That all looks like hippocampal subfield stuff, which is Eugenio's realm.
On 01/15/2016 11:41 AM, Fengji Geng wrote:
> Hi Doug,
>
> After reading your most recent reply, I just found that many of
> previous freesurfer emails had gone to my junk box automatically, so I
> missed some of your replies. Sorry!
>
> Looking at the strace output I generated last time, here are the lines
> where the program tries to stat and mkdir something in/scratch. And,
> the prev execve() system call.
>
> So, I'm guessing that bin/segmentSubjectT1_autoEstimateAlveusML
> or something it in turn runs is leading to "/scratch" directory problem.
>
> =========================
> 13174
> execve("/cell_root/software/freesurfer/dev/sys/bin/segmentSubjectT1_autoEstimateAlveusML",
>
> ["/cell_root/software/freesurfer/d"..., "HMN042",
> "/export/extra/pkd-fstest/FG_Temp",
> "0.333333333333333333333333333333"...,
> "/cell_root/software/freesurfer/d"...,
> "/cell_root/software/freesurfer/d"...,
> "/cell_root/software/freesurfer/d"..., "0.05", "left", "ConjGrad",
> "v10", "/cell_root/software/freesurfer/d"..., "0"], [/* 86 vars */]) = 0
> 13182 stat("/scratch/", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0
> 13182 stat("/scratch/HMN042_hippoSF_T1_v10_left/", 0x7f4e226015b0) =
> -1 ENOENT (No such file or directory)
> 13182 stat("/scratch/HMN042_hippoSF_T1_v10_left/", 0x7f4e226015e0) =
> -1 ENOENT (No such file or directory)
> 13182 lstat("/scratch", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0
> 13182 lstat("/scratch/HMN042_hippoSF_T1_v10_left", 0x7f4e226004b0) =
> -1 ENOENT (No such file or directory)
> 13182 stat("/scratch", {st_mode=S_IFDIR|0555, st_size=512, ...}) = 0
> 13182 mkdir("/scratch/HMN042_hippoSF_T1_v10_left", 0775) = -1 EROFS
> (Read-only file system)
> =========================
>
> I do see, however, MCRv80 references to before
> the mkdir("/scratch/HMN042_hippoSF_T1_v10_left" call. So, it could be
> something in the MCRv80 addition that's causing this issue.
>
> And, things like this:
> =========================
> 13182
> open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/gdcm.dic",
>
> O_RDONLY) = -1 ENOENT (No such file or directory)
> 13182
> open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/dicomVR.dic",
>
> O_RDONLY) = -1 ENOENT (No such file or directory)
> 13182
> open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/dicomTS.dic",
>
> O_RDONLY) = -1 ENOENT (No such file or directory)
> 13182
> open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/DictGroupName.dic",
>
> O_RDONLY) = -1 ENOENT (No such file or directory)
> 13182
> open("/mathworks/BLR/devel/bat/A3p1/build/3p/install/319992/glnxa64/ITK/share/gdcm/DicomDir.dic",
>
> O_RDONLY) = -1 ENOENT (No such file or directory)
> =========================
>
> are probably more MCRv80 (matlab runtime) package related
> and referencing a /mathworks/BLR directory on the machine that it
> was built, but not on our systems.
>
> Please let me know if you need more information. I will keep my eyes
> wide open this time.
>
> Thanks!!
>
>
> ---------------------------------------------------------------------------------------------------------------------------------------
> 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
>
> -----
> Fengji
>
> ------------------------------------------------------------------------
> *From:* Fengji Geng
> *Sent:* Thursday, January 14, 2016 1:46 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* FW: [Freesurfer] FW: problem with hard coded directory
> (/scratch)
>
> 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
>
>
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
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