Hi Mel
I had forgotten. Sure, upload them and people can grab them Bruce On Thu, 19 Oct 2017, Melanie Ganz wrote:
Hi Sean, Satra and Bruce, We just recently ran them all with v5.3 and did quite a few edits, especially to the subject ending in 10. Remember, we asked you for help, Bruce? 5 I had asked before if someone was interested in us uploading the work since we took quite some care in doing it, but there was no answer. I can upload them to a Martinos file drop tomorrow morning if you want.
Cheers, Mel
On Oct 19, 2017 9:41 PM, Satrajit Ghosh satra@mit.edu wrote: hi sean, i think i ran those in june 2013 at ohbm. however, my recollection of how it failed is encoded in that mail thread.
it may be worthw hile to just run through those images with freesurfer 6.0.
since it's only 6 brains, we can try running it through again.
cheers,
satra
On Thu, Oct 19, 2017 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Seán
I'm not sure. I think Satra posted the original issue, so maybe he knows. Satra? cheers Bruce On Thu, 19 Oct 2017, Seán Froudist Walsh wrote: Hi, Was the following issue ever solved? (sorry hit send too early!) https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html I tried and, like the previous two people it fails on mri_watershed. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html Best wishes, Sean Hi Mike it's hard to say without looking at the data. if you upload the subject dir we will take a look Bruce On Thu, 24 Nov 2016, Michael Craig wrote: Hi All, I am trying to run recon-all on the Allen Brain Institute T1 images. It works without any issue on all but one subject (H0351.1009). I saw this post from a few years ago describing the exact problem I’m having, but don’t see a solution. Has anyone figured out how to get this subject to run in recon-all? Or is it simply a matter of there not being enough contrast between grey and white matter? Thanks for the help! https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-July/031482.html Best wishes, Mike On 19 October 2017 at 15:05, Seán Froudist Walsh <froudiss@tcd.ie> wrote: Hi, Was the following issue ever solved? The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
hey melanie,
awesome - if you've already done edits, it should be quite straightforward to rerun with freesurfer 6. any chance you can run it through? otherwise i can send you a filedrop link off the list.
cheers,
satra
On Thu, Oct 19, 2017 at 4:13 PM, Melanie Ganz melanie.ganz@nru.dk wrote:
Hi Sean, Satra and Bruce,
We just recently ran them all with v5.3 and did quite a few edits, especially to the subject ending in 10. Remember, we asked you for help, Bruce? 5 I had asked before if someone was interested in us uploading the work since we took quite some care in doing it, but there was no answer. I can upload them to a Martinos file drop tomorrow morning if you want.
Cheers, Mel
On Oct 19, 2017 9:41 PM, Satrajit Ghosh satra@mit.edu wrote:
hi sean,
i think i ran those in june 2013 at ohbm. however, my recollection of how it failed is encoded in that mail thread.
it may be worthw hile to just run through those images with freesurfer 6.0.
since it's only 6 brains, we can try running it through again.
cheers,
satra
On Thu, Oct 19, 2017 at 3:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Seán
I'm not sure. I think Satra posted the original issue, so maybe he knows. Satra?
cheers Bruce On Thu, 19 Oct 2017, Seán Froudist Walsh wrote:
Hi, Was the following issue ever solved? (sorry hit send too early!) https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html I tried and, like the previous two people it fails on mri_watershed. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50297.html Best wishes, Sean
Hi Mike
it's hard to say without looking at the data. if you upload the subject dir we will take a look
Bruce On Thu, 24 Nov 2016, Michael Craig wrote:
Hi All, I am trying to run recon-all on the Allen Brain Institute T1 images. It works without any issue on all but one subject (H0351.1009).
I saw this post from a few years ago describing the exact problem I’m having, but don’t see a solution. Has anyone figured out how to get this subject to run in recon-all? Or is it simply a matter of there not being enough contrast between grey and white matter? Thanks for the help!
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013- July/031482.html
Best wishes, Mike
On 19 October 2017 at 15:05, Seán Froudist Walsh froudiss@tcd.ie wrote: Hi, Was the following issue ever solved?
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Melanie Ganz -
Satrajit Ghosh