External Email - Use Caution

Hi Greve,

Thank you very much for your reply.

How do I add data to the link you sent me? When I click on it, a pop up appears and I need to fill in a password to connect to the server. Which password should I use? If I copy the link on a browser, I see two folders: incoming and outcoming, but I cannot add files. Shall I send the all freesurfer output folder of two cases or just the aseg.presurf.mgz?

Best regards Ileana

Ileana Camerino

PhD candidate Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

On 16/04/2019, 21:14, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu> wrote:

Unfortunately, it usually means that you need to go in and manually fix the problems that you are seeing. Probably the best thing is to look at the aseg.presurf.mgz to see how the WM lesions are getting labeled. You may have to go in an label them manually. Can you upload a case or two here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming

On 4/16/19 11:05 AM, Camerino, .I.L. (Ileana) wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > > I am running recon all from the terminal of a linux machine: > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. > > > I tried recon all on an image dataset of small vessel disease > patients. I tried the command on several subjects and I got the same > outcome: a soft fallure. > > Please, find the recon all log in the attachment. > > Even though in the "recon all.log": it says: recon-all -s sub025 > finished without errors, after checking the pial and white matter > segmentations, very clear misplacement failures and part of dura mater > are present (see attachment: segmenation misplacement and dura). > > > I am also wandering how to avoid that white matter lesions are taken > into the aseg segmentation? > > > I checked the documentation and this kind of errors is not mentioned > anywhere. Can be the case, that this error is due to the fact that > these are clinical images? Can this problem be fixed? > > > For sake of curiosity, I tried the recon all command on another > dataset (stroke) and with these data I got an hard failure. > > recon all exited with errors: > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second > recon all o35403143 with errors) > > > Please, can anyone give me some ideas how to fix both errors? > > Thank you in advance > > Ileana > > > _______________________________________________ > 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

External Email - Use Caution

Hi Bruce,

I dragged into the folder "incoming" a folder called "sub025" (soft failure) for the first problem and a folder called "sub-31" (hard failure) for the second problem Can you see them?

Thanks Looking forward to hear from you Ileana

Ileana Camerino

PhD candidate Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

On 17/04/2019, 16:55, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

Hi Ileana

you use "anonymous" for the user name and your email for the password I believe.

cheers Bruce On Wed, 17 Apr 2019, Camerino, .I.L. (Ileana) wrote:

> External Email - Use Caution > > Hi Greve, > > Thank you very much for your reply. > > How do I add data to the link you sent me? When I click on it, a pop up appears and I need to fill in a password to connect to the server. Which password should I use? > If I copy the link on a browser, I see two folders: incoming and outcoming, but I cannot add files. > Shall I send the all freesurfer output folder of two cases or just the aseg.presurf.mgz? > > Best regards > Ileana > > Ileana Camerino > > PhD candidate > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognition > Spinozabuilding > Room B02.25 > Montessorilaan 3, 6525 HR Nijmegen > The Netherlands > Tel. +31-24 3612618 > > > > > > On 16/04/2019, 21:14, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu> wrote: > > Unfortunately, it usually means that you need to go in and manually fix > the problems that you are seeing. Probably the best thing is to look at > the aseg.presurf.mgz to see how the WM lesions are getting labeled. You > may have to go in an label them manually. Can you upload a case or two > here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming > > On 4/16/19 11:05 AM, Camerino, .I.L. (Ileana) wrote: > > > > External Email - Use Caution > > > > Dear Freesurfer experts, > > > > > > I am running recon all from the terminal of a linux machine: > > freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. > > > > > > I tried recon all on an image dataset of small vessel disease > > patients. I tried the command on several subjects and I got the same > > outcome: a soft fallure. > > > > Please, find the recon all log in the attachment. > > > > Even though in the "recon all.log": it says: recon-all -s sub025 > > finished without errors, after checking the pial and white matter > > segmentations, very clear misplacement failures and part of dura mater > > are present (see attachment: segmenation misplacement and dura). > > > > > > I am also wandering how to avoid that white matter lesions are taken > > into the aseg segmentation? > > > > > > I checked the documentation and this kind of errors is not mentioned > > anywhere. Can be the case, that this error is due to the fact that > > these are clinical images? Can this problem be fixed? > > > > > > For sake of curiosity, I tried the recon all command on another > > dataset (stroke) and with these data I got an hard failure. > > > > recon all exited with errors: > > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > > ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second > > recon all o35403143 with errors) > > > > > > Please, can anyone give me some ideas how to fix both errors? > > > > Thank you in advance > > > > Ileana > > > > > > _______________________________________________ > > 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 > > >