Hi Richard
no, that won't conform it. You need to explicitly tell mri_convert to do so:
mri_convert --help |grep conform -c, --conform conform to 1mm voxel size in coronal -cm, --conform_min conform to the src min direction size -cs, --conform_size size_in_mm conform to the size given in mm
you can check that it is conformed with mri_info (it should be 1mm isotropic, 256^3 and type UCHAR)
cheers Bruce
On Mon, 8 Jul 2013, Lin, Richard Lee-Tsong wrote:
Hi Bruce,
I ran the command "mri_convert structural_brain.nii.gz {FS_directory}/{subjid}/mri/brainmask.mgz" before running my recon-all. Would that not conform my skull-stripped image, or is there an option that I need to turn on with mri_convert?
Thanks, Richard
On 8 Jul 2013, at 09:35, Bruce Fischl wrote:
Hi Richard
did you "conform" (resample to 1mm isotropic, 256^3, 8 bits/voxel) your skull stripped image? That's probably what's causing you problems. You can do this with mri_convert
cheers Bruce On Mon, 8 Jul 2013, Lin, Richard Lee-Tsong wrote:
Hi Bruce,
Thanks for the advice. The recon-all.log I sent you in the first email of the thread (attached in this email again) was generated after I completed all recon-all stages (1, 2, and 3), and it says at the end of the log file that my recon-all finished with errors.
I visually inspected the surfaces following the steps 5-8 specified here (https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) to "make sure the recon was successful." All the segmentations and brain images look great. However, error message popped up when I ran step 6 ("Check the skull strip") in GUI:
Command: tkmedit {subjid} brainmask.mgz -aux T1.mgz "Error: Loading volume T1.mgz The aux volume must be the same size as the main volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size."
A similar error message showed up in step 7 ("Check the white and pial surfaces") when the GUI popped up:
Command: tkmedit {subjid} brainmask.mgz -aux wm.mgz -surfs "Error: Loading volume wm.mgz The aux volume must be the same size as the main volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size."
Steps 5 (tkregister2 --mgz --s {subjid} --fstal --surf orig) and 8 (tkmedit {subjid} brainmask.mgz -surfs -aseg) all ran great.
Is this something I should be concerned about, or could I consider my recon successful? Thanks.
Richard
On 7 Jul 2013, at 10:02, Bruce Fischl wrote:
check the end of the recon-all.log file to see if it completed without error, then visually inspect the surfaces and such to see if they are reasonable cheers Bruce On Sun, 7 Jul 2013, Lin, Richard Lee-Tsong wrote: Thanks Bruce. I did run that particular analysis to completion, after which it sent me an email with the text "recon-all -s {subjid} finished with errors". If I can just ignore that error message, I have a follow-up question - in the absence of an email stating that recon-all is completed without error, how can I confirm that my recon-all stages 2 and 3 ran successfully? Are there some files that, if generated in a subdirectory under {subjid}, can give me a final confirmation? Thanks! Richard On Jul 6, 2013, at 8:34 PM, "Bruce Fischl" <fischl@nmr.mgh.harvard.edu> wrote: p.s. I think that is a warning embedded in the depths of some open source numerical minimization code we use that seems benign On Sat, 6 Jul 2013, Lin, Richard Lee-Tsong wrote: Attaching other log outputs from recon-all. Thanks. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lin, Richard Lee-Tsong [Richard_Lin@hms.harvard.edu] Sent: Saturday, July 06, 2013 3:35 PM To: free surfer Subject: [Freesurfer] Error after recon_all on pre-BETed image Hi FS gurus, For whatever reason, BET worked better on my structural image than mri_watershed, so I used a BET image with recon-all -autorecon1 -noskullstrip. Here is a summary of the codes that I used: bet structural.nii structural_brain.nii.gz recon-all -i structural.nii -s {subjid} recon-all -autorecon1 -noskullstrip -s {subjid} mri_convert structural_brain.nii.gz {FS_directory}/{subjid}/mri/brainmask.mgz recon-all -autorecon2 -autorecon3 -subjid {subjid} Stage 1 ran without errors. Stage 2 ran with errors, but when I checked the log (see attached), and the only message that resembled error to me was the following: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH Is there something I did wrong? Thanks. Best, Richard 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.