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:
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I 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:
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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 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:
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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 <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
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... 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 >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>>>> 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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >>> 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 >
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