No, that is the average of 40 subjects distributed with FS On 8/3/15 11:47 AM, Lim, Lena wrote: > But is the fsaverage file the group norm for all the final 68 subjects I have > so far ? > > > > -----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 16:41 > To: Freesurfer support list > Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls > > I think you should be all set. I meant don't delete fsaverage and all > > On > Mon, 3 Aug 2015, Lim, Lena wrote: > >> 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 >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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