External Email - Use Caution 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.fav...@unipd.it> > ha scritto: > > 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 <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> 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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