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 > <dgr...@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 Caution >> >> 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.fav...@unipd.it <mailto:angela.fav...@unipd.it>> ha scritto: >>> >>> 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 <mailto: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 <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 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 <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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