Hi Mia you need to run it with the full path of the dicom you are trying to give to recon-all
cheers Bruce On Tue, 13 Jan 2015, Borzello, Mia wrote: > Okay, just ran ls-l and don't see it- image attached. > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, January 12, 2015 8:39 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error > > does that dicom exist? Can you run ls -l on it? > On Sat, 10 Jan 2015, > Borzello, Mia wrote: > >> I just fixed that but I'm still getting an error. I attached a screenshot. >> >> Thanks, >> Mia >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Krieger, Donald N. >> [krieg...@upmc.edu] >> Sent: Friday, January 09, 2015 5:39 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all error >> >> It looks like there's a typo in your recon-all command - there's a space >> between "-" and autorecon3 . >> >> Regards, >> >> Don >> >> >> Don Krieger, Ph.D. >> Department of Neurological Surgery >> University of Pittsburgh >> (412)648-9654 Office >> (412)521-4431 Cell/Text >> >> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- >>> boun...@nmr.mgh.harvard.edu] On Behalf Of Borzello, Mia >>> Sent: Friday, January 09, 2015 5:30 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all error >>> >>> Yea I didn't see it in /autofs/space/huygens_001/users/mia/subjects. >>> I attached the output error for recon-all. >>> >>> Thanks, >>> m >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer- >>> boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...@nmr.mgh.harvard.edu] >>> Sent: Thursday, January 08, 2015 4:27 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all error >>> >>> did you look in >>> >>> /autofs/space/huygens_001/users/mia/subjects >>> >>> Can you send us the screen output of recon-all? >>> >>> On Thu, 8 Jan 2015, Borzello, >>> Mia wrote: >>> >>>> I looked for that file and did not see a BI22_SurferOutput folder at all. >>>> ________________________________________ >>>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>> [fis...@nmr.mgh.harvard.edu] >>>> Sent: Thursday, January 08, 2015 2:34 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] recon-all error >>>> >>>> Hi Mia >>>> >>>> can you send us the recon-all.log? I don't think you included the >>>> error message in your email so there isn't much for us to go on. >>>> >>>> thanks >>>> Bruce >>>> >>>> On Thu, 8 Jan 2015, Borzello, Mia wrote: >>>> >>>>> >>>>> Hi Freesurfers, >>>>> >>>>> I'm wondering if you can help with the following error that occurred >>>>> when trying to create a reconstruction: >>>>> >>>>> FREESURFER_HOME: /usr/local/freesurfer/stable5_3_0 >>>>> >>>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>>> >>>>> RedHat release: CentOS release 6.5 (Final) >>>>> >>>>> Kernel info: Linux 2.6.32-431.20.3.el6.x86_64 x86_64 >>>>> >>>>> NMR Center info (/space/freesurfer exists): >>>>> >>>>> machine: huygens >>>>> >>>>> SUBJECTS_DIR: /autofs/space/huygens_001/users/mia/subjects >>>>> >>>>> PWD: /autofs/space/huygens_001/users/mia/subjects >>>>> >>>>> ssh huygens >>>>> setenv SUBJECTS_DIR /autofs/space/huygens_001/users/mia/subjects >>>>> cd /autofs/space/huygens_001/users/mia/subjects >>>>> >>>>> >>>>> 1)BI22 >>>>> 2)recon-all -autorecon1 -autorecon2 - autoreon3 -subject >>>>> BI22_SurferOutput >>>>> - >>> i/autofs/space/huygens_001/users/mia/subjects/BI22_PreOp_MRI/DICOM_B >>>>> I19/4571 >>>>> /4571157.dcm >>>>> 3)recon-all -s exited with ERRORS at Thu Jan 8 13:08:33 EST 2015 >>>>> >>>>> >>>>> Thanks, >>>>> m >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> 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 >> > _______________________________________________ > 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. 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