Re: [Freesurfer] LGI problem

External Email - Use Caution 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

Re: [Freesurfer] LGI problem

External Email - Use Caution 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

Re: [Freesurfer] LGI problem

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

Re: [Freesurfer] LGI problem

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 > ha scritto: > > External Email - Use Caution > > > Hi

Re: [Freesurfer] LGI problem

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

Re: [Freesurfer] LGI problem

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:

Re: [Freesurfer] LGI problem

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

Re: [Freesurfer] LGI problem

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

Re: [Freesurfer] LGI problem

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

Re: [Freesurfer] LGI problem

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 > ha scritto: > > Does it run under version 6? We are not really supporting

Re: [Freesurfer] LGI problem

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

[Freesurfer] LGI problem

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

[Freesurfer] LGI problem

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}

Re: [Freesurfer] LGI problem

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] LGI problem

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

Re: [Freesurfer] LGI problem

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 alandarkene...@gmail.commailto:alandarkene...@gmail.com wrote: Hi Marie: I am trying to run the LGI post processing