External Email - Use Caution Hi Doug, I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs Catalina and, although I am able to connect to the FTP site and open the incoming window (also in binary mode), commands are not working...
I am trying to overcome the problem. Is there any other method to transfer the data set? Thank you Angela > Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve > <dgr...@mgh.harvard.edu> ha scritto: > > Hmmm, I don't know. Can you upload the data set? Follow these instructions > > From the linux command line, > Create the file you want to upload, eg, > cd $SUBJECTS_DIR > tar cvfz subject.tar.gz ./subject > Now log into our anonymous FTP site: > ftp surfer.nmr.mgh.harvard.edu > It will ask you for a user name: use "anonymous" (no quotes) > It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > On 5/14/2020 5:03 PM, Angela Favaro wrote: >> External Email - Use Caution >> >> Thank you Doug! >> It works! Great! >> >> >> I have another problem: I am reprocessing all my database with freesurfer >> 7.1.0, but in one subject segmentation failed. >> I had no problem with this subjects using freesurfer 6 >> What can be the problem? >> >> I attach the log >> >> Thank you for any help! >> >> Angela >> >> >> >>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto: >>> >>> >>> Someone just pointed out that I posted the wrong file. Here is the correct >>> one. Copy it to the same folder >>> >>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m >>> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m> >>> >>> >>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote: >>>> >>>> Download this file >>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m >>>> >>>> <https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m> >>>> and copy it into $FREESURFER_HOME/matlab >>>> and rerun. Let me know if that fixes it. >>>> >>>> >>>> >>>> On 5/13/2020 5:57 PM, Angela Favaro wrote: >>>>> External Email - Use Caution >>>>> >>>>> Please find attached the log >>>>> Thank you >>>>> Angela >>>>> >>>>> >>>>> >>>>>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve >>>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto: >>>>>> >>>>>> Are you running this from recon-all? If so send the recon-all.log. If >>>>>> from the command line, send the command-line and all terminal output >>>>>> >>>>>> On 5/13/2020 5:28 PM, Angela Favaro wrote: >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Hi Doug! >>>>>>> yes, it run under version 6! >>>>>>> Please let me know if it is something that can be solved >>>>>>> Thank you >>>>>>> Angela >>>>>>> >>>>>>> >>>>>>>> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve >>>>>>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> ha scritto: >>>>>>>> >>>>>>>> Does it run under version 6? We are not really supporting lGI anymore, >>>>>>>> but maybe we can get it to work >>>>>>>> >>>>>>>> On 5/13/2020 4:24 PM, Angela Favaro wrote: >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi all, >>>>>>>>> I am using the new version of Freesurfer 7.1.0 >>>>>>>>> And I am finding problems in running gyrification analysis. >>>>>>>>> I have Matlab 2016a (and 2019b) with the toolbox image processing >>>>>>>>> >>>>>>>>> The error is after the command find_corresponding_center_FSformat >>>>>>>>> >>>>>>>>> Matlab seems to start, but then the following message appears: >>>>>>>>> >>>>>>>>> >> Warning: Input argument must be a string. >>>>>>>>> > In ver (line 41) >>>>>>>>> In freesurfer_read_surf (line 70) >>>>>>>>> In find_corresponding_center_FSformat (line 26) >>>>>>>>> Error using fprintf >>>>>>>>> Function is not defined for 'struct' inputs. >>>>>>>>> >>>>>>>>> Error in freesurfer_read_surf (line 70) >>>>>>>>> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15)); >>>>>>>>> >>>>>>>>> Error in find_corresponding_center_FSformat (line 26) >>>>>>>>> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); >>>>>>>>> >>>>>>>>> >> >>>>>>>>> ERROR: find_corresponding_center_FSformat did not complete >>>>>>>>> successfully! >>>>>>>>> >>>>>>>>> I tried with both the Matlab version, but the error is the same >>>>>>>>> Any help is appreciated. Thank you so much >>>>>>>>> >>>>>>>>> Angela >>>>>>>>> >>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <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
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