Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro <angela.favaro@unipd.it> ha scritto:

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Hi Doug, 

I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs Catalina and, although I am able to connect to the FTP site and open the incoming window (also in binary mode), commands are not working...

I am trying to overcome the problem.

Is there any other method to transfer the data set?

Thank you

Angela

Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve <dgreve@mgh.harvard.edu> 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:

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Thank you Doug!

It works! Great!

I have another problem: I am reprocessing all my database with freesurfer 7.1.0, but in one subject segmentation failed.

I had no problem with this subjects using freesurfer 6

What can be the problem?

I attach the log

Thank you for any help!

Angela

Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve <dgreve@mgh.harvard.edu> 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_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:

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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:

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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:

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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

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