External Email - Use Caution
Hi doug, I tried to re-run 3 or 4 times and always failed at the segmentation stage… I have no linux machine, but I can try in a mac computer with a different OS... thank you!
Angela
Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve dgreve@mgh.harvard.edu ha scritto:
Hi Angela, I cannot replicate this error. If you re-run, does it always exit with error? You can try this quickly be running
setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen cd /Users/angelafavaro/Desktop/Aachen/subj220/mri mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
One factor may be that I'm using CentOS and not Mac. Do you have a linux machine you can try it on?
On 5/15/2020 10:59 AM, Angela Favaro wrote:
External Email - Use CautionI have uploaded to you the data using the Martinos Center FileDrop Hope is a good option for you
Thank you Angela
Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> ha scritto:
External Email - Use CautionHi 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 mailto: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 http://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 Caution >> >> Please 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 >
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