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Hi Doug, I had the identical problem (failure at segmentation stage, as described below) in 4 subjects of my dataset. I have no possibility to run analyses on a linux machine… Since all 4 subjects had no problem using Freesurfer 6, is it so wrong to use freesurfer 6 only for these 4 subjects? Or have you any other suggestions?
Thank you for any help
Angela
Il giorno 15 mag 2020, alle ore 23:26, Angela Favaro angela.favaro@unipd.it ha scritto:
External Email - Use CautionHi 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 mailto: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
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