Dear group,
If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data?
thank you,
kind wishes
Anna
Hi Anna,
for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi
for the analysis after that you use the long directories.
Best, Martin
On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsson09@gmail.com wrote:
Dear group,
If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data?
thank you,
kind wishes
Anna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ?
recon-all -s XXXX_long -localGI
Thank you
On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Anna,
for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long ...... -lgi
for the analysis after that you use the long directories.
Best, Martin
On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsson09@gmail.com wrote:
Dear group,
If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data?
thank you,
kind wishes
Anna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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.
Hi Anna,
no, you would still do:
recon-all -long tpid baseid -localGI
just not use the '-all'.
Best, Martin
On 03/26/2014 11:12 AM, Anna Jonsson wrote:
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s XXXX_long -localGI
Thank you
On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Anna, for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long ...... -lgi for the analysis after that you use the long directories. Best, Martin On Mar 15, 2014, at 10:04 AM, Anna Jonsson <ajonsson09@gmail.com <mailto:ajonsson09@gmail.com>> wrote:Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data? thank you, kind wishes Anna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web : http://reuter.mit.edu <http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s?
What I did (according to your suggestion)
recon-all -long XXX_1.long XXX_2.long -localGI
This did not work? Do you know why potentially?
On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
Hi Anna,
no, you would still do:
recon-all -long tpid baseid -localGI
just not use the '-all'.
Best, Martin
On 03/26/2014 11:12 AM, Anna Jonsson wrote:
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ?
recon-all -s XXXX_long -localGI
Thank you
On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:
Hi Anna,
for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi
for the analysis after that you use the long directories.
Best, Martin
On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsson09@gmail.com wrote:
Dear group,If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data?
thank you,
kind wishes
Anna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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.
-- Martin Reuter, Ph.D.
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652
Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
Hi Anna,
that was not my suggestion, I suggested to pass both the cross sectional time point ID and the base id (together with the long flag) and additionally the -localGI flag.
So if you time point 1 is XXX_1 and time point 2 is XXX_2 and your base is XXX_base then
recon-all -long XXX_1 XXX_base -localGI
and for the second time point
recon-all -long XXX_2 XXX_base -localGI
The base is not one of your time points, it gets created in the -base step and you give it a name (here XXX_base). In order for the above to work you need 5 directories per subject:
the 2 cross XXX_1 and XXX_2 the base XXX_base the results of the -long runs: XXX_1.long.XXX_base XXX_2.long.XXX_base
the last two are the ones where the GI will be created.
Best, Martin
On Jul 23, 2014, at 9:02 AM, Anna Jonsson ajonsson09@gmail.com wrote:
hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s?
What I did (according to your suggestion)
recon-all -long XXX_1.long XXX_2.long -localGI
This did not work? Do you know why potentially?
On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Anna,
no, you would still do:
recon-all -long tpid baseid -localGI
just not use the '-all'.
Best, Martin
On 03/26/2014 11:12 AM, Anna Jonsson wrote:
thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s XXXX_long -localGI
Thank you
On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Anna,
for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi
for the analysis after that you use the long directories.
Best, Martin
On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsson09@gmail.com wrote:
Dear group,
If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the "normal" baseline command on the .long data?
thank you,
kind wishes
Anna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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.
-- Martin Reuter, Ph.D.
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652
Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
freesurfer@nmr.mgh.harvard.edu
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Anna Jonsson -
Martin Reuter