I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud
2017-04-07 10:23 GMT-04:00 basile pinsard basile.pinsard@gmail.com:
---------- Forwarded message ---------- From: Douglas N Greve greve@nmr.mgh.harvard.edu Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu
what is your label2label command line?
On 04/06/2017 04:52 PM, Arnaud Boré wrote:
Dear Freesurfer's experts, I draw a specific region on fsaverage using QDEC, then I mapped this label on each subject using mri_label2label. I looked at these registered labels using freeview. Most of them are perfect but for some of them I would like to correct the segmentation. I would like to modify it using QDEC but when I overlay this label on the surface of my subject it has been shifted. I think this shift is because QDEC is using fsaverage as the standard space. I try opening QDEC using the "average" option and use the subject I want but I still get this shift. am I missing something ? Thank you in advance for your help. Arnaud Bore
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
-- Basile Pinsard
*PhD candidate, * Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS *Brain-Cognition-Behaviour Doctoral School **, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal
when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ?
On 04/07/2017 11:47 AM, Arnaud Boré wrote:
I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud
2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com mailto:basile.pinsard@gmail.com>:
---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
I try to view it on O_Nap_04MB.
I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label
I get the same results.
2017-04-07 12:03 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ?
On 04/07/2017 11:47 AM, Arnaud Boré wrote:
I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud
2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com mailto:basile.pinsard@gmail.com>:
---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Do you want me to attach/upload a screenshot of the shift ?
2017-04-07 13:10 GMT-04:00 Arnaud Boré arnaud.bore@gmail.com:
I try to view it on O_Nap_04MB.
I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label
I get the same results.
2017-04-07 12:03 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ?
On 04/07/2017 11:47 AM, Arnaud Boré wrote:
I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud
2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com mailto:basile.pinsard@gmail.com>:
---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mappedthis > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <(514)%20647-8649>
Not yet. Did you try to load it into freeview? If so, do you still see the shift?
On 04/07/2017 04:14 PM, Arnaud Boré wrote:
Do you want me to attach/upload a screenshot of the shift ?
2017-04-07 13:10 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com mailto:arnaud.bore@gmail.com>:
I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label I get the same results. 2017-04-07 12:03 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>: ---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:%28514%29%20647-8649>-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
There is no shift in freeview.
2017-04-07 16:35 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Not yet. Did you try to load it into freeview? If so, do you still see the shift?
On 04/07/2017 04:14 PM, Arnaud Boré wrote:
Do you want me to attach/upload a screenshot of the shift ?
2017-04-07 13:10 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com mailto: arnaud.bore@gmail.com>:
I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label I get the same results. 2017-04-07 12:03 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>: ---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/ <ftp://surfer.nmr.mgh. harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/>
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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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:%28514%29%20647-8649>-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Hi Douglas, What more can I do to help you figure out what's wrong ? Thank you in advance Arnaud
2017-04-07 16:50 GMT-04:00 Arnaud Boré arnaud.bore@gmail.com:
There is no shift in freeview.
2017-04-07 16:35 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Not yet. Did you try to load it into freeview? If so, do you still see the shift?
On 04/07/2017 04:14 PM, Arnaud Boré wrote:
Do you want me to attach/upload a screenshot of the shift ?
2017-04-07 13:10 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com mailto: arnaud.bore@gmail.com>:
I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label I get the same results. 2017-04-07 12:03 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>: ---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard .edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe r>
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/ <ftp://surfer.nmr.mgh.harvard .edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard .edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe r>
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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal
-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:%28514%29%20647-8649>-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <(514)%20647-8649>
Sorry, I don't know what is going on with qdec. Why do you need to do this in qdec? If it is to draw labels, then you can also use tksurfer.
On 04/10/2017 11:34 AM, Arnaud Boré wrote:
Hi Douglas, What more can I do to help you figure out what's wrong ? Thank you in advance Arnaud
2017-04-07 16:50 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com mailto:arnaud.bore@gmail.com>:
There is no shift in freeview. 2017-04-07 16:35 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Not yet. Did you try to load it into freeview? If so, do you still see the shift? On 04/07/2017 04:14 PM, Arnaud Boré wrote: Do you want me to attach/upload a screenshot of the shift ? 2017-04-07 13:10 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>>>: I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label I get the same results. 2017-04-07 12:03 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>>: ---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:%28514%29%20647-8649> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:%28514%29%20647-8649>-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
Hi Douglas,
Yes I would like to draw ROIs, I understand I can use tksurfer. I would like to know if your fs version has the same behaviour as mine. I use: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 Can you replicate this command line and tell me if the label is well aligned to the surface ? qdec --surface $SUBJECTS_DIR/bert/surf/rh.pial --label $SUBJECTS_DIR/bert/label/rh.V1_exvivo.label
Thank you in advance Arnaud
2017-04-10 11:54 GMT-04:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Sorry, I don't know what is going on with qdec. Why do you need to do this in qdec? If it is to draw labels, then you can also use tksurfer.
On 04/10/2017 11:34 AM, Arnaud Boré wrote:
Hi Douglas, What more can I do to help you figure out what's wrong ? Thank you in advance Arnaud
2017-04-07 16:50 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com mailto: arnaud.bore@gmail.com>:
There is no shift in freeview. 2017-04-07 16:35 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Not yet. Did you try to load it into freeview? If so, do you still see the shift? On 04/07/2017 04:14 PM, Arnaud Boré wrote: Do you want me to attach/upload a screenshot of the shift ? 2017-04-07 13:10 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>>>: I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label I get the same results. 2017-04-07 12:03 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>>: ---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvar d.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvar d.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh. harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.e du/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.e du/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/ <ftp://surfer.nmr.mgh. harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/> < ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/ <ftp://surfer.nmr.mgh. harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/>>
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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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2 https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.e du/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/ <ftp://surfer.nmr.mgh. harvard.edu/transfer/outgoing/flat/greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/gre ve/>
-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:%28514%29%20647-8649> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:%28514%29%20647-8649>-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Yes, the label is shifted off the brain when I run that command
On 04/11/2017 10:13 AM, Arnaud Boré wrote:
Hi Douglas,
Yes I would like to draw ROIs, I understand I can use tksurfer. I would like to know if your fs version has the same behaviour as mine. I use: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118 Can you replicate this command line and tell me if the label is well aligned to the surface ? qdec --surface $SUBJECTS_DIR/bert/surf/rh.pial --label $SUBJECTS_DIR/bert/label/rh.V1_exvivo.label
Thank you in advance Arnaud
2017-04-10 11:54 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Sorry, I don't know what is going on with qdec. Why do you need to do this in qdec? If it is to draw labels, then you can also use tksurfer. On 04/10/2017 11:34 AM, Arnaud Boré wrote: Hi Douglas, What more can I do to help you figure out what's wrong ? Thank you in advance Arnaud 2017-04-07 16:50 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>>>: There is no shift in freeview. 2017-04-07 16:35 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: Not yet. Did you try to load it into freeview? If so, do you still see the shift? On 04/07/2017 04:14 PM, Arnaud Boré wrote: Do you want me to attach/upload a screenshot of the shift ? 2017-04-07 13:10 GMT-04:00 Arnaud Boré <arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>> <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com> <mailto:arnaud.bore@gmail.com <mailto:arnaud.bore@gmail.com>>>>: I try to view it on O_Nap_04MB. I've tried these two command lines: qdec --table qdec.all_subjs.table.dat --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB --surface O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label I get the same results. 2017-04-07 12:03 GMT-04:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>: when you view it in qdec, are you viewing it on fsaverage or on O_Nap_04MB ? On 04/07/2017 11:47 AM, Arnaud Boré wrote: I used this command line: mri_label2label --srclabel rh.M1_v4.label --srcsubject fsaverage --trgsubject O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface --hemi rh The output label overlaps the surface using freeview but using qdec it is shifted. Thank you for your help. Arnaud 2017-04-07 10:23 GMT-04:00 basile pinsard <basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com> <mailto:basile.pinsard@gmail.com <mailto:basile.pinsard@gmail.com>>>>>: ---------- Forwarded message ---------- From: *Douglas N Greve* <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> Date: Thu, Apr 6, 2017 at 4:53 PM Subject: Re: [Freesurfer] QDEC and ROI drawing To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>>> what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of them are perfect but for > some of them I would like to correct the segmentation. I would like to > modify it using QDEC but when I overlay this label on the surface of > my subject it has been shifted. I think this shift is because QDEC is > using fsaverage as the standard space. I try opening QDEC using the > "average" option and use the subject I want but I still get this > shift. am I missing something ? > Thank you in advance for your help. > Arnaud Bore > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>> -- Douglas N. 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<tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>>> 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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 <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> <http://www.partners.org/complianceline <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. -- Basile Pinsard /PhD candidate, / Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS /Brain-Cognition-Behaviour Doctoral School /*, *ED3C*, *UPMC, Sorbonne Universités Biomedical Sciences Doctoral School, Faculty of Medicine, Université de Montréal CRIUGM, Université de Montréal -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>> <tel:514-647-8649 <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>>> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>> <tel:%28514%29%20647-8649> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:514-647-8649 <tel:514-647-8649>> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> <https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> <tel:%28514%29%20647-8649> -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649 <tel:514-647-8649> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>-- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
freesurfer@nmr.mgh.harvard.edu
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Arnaud Boré -
Douglas N Greve