Re: [Freesurfer] fsaverage error with recon-all

Hi Jiachen does the fsaverage dir exist? It should be symlinked from you $SUBJECTS_DIR to $FREESUFER_HOME/subjects/fsaverage. cheers Bruce On Sun, 16 Jun 2019, chen wrote: External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set, but batching ex

Re: [Freesurfer] fsaverage error with recon-all

What is the output of running: ls -ld /home/dujiachen/HCP/human_connectome/female_processed/fsaverage From: on behalf of chen <824247...@qq.com> Reply-To: FS Help Date: Thursday, April 25, 2019 at 7:46 AM To: FS Help Subject: [Freesurfer] fsaverage error with recon-all Ex

Re: [Freesurfer] fsaverage error with recon-all

Thanks Douglas Now it's ok. I checked the OSX version. My OSX version was 10.9.5. I removed the XQuartz 2.7.7 and installed 2.7.5 I run this command is below recon-all -all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s S002_20151005 ( remove -sd and -ba_labels) thank you

Re: [Freesurfer] fsaverage error with recon-all

Try removing -ba_labels (it will do that with -all anyway) On 9/29/15 9:02 PM, 葉丁瑞 wrote: Dear All, I ran the following script: recon-all -i /Volumes/yang/S002_AD1118_20090116/NCKU-0003--1.dcm -s S002_ba -sd /Volumes/yang/S002_AD1118_20090116/ -all -ba_labels and got the error below at

Re: [Freesurfer] fsaverage error with recon-all

: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2011 8:48 AM To: Ayaz, Muhammad Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] fsaverage error with recon-all Hi Ayaz you need to create a symlink to the fsaverage subject we distribute in your SUBJE

Re: [Freesurfer] fsaverage error with recon-all

Hi Ayaz, > #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 > INFO: fsaverage subject does not exist in SUBJECTS_DIR > INFO: Creating symlink to fsaverage subject... > > ln -s /usr/local/freesurfer/subjects/fsaverage > /usr/local/subjects/fsaverage > > ln: creating symbolic link `/usr/local/subjec

Re: [Freesurfer] fsaverage error with recon-all

Hi Ayaz you need to create a symlink to the fsaverage subject we distribute in your SUBJECTS_DIR if you want to get the estimate Brodmann area labels. cheers Bruce On Tue, 31 May 2011, Ayaz, Muhammad wrote: > Dear All, > I ran recon-all using single MPRAGE data set. Processing exited with an

[Freesurfer] fsaverage error with recon-all

Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage. Thanks Ayaz #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...