External Email - Use Caution Could you elaborate what you mean by volumes and would I get the volumes within the recon-all log file I sent your way?
So I am inputting MRI and CT scans that are given to us via DICOMS. I used 3D slicer to look and see which is the best looking series and then I upload those dicoms into iEEGview in order to do segmentation-->coregistration--> and then electrode localization. Best, Katie On Mon, Feb 8, 2021 at 11:05 AM Fischl, Bruce <bfis...@mgh.harvard.edu> wrote: > Hi Katie > > > > I defer to others for this particular problem, but I would strongly advise > looking at the various volumes recon-all outputted prior to that and make > sure that they are all reasonable-looking. Can you also tell us what your > input data is? > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Katherine Andrade > *Sent:* Monday, February 8, 2021 1:05 PM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] Issue with Segmentation > > > > * External Email - Use Caution * > > Hi Bruce, > > > > Thank you for your prompt response. We were able to successfully run > segmentation on another dataset that we've received from one University but > when we attempt to run the segmentation from the dataset from another > University, we can't complete segmentation. > > > > This is what Matlab says: > > > --------------------------------------------------------------------------------------- > > Checking to see if freesurfer segmentation has started... > Freesurfer segmentation has started; this process may take more than 24 > hours... > The progress of the segmentation process can be observed by opening > /home/bdl/freesurfer/subjects/SD06/scripts/recon-all.log > When the segmentation is complete the results are saved in > /home/bdl/freesurfer/subjects/SD06/...The pial surfaces are saved as > rh.pial and lh.pial in SD06/surf/... > > Segmentation processing... Please don't turn off your computer! > > > > > ----------------------------------------------------------------------------------------- > > > > I've attached the recon-all.log below and it mentions there is an Error > that says "don't know how to get DWI parameters from. > > > > Is there anyway you can help me debug this issue. I know this process > shouldn't be taking so long. > > > > Best, > > Katie > > > > On Sun, Feb 7, 2021 at 2:38 PM Fischl, Bruce <bfis...@mgh.harvard.edu> > wrote: > > Hi Katie > > > > Can you give us more info? What command line did you run? Can you send us > the recon-all.log file from the subject so we can see what step it is on? > Usually this means the topology fixer is trying to fix something giant, > like the cerebellum attached to cortex or skull left around or something > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Katherine Andrade > *Sent:* Sunday, February 7, 2021 5:22 PM > *To:* Freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] Issue with Segmentation > > > > * External Email - Use Caution * > > To whom this may concern, > > > > I've been running segmentation for over 100 hours and I'm not entirely > sure how to fix this issue. Is this the right address to ask for help? > > > > Best, > > Katie > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1TdqPTLOIn9SKhxIYwJNGfRnQNqKDdOiRIZC8Ftex92kxPIZ2RxsrEl6sAq31whdaRZme02QqA6xHsSUPG62exw4iskrTDXuiEQOD81QPuZdNoosC0Ne7c9p52l6n_zWygHLRrtAth3LlNzCMvMrlNrVthzOOT46fHpyf7-GCSfUijl35DuiJy244LGvWZSFJ806OSWdazQQ-bsitjnVBuQBe9hBgPowurrigCTcuWejalt5NaXaMwDbHpYjh38SkNzY4HwWjiJoEIk0Gf_OfKg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > <https://secure-web.cisco.com/1Jd7b1IvlEoc6Uzt6G4C0NG7kEU-FRPsu8F_NSo7MVHWgJMSKSM5PC8jSIJr6n1w0eCS6VVI8scXvCscN-ooP6UmueBKGZaZ3kdowAbyU-z-XYpbPPI0I92nRzRf4iHJyEXqQEf2KdjxBn-LKDHy0te69p-rj1P-6o7DnaahuqZ2LhebZKp36-8Qtm5a2mnOHtZKI3MeyPFOQEZVkyL2_dpLiZP4j88vzDmppMOBS5g64qbBFPS9pf4isHCMpILeVI0wC1wHdg8bK6EQRTlFajw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1TdqPTLOIn9SKhxIYwJNGfRnQNqKDdOiRIZC8Ftex92kxPIZ2RxsrEl6sAq31whdaRZme02QqA6xHsSUPG62exw4iskrTDXuiEQOD81QPuZdNoosC0Ne7c9p52l6n_zWygHLRrtAth3LlNzCMvMrlNrVthzOOT46fHpyf7-GCSfUijl35DuiJy244LGvWZSFJ806OSWdazQQ-bsitjnVBuQBe9hBgPowurrigCTcuWejalt5NaXaMwDbHpYjh38SkNzY4HwWjiJoEIk0Gf_OfKg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
