Hi Fengji, you have sent several emails. I keep asking you to give us a specific binary that has the problem, but you seem to ignore my request, wait a couple of weeks, then post the question back to the list. I'm happy to take look, but please send me something more specific! thanks doug
On 01/14/2016 01:46 PM, Fengji Geng wrote: > Hi FS's experts, > I sent out a couple of emails to seek for help on an error from > running recon-all using freesurfer 6.0 beta. Could anyone help with > the question? > Thank you! > > > > ----- > Fengji > > ------------------------------------------------------------------------ > *From:* Fengji Geng > *Sent:* Thursday, January 07, 2016 8:15 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] FW: problem with hard coded directory > (/scratch) > > Hi Douglas, > You asked us to give you an example of the problem program. I will try > to do it here, but if it is not what you want, please let me know. > > we ran recon-all -all -s <subject_name> -hippocampal-subfields-T1T2 > <file name of additional scan> <analysisID>. We saw the program tried > to create /scratch/$subject_hippoSF_T1_v10_right directory > and failing with (Read-only file system) because the user does not > have permission to write to /scratch. > > I can also send you the strace output if needed. > > Thank you! > > --------------------------------------------------------------------------------- > Message: 4 > Date: Mon, 4 Jan 2016 13:37:48 -0500 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] FW: problem with hard coded directory > (/scratch) > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Can you give us specific examples of problem programs? > > On 01/04/2016 09:54 AM, Fengji Geng wrote: > > Hello Bruce, > > > > Happy New Year! > > > > After we reported the error related to '/scratch' several weeks ago > > (see the email attached below), we tested the newest version of > > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > > /scratch)" have been changed to "if (-dw /scratch)". However, there > > are still a lot of binaries in the bin directory that match the string > > "scratch", which cause the same error that I encountered before. I am > > wondering if it is possible for you to fix '/scratch' in the bin > > directory. > > > > Thank you! > > ----- > Fengji > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
