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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
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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
> ha s
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/a
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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
> ha scritto:
>
> External Email - Use Caution
>
>
> Hi Doug,
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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 overcom
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:
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/gr
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
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 somethin
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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
> ha scritto:
>
> Does it run under version 6? We are not really supporting lG
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 anal
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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
Matl
Hi Marie:
I am trying to run the LGI algorithm on 32 brains. As shown in the
archives, I set the environment (on tcsh) and provided the MATLAB pathway.
[afrancis-mac:~] afrancis% setenv MATLABPATH
/Applications/MATLAB_R2015a.app/
[afrancis-mac:~] afrancis% setenv PATH ${MATLABPATH}/bin:${PATH}
I
Hi Marie:
I just had another problem with the LGI processing. Here is the log:
thanks,
Alan
[alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514
Current Stamp: freesurfer-
Hi Alan,
Do you have the image processing toolbox installed in matlab? If not, I guess
this is the source of the error.
Best,
Marie
On Apr 30, 2015, at 7:51 AM, Alan Francis
mailto:alandarkene...@gmail.com>> wrote:
Hi Marie:
I am trying to run the LGI post processing step on 60 ASD subject
Hi Marie:
I am trying to run the LGI post processing step on 60 ASD subjects. I am
using FreeSurfer 5.3. The recons went well and the processed brains look
great. However when I run the LGI step, I am getting the following error
which is as follows: Could you please help me?
[alanf@micc FreeSurfe
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