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Hi doug,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:
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I have uploaded to you the data using the Martinos Center FileDropHope is a good option for you
Thank youAngela
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 6What 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:
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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 logThank youAngela
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 solvedThank youAngela
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 7.1.0And 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 fprintfFunction 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 sameAny help is appreciated. Thank you so much
Angela
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