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Hi teams, After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing guid in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh: command not found: tksurfer", "zsh: command not found: tkmedit". Could you please give some advice about how to solve this? Thanks.
Bo
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using freeview instead.
cheers Bruce On Wed, 13 May 2020, ZhangBo wrote:
External Email - Use Caution
Hi teams, After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing guid in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh: command not found: tksurfer", "zsh: command not found: tkmedit". Could you please give some advice about how to solve this? Thanks.
Bo
You can also use tkmeditfv and tksurferfv. They take the tkmedit/tksurfer arguments but run freeview
On 5/13/2020 11:48 AM, Bruce Fischl wrote:
Hi Bo
tkmedit and tksurfer have been deprecated for years. Try using freeview instead.
cheers Bruce On Wed, 13 May 2020, ZhangBo wrote:
External Email - Use Caution
Hi teams, After installing freesurfer-7.0.0 in MacOS 10.15.4, I followed the testing guid in https://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer. It is ok for freeview, however for tksurfer and tkmedit, I get errors "zsh: command not found: tksurfer", "zsh: command not found: tkmedit". Could you please give some advice about how to solve this? Thanks.
Bo
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 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 CautionHi 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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
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 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 CautionHi 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 CautionHi 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
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 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 CautionPlease 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 CautionHi 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 <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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 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 CautionPlease 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.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 CautionPlease 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.favaro@unipd.it mailto:angela.favaro@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 <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 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 <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 >
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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 >
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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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Dear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
Angela
External Email - Use Caution
Dear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems 1. About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these cases in one of my previous mails) 2. After the building of the template during the longitudinal processing, at the recon-all -long I found the following error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
Can you please help me with this two issues? Thank you so much!
Angela
Inizio messaggio inoltrato:
Da: Angela Favaro angela.favaro@unipd.it Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 Data: 23 maggio 2020 10:41:02 CEST A: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Rispondi a: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
External Email - Use CautionDear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
Angela _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Angela,
This is a bug on osx, which does not have the --preserve=timestamps flag available to cp. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via:
cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long... -o rca-long-tp-init sudo chmod +x rca-long-tp-init
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Angela Favaro angela.favaro@unipd.it Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Wednesday, May 27, 2020 at 4:27 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Problems with freesurfer 7.1.0
External Email - Use Caution Dear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems 1. About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these cases in one of my previous mails) 2. After the building of the template during the longitudinal processing, at the recon-all -long I found the following error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
Can you please help me with this two issues? Thank you so much!
Angela
Inizio messaggio inoltrato:
Da: Angela Favaro <angela.favaro@unipd.itmailto:angela.favaro@unipd.it> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 Data: 23 maggio 2020 10:41:02 CEST A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Rispondi a: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>
External Email - Use Caution
Dear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
Angela _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you!
Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew AHOOPES@mgh.harvard.edu ha scritto:
Hi Angela,
This is a bug on osx, which does not have the --preserve=timestamps flag available to cp. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via:
cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long... https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init -o rca-long-tp-init sudo chmod +x rca-long-tp-init
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Angela Favaro angela.favaro@unipd.it Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Wednesday, May 27, 2020 at 4:27 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Problems with freesurfer 7.1.0
External Email - Use CautionDear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems
- About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these cases in one of my previous mails)
- After the building of the template during the longitudinal processing, at the recon-all -long I found the following error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
Can you please help me with this two issues? Thank you so much!
Angela
Inizio messaggio inoltrato:
Da: Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 Data: 23 maggio 2020 10:41:02 CEST A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Rispondi a: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
External Email - Use CautionDear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Freesurfer experts, I continued to go on with my data set using 7.1.0 (with a Catalina MacOS 10.15) and in more than 10% of subjects recon-all -all failed. Failures were always at the segmentation stage (as I showed you in a previous mail) and all these subjects were processed without errors using Freesurfer 6. What do you think is the problem and do you have any suggestion on how to overcome it? Thank you
Angela
Il giorno 28 mag 2020, alle ore 23:18, Angela Favaro angela.favaro@unipd.it ha scritto:
External Email - Use CautionThank you!
Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@mgh.harvard.edu> ha scritto:
Hi Angela,
This is a bug on osx, which does not have the --preserve=timestamps flag available to cp. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via:
cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long... https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init -o rca-long-tp-init sudo chmod +x rca-long-tp-init
Best Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 4:27 PM To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Problems with freesurfer 7.1.0
External Email - Use CautionDear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems
- About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these cases in one of my previous mails)
- After the building of the template during the longitudinal processing, at the recon-all -long I found the following error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
Can you please help me with this two issues? Thank you so much!
Angela
Inizio messaggio inoltrato:
Da: Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 Data: 23 maggio 2020 10:41:02 CEST A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Rispondi a: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
External Email - Use CautionDear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear freesurfer experts, I found the same problems with recon-all (segmentation failure) using a Mac OS Sierra (10.12) and the same failures (more than 10% of cases) with the command: recon-all -base template -tp subj001 -tp subj002 -all
Hope it is possible to find a solution Thank you
Angela
Il giorno 30 mag 2020, alle ore 12:47, Angela Favaro angela.favaro@unipd.it ha scritto:
External Email - Use CautionDear Freesurfer experts, I continued to go on with my data set using 7.1.0 (with a Catalina MacOS 10.15) and in more than 10% of subjects recon-all -all failed. Failures were always at the segmentation stage (as I showed you in a previous mail) and all these subjects were processed without errors using Freesurfer 6. What do you think is the problem and do you have any suggestion on how to overcome it? Thank you
Angela
Il giorno 28 mag 2020, alle ore 23:18, Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> ha scritto:
External Email - Use CautionThank you!
Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@mgh.harvard.edu> ha scritto:
Hi Angela,
This is a bug on osx, which does not have the --preserve=timestamps flag available to cp. This will be fixed in the next 7.1 patch, but in the meantime, you can fix this manually via:
cd $FREESURFER_HOME/bin sudo rm rca-long-tp-init sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long... https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init -o rca-long-tp-init sudo chmod +x rca-long-tp-init
Best Andrew
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 4:27 PM To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Problems with freesurfer 7.1.0
External Email - Use CautionDear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems
- About a 10% of cases failed at the segmentation stage during the recon-all processing (I uploaded one of these cases in one of my previous mails)
- After the building of the template during the longitudinal processing, at the recon-all -long I found the following error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
Can you please help me with this two issues? Thank you so much!
Angela
Inizio messaggio inoltrato:
Da: Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 Data: 23 maggio 2020 10:41:02 CEST A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Rispondi a: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
External Email - Use CautionDear Freesurfer experts, I am trying to process a dataset with a longitudinal design. However, after building the template, at the “recon-all -long” command I got this error:
longmc Done /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri \n cp -f --preserve=timestamps /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz ./brainmask_template4.mgz \n cp: illegal option -- - usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory ERROR: Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64
recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 03:47:31 CEST 2020
For more details, see the log file /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log
Thank you for any help!
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Angela Favaro -
Bruce Fischl -
Douglas N. Greve -
Hoopes, Andrew -
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