Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
1. Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
2. Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
3. Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
4. then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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.
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer.
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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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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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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freeview -v norm.mgz aparc+aseg.mgh:colormap=lut
should do the trick (or another volume)
cheers Bruce On Thu, 27 Apr 2017, Das S. wrote:
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt.
Still the voxel in apar+aseg.mgh does not showing value from my parcellation table.
Extract from FreesurferLUT.txt # Below is the color table for the cortical labels of the seg volume # created by mri_aparc2aseg in which the aseg cortex label is replaced # by the labels in the aparc. It also supports wm labels that will # eventually be created by mri_aparc2aseg. Otherwise, the aseg labels # do not change from above. The cortical lables are the same as in # colortable_desikan_killiany.txt, except that left hemisphere has # 1000 added to the index and the right has 2000 added. The label # names are also prepended with ctx-lh or ctx-rh. The white matter # labels are the same as in colortable_desikan_killiany.txt, except # that left hemisphere has 3000 added to the index and the right has # 4000 added. The label names are also prepended with wm-lh or wm-rh. # Centrum semiovale is also labled with 5001 (left) and 5002 (right). # Even further below are the color tables for aparc.a2005s and aparc.a2009s. Thanks Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 27 April 2017 21:00 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
freeview -v norm.mgz aparc+aseg.mgh:colormap=lut
should do the trick (or another volume)
cheers Bruce On Thu, 27 Apr 2017, Das S. wrote:
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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
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 Can you please explain what the flags mean here, I don't find them in help.
mri_aparc2aseg --s 100307 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
--s : subject --volmask : ? --aseg: ? --relabel: ? and what are the /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca and mri/aseg.auto_noCCseg.label_intensities.txt files?
I am really stuck to put my colortable in aparc+aseg.mgz file. Please help. Thanks Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 28 April 2017 12:16 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt.
Still the voxel in apar+aseg.mgh does not showing value from my parcellation table.
Extract from FreesurferLUT.txt # Below is the color table for the cortical labels of the seg volume # created by mri_aparc2aseg in which the aseg cortex label is replaced # by the labels in the aparc. It also supports wm labels that will # eventually be created by mri_aparc2aseg. Otherwise, the aseg labels # do not change from above. The cortical lables are the same as in # colortable_desikan_killiany.txt, except that left hemisphere has # 1000 added to the index and the right has 2000 added. The label # names are also prepended with ctx-lh or ctx-rh. The white matter # labels are the same as in colortable_desikan_killiany.txt, except # that left hemisphere has 3000 added to the index and the right has # 4000 added. The label names are also prepended with wm-lh or wm-rh. # Centrum semiovale is also labled with 5001 (left) and 5002 (right). # Even further below are the color tables for aparc.a2005s and aparc.a2009s. Thanks Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 27 April 2017 21:00 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
freeview -v norm.mgz aparc+aseg.mgh:colormap=lut
should do the trick (or another volume)
cheers Bruce On Thu, 27 Apr 2017, Das S. wrote:
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/left
Content of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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
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Answers below
On 04/28/2017 07:34 AM, Das S. wrote:
Hi Can you please explain what the flags mean here, I don't find them in help.
mri_aparc2aseg --s 100307 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt
--s : subject --volmask : --> use the ribbon.mgz file as the mask for cortex (probably redundant now) --aseg: --> specifies which file to use for the subcort seg --relabel: --> this will relabel some voxels depending on their intensity. This should only affect WM. and what are the /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca and mri/aseg.auto_noCCseg.label_intensities.txt files? --> those are also for the WM relabeling to CSF
I am really stuck to put my colortable in aparc+aseg.mgz file. Please help. Thanks Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 28 April 2017 12:16 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt.
Still the voxel in apar+aseg.mgh does not showing value from my parcellation table.
Extract from FreesurferLUT.txt # Below is the color table for the cortical labels of the seg volume # created by mri_aparc2aseg in which the aseg cortex label is replaced # by the labels in the aparc. It also supports wm labels that will # eventually be created by mri_aparc2aseg. Otherwise, the aseg labels # do not change from above. The cortical lables are the same as in # colortable_desikan_killiany.txt, except that left hemisphere has # 1000 added to the index and the right has 2000 added. The label # names are also prepended with ctx-lh or ctx-rh. The white matter # labels are the same as in colortable_desikan_killiany.txt, except # that left hemisphere has 3000 added to the index and the right has # 4000 added. The label names are also prepended with wm-lh or wm-rh. # Centrum semiovale is also labled with 5001 (left) and 5002 (right). # Even further below are the color tables for aparc.a2005s and aparc.a2009s. Thanks Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 27 April 2017 21:00 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
freeview -v norm.mgz aparc+aseg.mgh:colormap=lut
should do the trick (or another volume)
cheers Bruce On Thu, 27 Apr 2017, Das S. wrote:
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
1. Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
- Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/leftContent of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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.
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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You will need to create your own LUT, the FreeSurferColorLUT.txt will not be updated. Can you figure out how to do that from the extracted text below?
On 04/28/2017 07:16 AM, Das S. wrote:
Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt.
Still the voxel in apar+aseg.mgh does not showing value from my parcellation table.
Extract from FreesurferLUT.txt # Below is the color table for the cortical labels of the seg volume # created by mri_aparc2aseg in which the aseg cortex label is replaced # by the labels in the aparc. It also supports wm labels that will # eventually be created by mri_aparc2aseg. Otherwise, the aseg labels # do not change from above. The cortical lables are the same as in # colortable_desikan_killiany.txt, except that left hemisphere has # 1000 added to the index and the right has 2000 added. The label # names are also prepended with ctx-lh or ctx-rh. The white matter # labels are the same as in colortable_desikan_killiany.txt, except # that left hemisphere has 3000 added to the index and the right has # 4000 added. The label names are also prepended with wm-lh or wm-rh. # Centrum semiovale is also labled with 5001 (left) and 5002 (right). # Even further below are the color tables for aparc.a2005s and aparc.a2009s. Thanks Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: 27 April 2017 21:00 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
freeview -v norm.mgz aparc+aseg.mgh:colormap=lut
should do the trick (or another volume)
cheers Bruce On Thu, 27 Apr 2017, Das S. wrote:
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer.
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Das S. [Sarbani.Das@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there
On 04/27/2017 02:55 PM, Das S. wrote:
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is)
On 04/27/2017 01:24 PM, Das S. wrote:
Dear Freesurfer Developer, I am using freesurfer to create a equal zone parcellation on cortical surface. I have used recon-all steps to create the aparc+aseg.mgz file. But in my aparc+aseg.mgz file I can't see the equal parcellation I have done.
Here are steps that I have followed:
1. Divided the vertex point from the sphere.reg into equal numbers and assigned them to label files.This way I have created n number of label files, n/2 for left and n/2 for right sphere. The label file names are as below lh.node-lh-1.label ........
- Then I run the mris_label2annot command to create the ?h.free40aparc.annot files. Before that I have created two color lookup table for left and right hemisphere.
mris_label2annot --s 100307 --h rh --no-unknown --ctab 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc --ldir 100307/label/eq_parcellation_label/right
mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc --ldir 100307/label/eq_parcellation_label/leftContent of ColorLUT.txt 801 node-lh-1 70 130 180 0 802 node-lh-2 245 245 245 0 803 node-lh-3 205 62 78 0.....
Then I am using the mris_ca_train to create the .gcs file.
mris_ca_train -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 100307/label/lh.leftaparc.gcs
mris_ca_train -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 100307/label/rh.righttaparc.gcs
then I am following the recon-all steps and call the mris_ca_label command as below: mris_ca_label -t 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs 100307/label/rh.aparc.annot mris_ca_label -t 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs 100307/label/lh.aparc.annot
Then I followed the rest of recon-all steps to create the apar+aseg.mgz file as below: recon-all -pial -subjid 100307 recon-all -cortribbon -subjid 100307 recon-all -parcstats -subjid 100307 recon-all -pctsurfcon -subjid 100307 recon-all -hyporelabel -subjid 100307 recon-all -aparc2aseg -subjid 100307
I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that the file is not reflecting valueof my equal parcellation lookup table. I tried many ways but coundn't figure out. Any help will be much appreciated. Thanks Sarbani Das
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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Das S. -
Douglas N Greve