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 The information in this e-mail is intended only for the person to whom it is addressed. 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