Hi,
I am trying to inflate right hemisphere only using the commands:
recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526
The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526
SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file
The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly?
Thank you for your help.
XJ Kang
Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce
On Thu, 7 Jul 2016, Kang, XJ wrote:
Hi,
I am trying to inflate right hemisphere only using the commands:
recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526
The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526
SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file
The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly?
Thank you for your help.
XJ Kang
Thank you for your reply.
The image "wmparc.mgz" does not have the correct values. I am not sure if that because of the interruption of the procedures or not. Also I need to use some other files.
Thank you for your explanations. I will wait for the future corrections on the problem.
On 7/7/2016 11:11 AM, Bruce Fischl wrote:
Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce
On Thu, 7 Jul 2016, Kang, XJ wrote:
Hi,
I am trying to inflate right hemisphere only using the commands:
recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526
The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526
SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file
The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly?
Thank you for your help.
XJ Kang
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.
what values does the wmparc have? On Thu, 7 Jul 2016, Kang, XJ wrote:
Thank you for your reply.
The image "wmparc.mgz" does not have the correct values. I am not sure if that because of the interruption of the procedures or not. Also I need to use some other files.
Thank you for your explanations. I will wait for the future corrections on the problem.
On 7/7/2016 11:11 AM, Bruce Fischl wrote: Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce On Thu, 7 Jul 2016, Kang, XJ wrote: Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
For the normal inflated brain, wmparc.mgz has values: 0~85, 251~255, 1000~1035, 2000~2035, 3000~3035, 4000~4035, and 5001, 5002.
I have two unfinished one hemi inflation brains, one wmparc.mgz has values 0 ~176, and the other has 0~156. No other values found.
On 7/7/2016 11:25 AM, Bruce Fischl wrote:
what values does the wmparc have? On Thu, 7 Jul 2016, Kang, XJ wrote:
Thank you for your reply.
The image "wmparc.mgz" does not have the correct values. I am not sure if that because of the interruption of the procedures or not. Also I need to use some other files.
Thank you for your explanations. I will wait for the future corrections on the problem.
On 7/7/2016 11:11 AM, Bruce Fischl wrote: Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce On Thu, 7 Jul 2016, Kang, XJ wrote: Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/SubjectsMRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file
The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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.
Hi Experts,
I am trying to inflate the brains with lesions in the LHs. The inflation failed because of those lesions. I need the RH data from the files "mri/wmparc.mgz" and "stats/rh.aparc.stats". Here are what I did:
1. Use "recon-all -hemi rh" to inflate the RH only but the inflation stopped at the step "mris_volmask". it needs the "lh.white" file. Then I tried to run the following steps manually, but not succeed.
2. Replace the LH by RH to construct a new brain image (RH+RH) for inflation. Yes the inflation finished. I can find the RH data. However, I'd like to verify the RH data from the inflation of "RH+RH" are the same as those from "LH+RH" by comparing the two inflations of a healthy brain. What I found is that the parcellations of the same RH are little different with different LH structures, especially curvature and thickness. I'd like to know if this is true. In other words, are the inflations of LH and RH are correlated?
Any more suggestions to get the RH parcellation data for brains with lesions in LH? Thank you for your time.
XJ Kang
On 7/7/2016 11:11 AM, Bruce Fischl wrote:
Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce
On Thu, 7 Jul 2016, Kang, XJ wrote:
Hi,
I am trying to inflate right hemisphere only using the commands:
recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526
The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526
SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file
The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly?
Thank you for your help.
XJ Kang
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 XJ
your approach sounds reasonable.
cheers Bruce
On Thu, 9 Mar 2017, XJ Kang wrote:
Hi Experts,
I am trying to inflate the brains with lesions in the LHs. The inflation failed because of those lesions. I need the RH data from the files "mri/wmparc.mgz" and "stats/rh.aparc.stats". Here are what I did:
- Use "recon-all -hemi rh" to inflate the RH only but the inflation stopped
at the step "mris_volmask". it needs the "lh.white" file. Then I tried to run the following steps manually, but not succeed.
- Replace the LH by RH to construct a new brain image (RH+RH) for
inflation. Yes the inflation finished. I can find the RH data. However, I'd like to verify the RH data from the inflation of "RH+RH" are the same as those from "LH+RH" by comparing the two inflations of a healthy brain. What I found is that the parcellations of the same RH are little different with different LH structures, especially curvature and thickness. I'd like to know if this is true. In other words, are the inflations of LH and RH are correlated?
Any more suggestions to get the RH parcellation data for brains with lesions in LH? Thank you for your time.
XJ Kang
On 7/7/2016 11:11 AM, Bruce Fischl wrote: Hi XJ
this is a known problem but we haven't gotten to fixing it yet. Do you need it to complete that step? It is pretty close to the end so it may be that the error doesn't effect you cheers Bruce On Thu, 7 Jul 2016, Kang, XJ wrote: Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Kang, XJ -
XJ Kang