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
<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
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:
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
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