/subjects/5095/mri/orig/T2.niiConstructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)MATLAB:subsassignnumelmismatchDarwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35 CESTFor more details, see the log file /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log* What could be the problem? Thanks in advance. Best wishes, El dom., 16 sept. 2018 a las 19:20, Miguel Ángel Rivas Fernández (< miguelrivasf...@gmail.com>) escribió: > Hi Eugenio, > > It was happened in only in 17 subjects (sample size is 295). I repeated > the process several times and I got always the same error. > > Thank you very much for your help!. > > > Cheers, > > El dom., 16 sept. 2018 a las 19:14, Iglesias Gonzalez, Eugenio (< > e.igles...@ucl.ac.uk>) escribió: > >> External Email - Use Caution >> >> Wow sorry about this. I have to carefully check whether it’s a different >> / related bug, or if the fix only made it to the Linux version. Is it >> happening for all subjects, or only some? >> >> I’m traveling / on vacation these days but will take a look as soon as I >> can. >> >> Cheers, >> >> /E >> >> >> >> -- >> >> Juan Eugenio Iglesias >> >> ERC Senior Research Fellow >> >> Centre for Medical Image Computing (CMIC) >> >> University College London >> >> http://www.jeiglesias.com >> >> http://cmictig.cs.ucl.ac.uk/ >> >> >> >> >> >> *From: * on behalf of Miguel >> Ángel Rivas Fernández >> *Reply-To: *Freesurfer support list >> *Date: *Sunday, 16 September 2018 at 15:52 >> *To: *Freesurfer support list >> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error >> >> >> >> *External Email - Use Caution* >> >> >> >> Hi Eugenio, >> >> >> >> I have downloaded the most recent dev version ( >> freesurfer-darwin-OSX-ElCapitan-dev.tar.gz >> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz> >> ) from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev >> and I get the same error. >> >> >> >> My version of Mac is Mac OS High Sierra Version 10.13.3 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *Fitting mesh to image data mask took 683.6633 seconds Transforming >> points Transforming points Wrote image to file image.mgz INFO: dst volume >> info differs from the one stored in lta. gets modified now. volume >> geometry: extent : (691, 691, 473) voxel : ( 0., 0., 0.) >> x_(ras) : ( 0., -1., 0.) y_(ras) : (-0.0047, 0., 1.) >> z_(ras) : ( 1.000
[Freesurfer] Thalamic Nuclei segmentation
External Email - Use Caution Hi Freesurfer devs, Just a simple question, it´s possible make the thalamic nuclei segmentation using as input a simple T2 image as additional scan or by contrary, is always required use as input a more specific scan such as the FGATIR or a DBS scan. Best, -- *Miguel Ángel Rivas Fernández* ___ 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] Hippocampal-Amygdala subfields error
External Email - Use Caution Hi Eugenio, It was happened in only in 17 subjects (sample size is 295). I repeated the process several times and I got always the same error. Thank you very much for your help!. Cheers, El dom., 16 sept. 2018 a las 19:14, Iglesias Gonzalez, Eugenio (< e.igles...@ucl.ac.uk>) escribió: > External Email - Use Caution > > Wow sorry about this. I have to carefully check whether it’s a different / > related bug, or if the fix only made it to the Linux version. Is it > happening for all subjects, or only some? > > I’m traveling / on vacation these days but will take a look as soon as I > can. > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Sunday, 16 September 2018 at 15:52 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error > > > > *External Email - Use Caution* > > > > Hi Eugenio, > > > > I have downloaded the most recent dev version ( > freesurfer-darwin-OSX-ElCapitan-dev.tar.gz > <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz> > ) from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and > I get the same error. > > > > My version of Mac is Mac OS High Sierra Version 10.13.3 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *Fitting mesh to image data mask took 683.6633 seconds Transforming points > Transforming points Wrote image to file image.mgz INFO: dst volume info > differs from the one stored in lta. gets modified now. volume geometry: > extent : (691, 691, 473) voxel : ( 0., 0., 0.) x_(ras) : ( > 0., -1., 0.) y_(ras) : (-0.0047, 0., 1.) z_(ras) : ( > 1., 0., 0.0047) c_(ras) : ( 4.2397, 13.6233, 12.2196) file: > T2isotropic.mgz volume geometry: extent : (640, 640, 225) voxel : ( > 0.3594, 0.3594, 0.7000) x_(ras) : ( 0., -1., 0.) y_(ras) : > (-0.0047, 0., 1.) z_(ras) : ( 1., 0., 0.0047) c_(ras) : > ( 4.2397, 13.6234, 12.2196) file: > /Applications/freesurfer/subjects/5095/mri/orig/T2.nii Constructing > image-to-world transform from header information (asmr1.mgz) Constructing > image-to-world transform from header information > (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) > Wrote image to file asmr2.mgz This file does not contain MRI parameters > This file does not contain MRI parameters In an assignment A(:) = B, the > number of elements in A and B must be the same. Error in > segmentSubjectT2_autoEstimateAlveusML (line 2147) > MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es > <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 > 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2 > hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de > 2018, 15:35:35 CEST For more details, see the log file > /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log* > > > > > > > > > > > > > > *What could be the problem?* > > > > > > *Thanks in advance, * > > > > *Best wishes, * > > > > > > El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (< > e.igles...@ucl.ac.uk>) escribió: > > *External Email - Use Caution* > > Hi Miguel Angel, > > This bug was recently fixed in the dev version. If you download the most > recent one, you won’t have this problem. > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Thursday, 13 September 2018 at 21:12 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal-Amygdala subfields error > > > > *External Email - Use Caution* > > > > Hello Freesurfer devs, > > > > I
Re: [Freesurfer] Hippocampal-Amygdala subfields error
External Email - Use Caution Hi Eugenio, I have downloaded the most recent dev version ( freesurfer-darwin-OSX-ElCapitan-dev.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz> ) from here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and I get the same error. My version of Mac is Mac OS High Sierra Version 10.13.3 *Fitting mesh to image data mask took 683.6633 secondsTransforming pointsTransforming pointsWrote image to file image.mgzINFO: dst volume info differs from the one stored in lta. gets modified now.volume geometry:extent : (691, 691, 473)voxel : ( 0., 0., 0.)x_(ras) : ( 0., -1., 0.)y_(ras) : (-0.0047, 0., 1.)z_(ras) : ( 1., 0., 0.0047)c_(ras) : ( 4.2397, 13.6233, 12.2196)file: T2isotropic.mgzvolume geometry:extent : (640, 640, 225)voxel : ( 0.3594, 0.3594, 0.7000)x_(ras) : ( 0., -1., 0.)y_(ras) : (-0.0047, 0., 1.)z_(ras) : ( 1., 0., 0.0047)c_(ras) : ( 4.2397, 13.6234, 12.2196)file: /Applications/freesurfer/subjects/5095/mri/orig/T2.niiConstructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)MATLAB:subsassignnumelmismatchDarwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35 CESTFor more details, see the log file /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log* *What could be the problem?* *Thanks in advance, * *Best wishes, * El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (< e.igles...@ucl.ac.uk>) escribió: > External Email - Use Caution > > Hi Miguel Angel, > > This bug was recently fixed in the dev version. If you download the most > recent one, you won’t have this problem. > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Thursday, 13 September 2018 at 21:12 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal-Amygdala subfields error > > > > *External Email - Use Caution* > > > > Hello Freesurfer devs, > > > > I ran the hippocampal and amygdala subfields command in my sample and I > get the following error in several subjects: > > > > > > > > > > > > > > > > > > *Constructing image-to-world transform from header information (asmr1.mgz) > Constructing image-to-world transform from header information > (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) > Wrote image to file asmr2.mgz This file does not contain MRI parameters > This file does not contain MRI parameters In an assignment A(:) = B, the > number of elements in A and B must be the same. Error in > segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing > image-to-world transform from header information (asmr1.mgz) Constructing > image-to-world transform from header information > (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz) > Wrote image to file asmr2.mgz This file does not contain MRI parameters > This file does not contain MRI parameters In an assignment A(:) = B, the > number of elements in A and B must be the same. Error in > segmentSubjectT2_autoEstimateAlveusML (line 2147)* > > > > > > > *MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es > <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 > 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2 > hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de > 2018, 21:37:33 CEST* > > > > > > > > What would be the reason? > > > > > > Thanks in advance, > > > > > > Best wishes, > > > -- > > *Miguel Ángel Rivas Fernández* > _
[Freesurfer] Hippocampal-Amygdala subfields error
External Email - Use Caution Hello Freesurfer devs, I ran the hippocampal and amygdala subfields command in my sample and I get the following error in several subjects: *Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)* *MATLAB:subsassignnumelmismatchDarwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64T2 hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de 2018, 21:37:33 CEST* What would be the reason? Thanks in advance, Best wishes, -- *Miguel Ángel Rivas Fernández* ___ 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] Fwd: strange eTIV values
External Email - Use Caution Hi Douglas, Yes, I compared the eTIV values in the SPSS and in the individual aseg.stats files and I noticed that Freesurfer export this kind of measures with a precision of 6 decimals (eg. 1418761.222904) The problem is that when I send these values from the txt (that contain all the measures of the aseg.stats file) to SPSS. I will try to send the data from the txt to the SPSS without any distortion in the number of decimals. Any help will be appreciated. Best, El jue., 6 sept. 2018 a las 20:16, Douglas N. Greve () escribió: > Canyou give more info on how you arrived at those numbers? Eg, are those > the numbers after you imported into SPSS? If you look in an individual's > aseg.stats file, do you see the same value? > > On 09/06/2018 12:41 PM, Miguel Ángel Rivas Fernández wrote: > > > > External Email - Use Caution > > > > Hello Freesurfer developers, > > > > > > Did hoy have chance to read this question?. > > > > Thank you very much for your help! > > > > > > Best regards, > > > > -- Forwarded message - > > From: *Miguel Ángel Rivas Fernández* > <mailto:miguelrivasf...@gmail.com>> > > Date: mar., 4 sept. 2018 20:37 > > Subject: strange eTIV values > > To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > > > > > > Hello Freesurfer experts, > > > > > > When I exported the Destrieux and Desikian-Killiany volume values from > > Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as > > follows: > > > > 101,632,104,008. > > 134,253,072,953. > > 155,967,056,944. > > 142,085,122,028. > > 181,105,664,397. > > 118,051,287,519. > > 896,135,067,103. > > > > With how many decimals Freesurfer exports the eTIV values ?, that is, > > what is the precision of this measure? I do not know how many decimals > > this measure has. > > > > Another doubt, it is necessary to make some kind of numerical > > transformation on the eTIV values before including it as a covariate > > in the statistical analysis (for example, a logarithmic transformation). > > > > > > Best, > > > > -- > > *Miguel Ángel Rivas Fernández* > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > 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. > -- *Miguel Ángel Rivas Fernández* ___ 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] Amygdala subfields segmentation
External Email - Use Caution Hi Eugenio, Where can I find the link for download the latest dev version? The latest version is this?: *freesurfer-darwin-OSX-ElCapitan-dev.tar.gz* Thanks in advance, Best, El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio (< e.igles...@ucl.ac.uk>) escribió: > External Email - Use Caution > > Dear MA > Please download the latest dev version and the command will be there > Cheers > Eugenio > > Sent from my phone, please excuse brevity and typos > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas > Fernández > *Sent:* Tuesday, September 11, 2018 12:20:55 PM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Amygdala subfields segmentation > > > External Email - Use Caution > > > Hi Freesurfer developes, > > I am trying to execute the hippocampal and amygdala segmentation command " > segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 > [SUBJECTS_DIR]" but freesurfer gave to me this error > *command not found. * > > > However, when I use the command that segment only the hippocampal > subfields (recon-all -s -hippocampal-subfields-T2 of additional scan> ) I don´t have any problem. > > > What would be the reason? > > > Thanks in advance. > > > Best, > > -- > *Miguel Ángel Rivas Fernández* > ___ > 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. > -- *Miguel Ángel Rivas Fernández* ___ 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] Amygdala subfields segmentation
External Email - Use Caution Hi Freesurfer developes, I am trying to execute the hippocampal and amygdala segmentation command " segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]" but freesurfer gave to me this error *command not found. * However, when I use the command that segment only the hippocampal subfields (recon-all -s -hippocampal-subfields-T2 ) I don´t have any problem. What would be the reason? Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández* ___ 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] Fwd: strange eTIV values
External Email - Use Caution Hello Freesurfer developers, Did hoy have chance to read this question?. Thank you very much for your help! Best regards, -- Forwarded message - From: Miguel Ángel Rivas Fernández Date: mar., 4 sept. 2018 20:37 Subject: strange eTIV values To: Freesurfer support list Hello Freesurfer experts, When I exported the Destrieux and Desikian-Killiany volume values from Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as follows: 101,632,104,008. 134,253,072,953. 155,967,056,944. 142,085,122,028. 181,105,664,397. 118,051,287,519. 896,135,067,103. With how many decimals Freesurfer exports the eTIV values ?, that is, what is the precision of this measure? I do not know how many decimals this measure has. Another doubt, it is necessary to make some kind of numerical transformation on the eTIV values before including it as a covariate in the statistical analysis (for example, a logarithmic transformation). Best, -- *Miguel Ángel Rivas Fernández* ___ 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] strange eTIV values
External Email - Use Caution Hello Freesurfer experts, When I exported the Destrieux and Desikian-Killiany volume values from Freesurfer to SPSS I obtained "strange" eTIV values with 16 digits as follows: 101,632,104,008. 134,253,072,953. 155,967,056,944. 142,085,122,028. 181,105,664,397. 118,051,287,519. 896,135,067,103. With how many decimals Freesurfer exports the eTIV values ?, that is, what is the precision of this measure? I do not know how many decimals this measure has. Another doubt, it is necessary to make some kind of numerical transformation on the eTIV values before including it as a covariate in the statistical analysis (for example, a logarithmic transformation). Best, -- *Miguel Ángel Rivas Fernández* ___ 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] Difference between Freesurfer and Voxel Based Morphometry
External Email - Use Caution Hi Freesurfer developers, I´m starting in structural MRI analysis with Freesurfer and i would like to know what is the main difference between freesurfer and the voxel based morphometry approach. It is more appropiate to use a method for some specific analysis? Thanks in advance. Best, -- *Miguel Ángel Rivas Fernández* ___ 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] Command to export hippocampal subfields segmentations
External Email - Use Caution Thank you Eugenio, it works but now I have a "absurd" question, the volume values that I obtained are mm with six decimals? For example, for the left_Hippocampal_tail I obtained 498.117062 Sorry for this absurd question but I would like be sure about this. Thanks in advance, Best 2018-05-29 16:50 GMT+02:00 Iglesias Gonzalez, Eugenio : > External Email - Use Caution > > Yes, it looks like that. You can try ~/Desktop/pruebaHipocampo.txt you > should be able to write there. > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 15:47 > > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Command to export hippocampal subfields > segmentations > > > > *External Email - Use Caution* > > Hi Eugenio, > > > > > > I ran the command and fs gave me the following error in all subjects > > > > Collecting data for subject: 5250 > > /Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 94: > pruebahipocampo.txt: Permission denied > > > > > > > > In order to gathering the hippocampus volumes I used this command > > > > > > rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh T2_3D_SAG > pruebahipocampo.txt /Applications/freesurfer/subjects > > > > > > > > Could be motivated this error due to read & write permissions on Mac > folders? > > > > > > > > Thanks > > > > Best, > > > > > > 2018-05-29 10:54 GMT+02:00 Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk>: > > *External Email - Use Caution* > > The results should be in pruebahipocampo.txt, which will be located in the > directory from which you ran the command. > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:46 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Command to export hippocampal subfields > segmentations > > > > *External Email - Use Caution* > > Hi Eugenio, > > > > I want to export the volumnes of all subjects, I used the > quantifyHippocampalSubfields.sh command and apparently it did work but > now I can´t find where Freesurfer saved the file. > > > > Here is the response of Freesurfer > > > > > > rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh T1-T2_3D_SAG > pruebahipocampo.txt /Applications/freesurfer/subjects > Gathering results from subjects in: >/Applications/freesurfer/subjects > Using the suffix name: >T1-T2_3D_SAG > And writing them to: >pruebahipocampo.txt > > > > I looked for it in the subjects folder but I can not find the file > anywhere. > > > > > > Thanks in advance > > > > 2018-05-29 10:34 GMT+02:00 Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk>: > > *External Email - Use Caution * > > Hola Miguel Ángel, > > What do you mean by exporting? The volumes? There is a command to gather > the volumes from all subjects in the subjects directory, which is: > > quantifyHippocampalSubfields.sh (in FreeSurfer 6.0) > > quantifyHAsubregions.sh (in dev version) > > Cheers, > > /Eugenio > > > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:32 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Command to export hippocampal subfields > segmentations > > > > *External Email - Use Caution* > > > > > > Hi Freesurfer developers, > > > > > > I was looking for the freesurfer command to export hippocampal sufields > segmentati
Re: [Freesurfer] Command to export hippocampal subfields segmentations
External Email - Use Caution Hi Eugenio, I ran the command and fs gave me the following error in all subjects Collecting data for subject: 5250 /Applications/freesurfer/bin/quantifyHippocampalSubfields.sh: line 94: pruebahipocampo.txt: Permission denied In order to gathering the hippocampus volumes I used this command rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh T2_3D_SAG pruebahipocampo.txt /Applications/freesurfer/subjects Could be motivated this error due to read & write permissions on Mac folders? Thanks Best, 2018-05-29 10:54 GMT+02:00 Iglesias Gonzalez, Eugenio : > External Email - Use Caution > > The results should be in pruebahipocampo.txt, which will be located in the > directory from which you ran the command. > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:46 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Command to export hippocampal subfields > segmentations > > > > *External Email - Use Caution* > > Hi Eugenio, > > > > I want to export the volumnes of all subjects, I used the > quantifyHippocampalSubfields.sh command and apparently it did work but > now I can´t find where Freesurfer saved the file. > > > > Here is the response of Freesurfer > > > > > > rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh T1-T2_3D_SAG > pruebahipocampo.txt /Applications/freesurfer/subjects > Gathering results from subjects in: >/Applications/freesurfer/subjects > Using the suffix name: >T1-T2_3D_SAG > And writing them to: >pruebahipocampo.txt > > > > I looked for it in the subjects folder but I can not find the file > anywhere. > > > > > > Thanks in advance > > > > 2018-05-29 10:34 GMT+02:00 Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk>: > > *External Email - Use Caution* > > Hola Miguel Ángel, > > What do you mean by exporting? The volumes? There is a command to gather > the volumes from all subjects in the subjects directory, which is: > > quantifyHippocampalSubfields.sh (in FreeSurfer 6.0) > > quantifyHAsubregions.sh (in dev version) > > Cheers, > > /Eugenio > > > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:32 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Command to export hippocampal subfields > segmentations > > > > *External Email - Use Caution* > > > > > > Hi Freesurfer developers, > > > > > > I was looking for the freesurfer command to export hippocampal sufields > segmentations but I did not found. What is the command to export this > measures and in what folder are exported the file? > > > > > > Thanks a lot. > > > > > > Best, > > > -- > > *Miguel Ángel Rivas Fernández* > > > ___ > 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. > > > > > -- > > *Miguel Ángel Rivas Fernández* > > ___ > 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
Re: [Freesurfer] Command to export hippocampal subfields segmentations
External Email - Use Caution Hi Eugenio, I want to export the volumnes of all subjects, I used the quantifyHippocampalSubfields.sh command and apparently it did work but now I can´t find where Freesurfer saved the file. Here is the response of Freesurfer rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh T1-T2_3D_SAG pruebahipocampo.txt /Applications/freesurfer/subjects Gathering results from subjects in: /Applications/freesurfer/subjects Using the suffix name: T1-T2_3D_SAG And writing them to: pruebahipocampo.txt I looked for it in the subjects folder but I can not find the file anywhere. Thanks in advance 2018-05-29 10:34 GMT+02:00 Iglesias Gonzalez, Eugenio : > External Email - Use Caution > > Hola Miguel Ángel, > > What do you mean by exporting? The volumes? There is a command to gather > the volumes from all subjects in the subjects directory, which is: > > quantifyHippocampalSubfields.sh (in FreeSurfer 6.0) > > quantifyHAsubregions.sh (in dev version) > > Cheers, > > /Eugenio > > > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Miguel > Ángel Rivas Fernández > *Reply-To: *Freesurfer support list > *Date: *Tuesday, 29 May 2018 at 09:32 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Command to export hippocampal subfields > segmentations > > > > *External Email - Use Caution* > > > > > > Hi Freesurfer developers, > > > > > > I was looking for the freesurfer command to export hippocampal sufields > segmentations but I did not found. What is the command to export this > measures and in what folder are exported the file? > > > > > > Thanks a lot. > > > > > > Best, > > > -- > > *Miguel Ángel Rivas Fernández* > > ___ > 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. > > -- *Miguel Ángel Rivas Fernández* ___ 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] Command to export hippocampal subfields segmentations
External Email - Use Caution Hi Freesurfer developers, I was looking for the freesurfer command to export hippocampal sufields segmentations but I did not found. What is the command to export this measures and in what folder are exported the file? Thanks a lot. Best, -- *Miguel Ángel Rivas Fernández* ___ 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] Problems Extending the Pial Surface
External Email - Use Caution Hi Bruce, I sent you the whole directory if one subject un which we had some problems extending the pial surface. Se would like extend the pial surface without affect the wm boundary. Did you have a chance to review It? Thanks in advance, Cheers, El vie., 4 may. 2018 1:02, Miguel Ángel Rivas Fernández < miguelrivasf...@gmail.com> escribió: > Hi Bruce, > > > I tried to upload the whole subject dir in the ftp site but i didn´t > works. I send you the file in 7zip format trough a google drive link . I > would know how can i extend the pial surface without affect the wm > boundaries because the pial surface segmentation in some subjects (as this > that i send to you) was incorrect. > > https://drive.google.com/open?id=11xcWuDlWzGeLLV4MvW-bJK3-rrlsIA8Q > > > > Thaks in advance > > > Cheers, > > 2018-05-01 16:26 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > >> why don't you tar and gzip the whole subject dir and upload it to our ftp >> site and we will take a look >> cheers >> Bruce >> >> On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote: >> >> >>> External Email - Use Caution >>> >>> >>> Hi Bruce, >>> >>> >>> The problem is that the reconstruction of the pial surface is incorrect. >>> I tried to put control >>> points on some voxels but did a wrong reconstruction because in this >>> region there is no voxel with >>> an intensity between 95-110. How can I improve the reconstruction of the >>> pial surface (in this case >>> extend) without modifying the boundaries of wm? . Sorry, I read the >>> answer you gave to Saum but I >>> could not understand very well how to modify the statistics that >>> FreeSurfer does in the >>> mri_make_surfaces. >>> >>> >>> >>> Hi Saum >>> >>> it is, but you need to figure out why it isn't getting out far enough. >>> The easiest way is to >>> override the intensity statistics that are computed automatically in >>> mris_make_surfaces. You can see >>> them if you look in your recon-all.log. For example if the lowest value >>> gm is allowed to be at the >>> pial surface is too high, then it will settle too far in >>> >>> >>> Thanks, >>> >>> >>> Cheers, >>> >>> >>> >>> 2018-04-29 17:33 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >>> that looks like a big temporal lobe bias field to me. Is the WM in >>> the temporal lobes >>> significantly darker than 110? I can't tell if some of the stuff >>> in e.g. the left medial >>> temporal lobe is WM or GM. Try putting some control points in >>> regions where the >>> intensity is in say [95, 110) and see if that helps >>> >>> cheers >>> Bruce >>> >>> >>> On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote: >>> >>> >>> External Email - Use Caution >>> >>> Hi guys, >>> >>> >>> I have the same problem as Saum, I executed the recon-all in >>> several >>> subjects and I did not obtain a >>> completely correct segmentation of the pial surface. To >>> solve this error >>> could I use the control >>> points? When I use the control points, will I also be able >>> to correct the >>> white matter segmentation? >>> >>> I send you a image if you want >>> to check it. >>> >>> Thank you very much! >>> >>> >>> Cheers, >>> >>> >>> >>> [IMAGE] >>> >>> >>> >>> 2018-04-27 21:28 GMT+02:00 Bruce Fischl < >>> fis...@nmr.mgh.harvard.edu>: >>> Hi Saum >>> >>> it is, but you need to figure out why it isn't getting >>> out far enough. >>> The easiest way >>> is to override the intensity statistics that are >>> computed >>> automatically in >>> mris_make_surfaces. You can see them if you look in >>> your >>>
[Freesurfer] Problems at exporting recon-all outputs
External Email - Use Caution Hi Freesurfer developers, After having executed the recon-all in several subjects I tried to export all measures of the Destrieux atlas (area, volume, curvind, foldind, gauscurv, meancurv, thickness and thicknesstd) but I got an error because in some variables only zeros appear and however, in the other variables I did obtain values when doing the export. I had the same error in some variables when exported the subcortical segmentation (aseg.stats) and the wm (wmparc.stats). Why do some variables appear without any value? Thanks in advance, Cheers, -- *Miguel Ángel Rivas Fernández* ___ 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] T2 weighted images as input for recon-all command
External Email - Use Caution Hi Eugenio, In my error free surfer say that cannot find the file, It´s necessary put the additional scan in a specific folder? I have this organization in the free surfer subjects directory 4235_T2 (main folder) mri (subfolder) orig (subfolder) Inside the subfolder orig i have two files T2.nii and T2.mgz (T2.mgz was previously generated using mir_convert command) Why don´t find the file? Thanks for your help Cheers, 2018-05-04 10:50 GMT+02:00 Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> : > External Email - Use Caution > > It depends on the version, but yes, in 6.0 it’d be that command. > > The file name of the additional scan should be an existing nii/nii.gz/mgz > file, though (right now you just have “T2”). > > Cheers, > > /E > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Translational Imaging Group > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel > Ángel Rivas Fernández <miguelrivasf...@gmail.com> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, 4 May 2018 at 09:46 > > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] T2 weighted images as input for recon-all > command > > > > *External Email - Use Caution* > > Hi, > > > > > > What would be the command for hippocampal subfields using only the T2 > images? > > > > This? > > > > recon-all -s -hippocampal-subfields-T2 additional scan> > > > > > > I tried but obtained the following error > > > > > > pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2 > -hippocampal-subfields-T2 T2 T2_3D_SAG > > ERROR: cannot find T2 > > Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan > 30 11:45:51 PST 2018; root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64 > > > > recon-all -s 4235_T2 exited with ERRORS at Fri May 4 10:43:04 CEST 2018 > > > > > > > > Thanks > > > > > > cheers, > > > > 2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio < > e.igles...@ucl.ac.uk>: > > *External Email - Use Caution* > > Sorry if I didn’t explain myself properly. > > T2 scans of the whole head can be used by recon-all to improve the > segmentation of the pial surface, but: a) They are not required (you can > use the T1 alone); and b) Cannot be run through recon-all independently > from the T1. > > For hippocampal subfields: the T2 scan is used in a separate stream. In > fact, their field of view doesn’t even have to cover the whole head – just > the hippocampi (this is what the ADNI highres T2 protocol does). > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Translational Imaging Group > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of M Janani < > janan...@hcl.com> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, 4 May 2018 at 08:26 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > *Subject: *Re: [Freesurfer] T2 weighted images as input for recon-all > command > > > > *External Email - Use Caution* > > Thanks for your reply Eugenio. > > You have mentioned like “No recon-all on the T2 required, as it's used in > a different way”. May I know the actual purpose of using T2 images for > reconstruction process. Why we should not T2 images as input for recon-all > command. > > Regards, > > Janani > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@ > nmr.mgh.harvard.edu] *On Behalf Of *Iglesias Gonzalez, Eugenio > *Sent:* 04 May 2018 12:50 > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; > Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all > command > > > > *External Email - Use Caution* > > Hola Miguel Ángel, > > First, you need to run the T1 through recon-all normally, as you have > already done. Next, you run the subfield module with the highres T2 as > input - no recon-all on the T2 req
Re: [Freesurfer] T2 weighted images as input for recon-all command
External Email - Use Caution Hi, What would be the command for hippocampal subfields using only the T2 images? This? recon-all -s -hippocampal-subfields-T2 I tried but obtained the following error pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2 -hippocampal-subfields-T2 T2 T2_3D_SAG ERROR: cannot find T2 Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan 30 11:45:51 PST 2018; root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64 recon-all -s 4235_T2 exited with ERRORS at Fri May 4 10:43:04 CEST 2018 Thanks cheers, 2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> : > External Email - Use Caution > > Sorry if I didn’t explain myself properly. > > T2 scans of the whole head can be used by recon-all to improve the > segmentation of the pial surface, but: a) They are not required (you can > use the T1 alone); and b) Cannot be run through recon-all independently > from the T1. > > For hippocampal subfields: the T2 scan is used in a separate stream. In > fact, their field of view doesn’t even have to cover the whole head – just > the hippocampi (this is what the ADNI highres T2 protocol does). > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Translational Imaging Group > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of M Janani < > janan...@hcl.com> > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Date: *Friday, 4 May 2018 at 08:26 > *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] T2 weighted images as input for recon-all > command > > > > *External Email - Use Caution* > > Thanks for your reply Eugenio. > > You have mentioned like “No recon-all on the T2 required, as it's used in > a different way”. May I know the actual purpose of using T2 images for > reconstruction process. Why we should not T2 images as input for recon-all > command. > > Regards, > > Janani > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@ > nmr.mgh.harvard.edu] *On Behalf Of *Iglesias Gonzalez, Eugenio > *Sent:* 04 May 2018 12:50 > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; > Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all > command > > > > *External Email - Use Caution* > > Hola Miguel Ángel, > > First, you need to run the T1 through recon-all normally, as you have > already done. Next, you run the subfield module with the highres T2 as > input - no recon-all on the T2 required, as it's used in a different way. > > Cheers > > Eugenio > > Sent from my phone, please excuse brevity and typos > > > -- > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas > Fernández <miguelrivasf...@gmail.com> > *Sent:* Thursday, May 3, 2018 11:08:17 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] T2 weighted images as input for recon-all > command > > > > *External Email - Use Caution* > > Hi Freesurfer developers, > > I have executed the recon-all command using the T1 images but I would be > interested in doing a reconstruction of the hippocampal subregions using > for that purpose a higher resolution images (eg T2 or FLAIR) as input. I > read here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields > <https://apac01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfields=02%7C01%7Cjananimj%40hcl.com%7C733fab39e9994ea213fb08d5b18f8582%7C189de737c93a4f5a8b686f4ca9941912%7C0%7C1%7C636610152364530300=H1MJaa6TKp%2BOBlGtJM%2F%2BjnQBIdhAWvUS94hG9a3kC8c%3D=0> > that is possible make hippocampal segmentation using the T2 images, but if > T2 images cannot be used as input to execute the recon-all in consecuence I > can´t do the segmentation of hippocampal subfields or on the contrary the > recon-all and the hippocampal subfields segmentation are two operations > that can be executed independently ? >
Re: [Freesurfer] Problems Extending the Pial Surface
External Email - Use Caution Hi Bruce, I tried to upload the whole subject dir in the ftp site but i didn´t works. I send you the file in 7zip format trough a google drive link . I would know how can i extend the pial surface without affect the wm boundaries because the pial surface segmentation in some subjects (as this that i send to you) was incorrect. https://drive.google.com/open?id=11xcWuDlWzGeLLV4MvW-bJK3-rrlsIA8Q Thaks in advance Cheers, 2018-05-01 16:26 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > why don't you tar and gzip the whole subject dir and upload it to our ftp > site and we will take a look > cheers > Bruce > > On Tue, 1 May 2018, Miguel Ángel Rivas Fernández wrote: > > >> External Email - Use Caution >> >> >> Hi Bruce, >> >> >> The problem is that the reconstruction of the pial surface is incorrect. >> I tried to put control >> points on some voxels but did a wrong reconstruction because in this >> region there is no voxel with >> an intensity between 95-110. How can I improve the reconstruction of the >> pial surface (in this case >> extend) without modifying the boundaries of wm? . Sorry, I read the >> answer you gave to Saum but I >> could not understand very well how to modify the statistics that >> FreeSurfer does in the >> mri_make_surfaces. >> >> >> >> Hi Saum >> >> it is, but you need to figure out why it isn't getting out far enough. >> The easiest way is to >> override the intensity statistics that are computed automatically in >> mris_make_surfaces. You can see >> them if you look in your recon-all.log. For example if the lowest value >> gm is allowed to be at the >> pial surface is too high, then it will settle too far in >> >> >> Thanks, >> >> >> Cheers, >> >> >> >> 2018-04-29 17:33 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> that looks like a big temporal lobe bias field to me. Is the WM in >> the temporal lobes >> significantly darker than 110? I can't tell if some of the stuff in >> e.g. the left medial >> temporal lobe is WM or GM. Try putting some control points in >> regions where the >> intensity is in say [95, 110) and see if that helps >> >> cheers >> Bruce >> >> >> On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote: >> >> >> External Email - Use Caution >> >> Hi guys, >> >> >> I have the same problem as Saum, I executed the recon-all in >> several >> subjects and I did not obtain a >> completely correct segmentation of the pial surface. To solve >> this error >> could I use the control >> points? When I use the control points, will I also be able to >> correct the >> white matter segmentation? >> >> I send you a image if you want >> to check it. >> >> Thank you very much! >> >> >> Cheers, >> >> >> >> [IMAGE] >> >> >> >> 2018-04-27 21:28 GMT+02:00 Bruce Fischl < >> fis...@nmr.mgh.harvard.edu>: >> Hi Saum >> >> it is, but you need to figure out why it isn't getting >> out far enough. >> The easiest way >> is to override the intensity statistics that are >> computed >> automatically in >> mris_make_surfaces. You can see them if you look in your >> recon-all.log. For example if >> the lowest value gm is allowed to be at the pial >> surface is too high, >> then it will >> settle too far in >> >> cheers >> Bruce >> >> >> On Fri, 27 Apr 2018, Saum Naderi wrote: >> >> >> External Email - Use Caution >> >> Hi guys, >> >> I'm having some trouble extending the pial >> surface of my bm >> volume. I am >> aware that the general >> procedure for extending the pial is to extend the >> wm first and >> the pial will >> follow. However, is it >>
Re: [Freesurfer] T2 weighted images as input for recon-all command
External Email - Use Caution Hi Freesurfer developers, I have executed the recon-all command using the T1 images but I would be interested in doing a reconstruction of the hippocampal subregions using for that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields that is possible make hippocampal segmentation using the T2 images, but if T2 images cannot be used as input to execute the recon-all in consecuence I can´t do the segmentation of hippocampal subfields or on the contrary the recon-all and the hippocampal subfields segmentation are two operations that can be executed independently ? I hope to have explained myself correctly Thanks in advance. Cheers 2018-05-03 18:28 GMT+02:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > No, not currently > > > On 05/03/2018 11:26 AM, M Janani wrote: > > > > Hi Team, > > > >I have one doubt. Can I input T2 weighted images for > > recon-all command? > > > > Regards, > > > > Janani > > > > ::DISCLAIMER:: > > > > > > -- > > The contents of this e-mail and any attachment(s) are confidential and > > intended for the named recipient(s) only. E-mail transmission is not > > guaranteed to be secure or error-free as information could be > > intercepted, corrupted, lost, destroyed, arrive late or incomplete, or > > may contain viruses in transmission. The e mail and its contents (with > > or without referred errors) shall therefore not attach any liability > > on the originator or HCL or its affiliates. Views or opinions, if any, > > presented in this email are solely those of the author and may not > > necessarily reflect the views or opinions of HCL or its affiliates. > > Any form of reproduction, dissemination, copying, disclosure, > > modification, distribution and / or publication of this message > > without the prior written consent of authorized representative of HCL > > is strictly prohibited. If you have received this email in error > > please delete it and notify the sender immediately. Before opening any > > email and/or attachments, please check them for viruses and other > defects. > > > > > > -- > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > 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. > > -- *Miguel Ángel Rivas Fernández* ___ 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] Problems Extending the Pial Surface
External Email - Use Caution Hi Bruce, The problem is that the reconstruction of the pial surface is incorrect. I tried to put control points on some voxels but did a wrong reconstruction because in this region there is no voxel with an intensity between 95-110. How can I improve the reconstruction of the pial surface (in this case extend) without modifying the boundaries of wm? . Sorry, I read the answer you gave to Saum but I could not understand very well how to modify the statistics that FreeSurfer does in the mri_make_surfaces. *Hi Saum it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in * Thanks, Cheers, 2018-04-29 17:33 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: > that looks like a big temporal lobe bias field to me. Is the WM in the > temporal lobes significantly darker than 110? I can't tell if some of the > stuff in e.g. the left medial temporal lobe is WM or GM. Try putting some > control points in regions where the intensity is in say [95, 110) and see > if that helps > > cheers > Bruce > > > On Sat, 28 Apr 2018, Miguel Ángel Rivas Fernández wrote: > > >> External Email - Use Caution >> >> Hi guys, >> >> >> I have the same problem as Saum, I executed the recon-all in several >> subjects and I did not obtain a >> completely correct segmentation of the pial surface. To solve this error >> could I use the control >> points? When I use the control points, will I also be able to correct the >> white matter segmentation? >> >> I send you a image if you want >> to check it. >> >> Thank you very much! >> >> >> Cheers, >> >> >> >> [IMAGE] >> >> >> >> >> 2018-04-27 21:28 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: >> Hi Saum >> >> it is, but you need to figure out why it isn't getting out far >> enough. The easiest way >> is to override the intensity statistics that are computed >> automatically in >> mris_make_surfaces. You can see them if you look in your >> recon-all.log. For example if >> the lowest value gm is allowed to be at the pial surface is too >> high, then it will >> settle too far in >> >> cheers >> Bruce >> >> >> On Fri, 27 Apr 2018, Saum Naderi wrote: >> >> >> External Email - Use Caution >> >> Hi guys, >> >> I'm having some trouble extending the pial surface of my bm >> volume. I am >> aware that the general >> procedure for extending the pial is to extend the wm first >> and the pial will >> follow. However, is it >> possible to extend the pial surface without affecting the wm >> boundary? >> >> Thanks, >> >> Saum >> >> >> >> ___ >> 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. >> >> >> >> >> -- >> Miguel Ángel Rivas Fernández >> >> > ___________ > 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. > > -- *Miguel Ángel Rivas Fernández* ___ 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.
