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 




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