Sorry, I don’t understand. Those files are now in the directory. What exactly should I run next?
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: 03 August 2015 16:04 To: Freesurfer support list Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls no! Don't delete those files - we need them. Just don't include them in your for loop cheers Bruce On Mon, 3 Aug 2015, Lim, Lena wrote: > Thanks, Bruce. So do I delete that files and run recon-all -qcache -subjid $i > for all the subjects again though they have already been smoothed? > > > Cheers, > > L > > ---------------------------------------------------------------- > Lena Lim, PhD > Department of Child & Adolescent Psychiatry (PO 85) Institute of > Psychiatry, Psychology & Neuroscience King's College London De > Crespigny Park London SE5 8AF lena....@kcl.ac.uk > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: 03 August 2015 15:38 > To: Freesurfer support list > Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls > > Hi Lena > > those aren't files that you need to recreate - they are distributed > with FS (which is also why you don't have permission to write into > their directories). You should leave them out of the list that you are > running -qcache on > > cheers > Bruce > > > On Mon, 3 Aug 2015, Lim, Lena wrote: > >> >> >> >> >> >> Thanks Bruce. >> >> >> >> I managed to get the hippo files for the 3 new subjects. >> >> >> >> However, when I ran >> >> >> >> #! /bin/bash >> >> >> >> for i in $ ( ls ) ; do >> >> >> >> recon-all -qcache -subjid $i >> >> >> >> done >> >> >> >> >> >> The smoothing for each individual subject was alright (e.g. recon-all >> -s >> PAC70 finished without error) but there were these errors messages >> below (please see log attached): >> >> >> >> ERROR: you do not have write permission to >> /home/spjwker_PAC/Lena/CT_SA/FSL/fsaverage >> >> ERROR: you do not have write permission to >> /home/spjwker_PAC/Lena/CT_SA/FSL/rh.EC_average >> >> ERROR: you do not have write permission to >> /home/spjwker_PAC/Lena/CT_SA/FSL/lh.EC_average >> >> >> >> I think the fsaverage, rh.EC_average and lh.EC_average files were >> already before I ran the above commands… >> >> >> >> How do I create the final fsaverage, rh.EC_average and lh.EC_average >> files for all the 68 subjects that I want in the final analysis? >> >> >> >> Thanks, >> >> >> >> Lena >> >> >> >> >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: 30 July 2015 18:02 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls >> >> >> >> Hi Lena >> >> >> >> you need to run the hippocampal subfield code. Depending on what >> version you are running it could mean adding something like: >> >> >> >> -hippocampal-subfields-<T1/T1T2/T2> >> >> >> >> and removing the -autorecon-all >> >> >> >> cheers >> >> Bruce >> >> >> >> >> >> On Thu, 30 Jul 2015, Lim, Lena wrote: >> >> >> >>> >> >>> Dear Freesurfer experts, >> >>> >> >>> >> >>> >> >>> My colleague (who has now left) told me that he has run the >> >>> preprocessing >> >>> autorecon1—3 and that I only have to run recon-all –qcache -subjid >>> $i >> >>> for all the subjects. However, I realised that there were 3 missing >> >>> subjects and so I tried to run the preprocessing for these 3 new >> >>> subjects with the following commands: >> >>> >> >>> >> >>> >> >>> #!/bin/bash >> >>> >> >>> >> >>> >> >>> files=( PAC03 PAC17 PAC57 ) >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> for i in ${files[*]}; do >> >>> >> >>> >> >>> >> >>> #echo $i >> >>> >> >>> >> >>> >> >>> recon-all -autorecon-all -subjid $i >> >>> >> >>> done >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> 1) The preprocessing finished without any errors but the outputs in >> >>> the mri folders seem slightly different from the others he did >>> (please >> >>> see screenshots attached, my PAC17 vs his PAC01). In particular, I >> >>> don’t have the 20 posterior_* files (e.g. posterior_left_CA1.mgz >>> etc) >> >>> in the mri folder, the hippo-subfield.log in the scripts folder and >> >>> the hippocampal_subfield.touch in the touch folder. How and when >>> were >> >>> they been created? Are they needed for subsequent analyses? >> >>> >> >>> >> >>> >> >>> 2) Shall I run the following for the 3 missing subjects all over again? >> >>> >> >>> >> >>> >> >>> #!/bin/bash >> >>> >> >>> >> >>> >> >>> files=( PAC03 PAC17 PAC57 ) >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> for i in ${files[*]}; do >> >>> >> >>> >> >>> >> >>> recon-all -autorecon-all –qcache -subjid $i >> >>> >> >>> >> >>> >> >>> done >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> 3) Finally, do I then run the following for all the subjects as the >> >>> final preprocessing step? >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> #!/bin/bash >> >>> >> >>> >> >>> >> >>> for i in $ ( ls ); do >> >>> >> >>> >> >>> >> >>> recon-all –qcache -subjid $i >> >>> >> >>> >> >>> >> >>> done >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> I am using Freesurfer v5.3.0 and have attached the recon-all log for >> >>> PAC17 and PAC01. >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> Many thanks, >> >>> >> >>> >> >>> >> >>> Lena >> >>> >> >>> >> >>> >> >>> >> >>> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
