Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
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/
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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 . 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.
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug I am using the 5.0, but I have followed the instructions and downloaded the new files as indicated.
the xhemi folder has some folders that are empty (bem, label, src, stats, tmp), while the others include files (mri, scripts, surf, touch)
Is it possible that the script fails to copy files in the xhemi/label directory? I noted that the script copies other files from the subj00X folders to the xhemi folders, but label files are not copied.
May I find the label files in other folders and manually copy them into the xhemi/label folder? which are the correct files?
Thank you for your help!
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
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.
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
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
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.
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
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 CEST 2014
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.
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
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 Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote:
Hi all, I have a problem with 'Surface-based Interhemispheric Registration'
I followed the instructions and all seem to work, but the command: 'surfreg --s $subject --t fsaverage_sym --lh --xhemi'
finish with the error below (indeed in the xhemi/label directory, there is no file)
What can I do? Thank you for any help! Angela
#@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 subj024/xhemi rh ../surf/rh.sphere.reg
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
../label/rh.aparc.annot \n No such file or directory mris_ca_label: could not open label file ../label/rh.cortex.label No such file or directory
No such file or directory Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel
Version
10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30
17:44:52
CEST 2014
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.
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
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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 . 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.
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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 . 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.
Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you!
Angela
Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
Can you send the log file (or the full terminal output)? On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote: > Hi all, > I have a problem with 'Surface-based Interhemispheric
Registration'
> > I followed the instructions and all seem to work, but the command: > 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' > > finish with the error below > (indeed in the xhemi/label directory, there is no file) > > What can I do? > Thank you for any help! > Angela > > #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 > /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts > \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz > -seed > 1234 subj024/xhemi rh ../surf/rh.sphere.reg >
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
> ../label/rh.aparc.annot \n > No such file or directory > mris_ca_label: could not open label file ../label/rh.cortex.label > No such file or directory > > No such file or directory > Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel
Version
> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; > root:xnu-1504.15.3~1/RELEASE_I386 > i386 > > recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30
17:44:52
> CEST > 2014 > > > > _______________________________________________ > 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.
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
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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Angela,
Have you tried just running the specific commands to get the output file you need?
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
Anthony
On 7/7/14, 10:52 AM, angela.favaro@unipd.it wrote:
Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you!
Angela
Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
> Can you send the log file (or the full terminal output)? > On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote: >> Hi all, >> I have a problem with 'Surface-based Interhemispheric
Registration'
>> I followed the instructions and all seem to work, but the command: >> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >> >> finish with the error below >> (indeed in the xhemi/label directory, there is no file) >> >> What can I do? >> Thank you for any help! >> Angela >> >> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts >> \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz >> -seed >> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >>
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>> ../label/rh.aparc.annot \n >> No such file or directory >> mris_ca_label: could not open label file ../label/rh.cortex.label >> No such file or directory >> >> No such file or directory >> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel
Version
>> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >> root:xnu-1504.15.3~1/RELEASE_I386 >> i386 >> >> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30
17:44:52
>> CEST >> 2014 >> >> >> >> _______________________________________________ >> 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. > > > > > > _______________________________________________ > 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
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.
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Hi Anthony, I am not sure I understood what you are saying, but I had no problems with recon-all commands (I already performed surface, curvature and gyrification analyses comparing cases and controls, etc...) until I tried to perform interhemispheric registration. I had the same problem (see attached logfiles in my previous messages) with both 'xhemireg' and 'surfreg --xhemi' commands. I followed the instruction in the web-page without success...
Thank you for any help you can give me
Angela
Hello Angela,
Have you tried just running the specific commands to get the output file you need?
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
Anthony
On 7/7/14, 10:52 AM, angela.favaro@unipd.it wrote:
Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you!
Angela
Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote: > sure! thank you > > >> Can you send the log file (or the full terminal output)? >> On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote: >>> Hi all, >>> I have a problem with 'Surface-based Interhemispheric
Registration'
>>> I followed the instructions and all seem to work, but the >>> command: >>> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >>> >>> finish with the error below >>> (indeed in the xhemi/label directory, there is no file) >>> >>> What can I do? >>> Thank you for any help! >>> Angela >>> >>> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts >>> \n mris_ca_label -l ../label/rh.cortex.label -aseg >>> ../mri/aseg.mgz >>> -seed >>> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >>>
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>>> ../label/rh.aparc.annot \n >>> No such file or directory >>> mris_ca_label: could not open label file ../label/rh.cortex.label >>> No such file or directory >>> >>> No such file or directory >>> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel
Version
>>> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >>> root:xnu-1504.15.3~1/RELEASE_I386 >>> i386 >>> >>> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30
17:44:52
>>> CEST >>> 2014 >>> >>> >>> >>> _______________________________________________ >>> 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. >> >> >> >> >> >> _______________________________________________ >> 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
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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 . 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.
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick@fiu.edu Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I have been able to replicate the error with the patch in 5.1 and I'm working on a fix. doug
On 07/07/2014 10:52 AM, angela.favaro@unipd.it wrote:
Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you!
Angela
Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote:
sure! thank you
> Can you send the log file (or the full terminal output)? > On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote: >> Hi all, >> I have a problem with 'Surface-based Interhemispheric
Registration'
>> I followed the instructions and all seem to work, but the command: >> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >> >> finish with the error below >> (indeed in the xhemi/label directory, there is no file) >> >> What can I do? >> Thank you for any help! >> Angela >> >> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts >> \n mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz >> -seed >> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >>
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>> ../label/rh.aparc.annot \n >> No such file or directory >> mris_ca_label: could not open label file ../label/rh.cortex.label >> No such file or directory >> >> No such file or directory >> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel
Version
>> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >> root:xnu-1504.15.3~1/RELEASE_I386 >> i386 >> >> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30
17:44:52
>> CEST >> 2014 >> >> >> >> _______________________________________________ >> 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. > > > > > > _______________________________________________ > 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
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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, thank you very much! Angela
I have been able to replicate the error with the patch in 5.1 and I'm working on a fix. doug
On 07/07/2014 10:52 AM, angela.favaro@unipd.it wrote:
Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you!
Angela
Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
I'm not sure why this is failing. Are there other things in the xhemi folder? What version of FS are you using? doug
On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote: > sure! thank you > > >> Can you send the log file (or the full terminal output)? >> On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote: >>> Hi all, >>> I have a problem with 'Surface-based Interhemispheric
Registration'
>>> I followed the instructions and all seem to work, but the >>> command: >>> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >>> >>> finish with the error below >>> (indeed in the xhemi/label directory, there is no file) >>> >>> What can I do? >>> Thank you for any help! >>> Angela >>> >>> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts >>> \n mris_ca_label -l ../label/rh.cortex.label -aseg >>> ../mri/aseg.mgz >>> -seed >>> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >>>
/Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
>>> ../label/rh.aparc.annot \n >>> No such file or directory >>> mris_ca_label: could not open label file ../label/rh.cortex.label >>> No such file or directory >>> >>> No such file or directory >>> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel
Version
>>> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >>> root:xnu-1504.15.3~1/RELEASE_I386 >>> i386 >>> >>> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30
17:44:52
>>> CEST >>> 2014 >>> >>> >>> >>> _______________________________________________ >>> 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. >> >> >> >> >> >> _______________________________________________ >> 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/
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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 . 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.
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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 . 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.
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-- 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
OK, I have updated
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi
with new versions of mri_surf2surf and xhemireg. Copy those into $FREESURFER_HOME/bin (after making backups of what is already there)
doug
On 07/07/2014 03:24 PM, angela.favaro@unipd.it wrote:
Hi Doug, thank you very much! Angela
I have been able to replicate the error with the patch in 5.1 and I'm working on a fix. doug
On 07/07/2014 10:52 AM, angela.favaro@unipd.it wrote:
Dear Freesurfer team I am sorry to bore you again with my problems, but I need your help (or opinion) about which is the best solution in my situation.
Is there any way to make xhemireg and surfreg (--xhemi) work in my Freesurfer version (5.0)? Or do I need to use the 5.3 version? I would prefer to avoid to install the 5.3 version, because I think that I would need to re-perform all the analyses from the beginning (that in my computer would be about two months at full-time working). If there is any other solution (or if I simply need to wait that you look for the best solution), please let me know. Thank you!
Angela
Hi Adam, thank you for your mail. I am quite demoralized because I cannot get out of my problem and I am not receiving support from the mailing list. Which is, according to you, the solution? Do I need to install 5.3 version and re-analyse all my subjects from the beginning? Or do you think that I can install the 5.3 xhemireg (and surfreg) only?
I would be very grateful to receive any help or opinion
Angela
Just to provide some additional insight,
I noticed that the xhemireg file was missing from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg the ftp on January 28th, 2014 and emailed the listserv: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg33639.html
Doug quickly emailed back after hosting it with "sorry, try now".
I downloaded the new xhemireg and installed it in my FS v5.1.0 directory, and got an identical error as Angela. Xhemireg fails at -cortparc, trying to generate the rh.aparc.annot (The label directory is empty).
For curiosity, I used v5.3.0 and compared log files.
Differences: *xhemireg that was hosted for versions below FSv5.2.0 is xhemireg v1.12* --> mri_convert {volumes}.mgz --> tkregister2 -> mri_surf2surf for each hemi --> copies only surfaces --> generate annots/cortex label from -cortparc
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.avg_curv {subject}/xhemi/surf/rh.avg_curv cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness Goes on to try -cortparc for right hemi to generate the rh.aparc.annot, but fails because rh.cortex.label does not exist in {subject}/label/ directory
*xhemireg that v5.3.0 uses is v1.12.4.3* and is much more efficient --> mri_vol2vol --> mri_surf2surf each hemi --> copies surfaces and annots/labels for each hemi
cp surf/lh.curv {subject}/xhemi/surf/rh.curv cp surf/lh.sulc {subject}/xhemi/surf/rh.sulc cp surf/lh.area {subject}/xhemi/surf/rh.area cp surf/lh.volume {subject}/xhemi/surf/rh.volume cp surf/lh.thickness {subject}/xhemi/surf/rh.thickness cp surf/lh.inflated.H {subject}/xhemi/surf/rh.inflated.H cp surf/lh.area.pial {subject}/xhemi/surf/rh.area.pial cp surf/lh.area.mid {subject}/xhemi/surf/rh.area.mid cp surf/lh.curv.pial {subject}/xhemi/surf/rh.curv.pial cp surf/lh.inflated.K {subject}/xhemi/surf/rh.inflated.K
*cp label/lh.aparc.annot {subject}/xhemi/label/rh.aparc.annotcp label/lh.BA.annot {subject}/xhemi/label/rh.BA.annotcp label/lh.aparc.a2009s.annot {subject}/xhemi/label/rh.aparc.a2009s.annot* (Not explicit, but the ?h.cortex.label appears at the same time; presumably just from the corresponding ?h.aparc.annot)
Hope that was helpful! Adam Martersteck
On 01/28/2014 11:26 AM, Adam Martersteck wrote:
Hi Freesurfer team,
I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg
On Thu, Jul 3, 2014 at 3:44 PM, angela.favaro@unipd.it wrote:
Hi all, I am trying again to perform Surface-based Interhemispheric Registration in another computer (same version of FS 5.0) and by building my own atlas. However, there is an error while running xhemireg command (please find the log attached).
I also noted that the command xhemireg took a lot of time to run (more than 30 min) while you wrote on the wiki that it would take a few minutes to finish.
If anyone can give some hints it would be great
thank you
Angela
> I'm not sure why this is failing. Are there other things in the > xhemi > folder? What version of FS are you using? > doug > > On 07/01/2014 11:06 AM, angela.favaro@unipd.it wrote: >> sure! thank you >> >> >>> Can you send the log file (or the full terminal output)? >>> On 06/30/2014 03:11 PM, angela.favaro@unipd.it wrote: >>>> Hi all, >>>> I have a problem with 'Surface-based Interhemispheric Registration' >>>> I followed the instructions and all seem to work, but the >>>> command: >>>> 'surfreg --s $subject --t fsaverage_sym --lh --xhemi' >>>> >>>> finish with the error below >>>> (indeed in the xhemi/label directory, there is no file) >>>> >>>> What can I do? >>>> Thank you for any help! >>>> Angela >>>> >>>> #@# Cortical Parc rh Mon Jun 30 17:44:52 CEST 2014 >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj024/xhemi/scripts >>>> \n mris_ca_label -l ../label/rh.cortex.label -aseg >>>> ../mri/aseg.mgz >>>> -seed >>>> 1234 subj024/xhemi rh ../surf/rh.sphere.reg >>>> /Applications/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs >>>> ../label/rh.aparc.annot \n >>>> No such file or directory >>>> mris_ca_label: could not open label file ../label/rh.cortex.label >>>> No such file or directory >>>> >>>> No such file or directory >>>> Darwin host-001.homenet.telecomitalia.it 10.8.0 Darwin Kernel Version >>>> 10.8.0: Tue Jun 7 16:33:36 PDT 2011; >>>> root:xnu-1504.15.3~1/RELEASE_I386 >>>> i386 >>>> >>>> recon-all -s subj024/xhemi exited with ERRORS at Mon Jun 30 17:44:52 >>>> CEST >>>> 2014 >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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
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