I think you need to ask that on the FreeSurfer list as that is not an HCP Pipeline issue. Please tell them what version of FreeSurfer you are using.
Matt. From: Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Monday, August 20, 2018 at 10:53 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: Niv Tik <niv...@gmail.com<mailto:niv...@gmail.com>> Subject: Re: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions thanks for the (very) quick response, added to this mail is the log file but actually I think now that the reason it carried out until the end is because I changed the 'set -e' to 'set -x' for debugging. so, here is the error that arises when we just run it with 'set -e': dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib thanks again Sahchar On Mon, 20 Aug 2018 at 18:38, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: 1. You can get the gradient distortion coefficients from your scanner. NONE can be set and for some scanners it does not make much difference (e.g. Trio). 2. recon_all_seed is a random number seed. Presumably this is an optional argument, but you could set 12345. 3. Need to look at the recon-all log to see what failed. 4. Give T1w and T2w from the ${StudyFolder}/${Subject}/T1w folder with acpc_dc_restore. Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal <gal.shac...@gmail.com<mailto:gal.shac...@gmail.com>> Date: Monday, August 20, 2018 at 10:34 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Cc: Niv Tik <niv...@gmail.com<mailto:niv...@gmail.com>> Subject: [HCP-Users] PreFreeSurfer and FreeSurfer pipelines questions Hello dear experts As I mentioned in an earlier message, we are trying to implement the HCP pipelines to our data, and we have a few questions. After some struggling, we successfully ran the PreSurfer Pipeline we tried running the FreeSurfer Pipeline. we ran in with 'gdcoeffs' set to 'NONE', because we don't have any file with the gradient distortion coefficients. is that a problem? After running the PreFreeSurfer, we tried to run the FreeSurfer pipeline, but didn't really know what to put as the 'recon_all_seed', so we tried to run the script without giving it any input. The script somehow completed running "successfully", but without producing anything really - the 'surf' folder in the subject's dir is completely empty... Which brings us to our question - what is the necessary input for 'recon_all_seed'? And another question just to make sure - the t1 and t2 images we should give the FreeSurfer pipeline are the acc_dc_restore ones, right? Hope to hear from you Shachar Gal, Tel Aviv University _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
