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 dgreve@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 CautionThank 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 <dgreve@mgh.harvard.edu mailto:dgreve@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_F... 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 CautionPlease find attached the log Thank you Angela
Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@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 <dgreve@mgh.harvard.edu mailto:dgreve@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
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