[Freesurfer] No voxel in mask using mri_binarize
Dear experts I want to create a mask for prefrontal gyrus. I used labels ( 1001, 1003, 1012,1014,1018 etc,)in FreeSurferColorLUT.txt and run the command like following mri_binarize --i con_sub01/mri/aparc.a2009s+aseg.mgz --out segment.nii.gz --match 1001, 1003, 1012,1014,1018 erode 1 But it found 0 voxels in final mask. How should I do ? Thank you Wang Kangcheng ___ 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.
Re: [Freesurfer] No voxel in mask using mri_binarize
The problem is probably the --erode 1. Cortex is very thin, so eroding by even one voxel may eliminate the entire ROI. Also, I'm not sure what the commas in the segmentation numbers will do On 8/17/14 9:11 AM, wang kangcheng wrote: Dear experts I want to create a mask for prefrontal gyrus. I used labels ( 1001, 1003, 1012,1014,1018 etc,)in FreeSurferColorLUT.txt and run the command like following mri_binarize --i con_sub01/mri/aparc.a2009s+aseg.mgz --out segment.nii.gz --match 1001, 1003, 1012,1014,1018 erode 1 But it found 0 voxels in final mask. How should I do ? Thank you Wang Kangcheng ___ 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] Removing dura fails to correct pial errors
Hi Freesurfer Team, I am encountering a situation where some pial errors in a few subjects persist even after removing the non-brain voxels. It appears that pial surface has not changed although the portion in the brainmask has been erased. What could be some of the reasons for this? I have attached a screenshot. Many thanks for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ 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] mri_glmfit group analyses in FDR in Freeview
Dear Surfers, In qdec, one can obtain a list of the significant clusters for a contrast by clicking the find clusters... button. Is there a file equivalent or button in Freeview that can give us that kind of information? Additionally, is there an option in Freeview to calculate and view clusters with FDR-corrected value? Thanks in advance, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health ___ 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.
Re: [Freesurfer] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file
On 08/15/2014 10:33 PM, Chung, Yoonho wrote: Hi, I am running Hippocampal subfield processing stream and I think I got all the appropriate posterior_*.mgz files I need to get the stats, but I am not seeing nonPartialVolumeStatsRight.txt anywhere as described in the wiki under $subjectsdir. What I am seeing is volumeStats_left.txt and volumeStats_right.txt files under the $subject/mri directory and one of the text files look like this. volumeInVoxels: Left-Hippocampus: 2616.97 left_presubiculum: 4050 left_CA1: 2880.55 left_CA2_3: 8120.59 left_fimbria: 212.439 left_subiculum: 5985.02 left_CA4_DG: 4459.07 left_hippocampal_fissure: 358.59 - If I look at the end of the hippo-subfields.log file, it is saying it is skipping the partial volume segmentation (see below). --- ... Debug: Off Observers: none Matrix: -0.5 0 0 0 0 0.5 0 -0.5 0 Offset: [41.7047, -40.8148, -4.10007] Center: [0, 0, 0] Translation: [41.7047, -40.8148, -4.10007] Inverse: -2 0 0 0 0 -2 0 2 0 Singular: 0 spacing: [0.5, 0.5, 0.5] origin: [41.7047, -40.8148, -4.10007] direction: -1 0 0 0 0 1 0 -1 0 done! Skipping the partial volume segmentation part --- Can please someone tell me what I am missing? Also, what do I need to do to extract the values to a spreadsheet? Should I use asegstats2table? under '-help' it doesn't say which options it should be used to get the subfields. Thank you so much for the help in advance. Cheers, Yoon Hi, i just checked, we have that last line in the log too, so that seems to be normal. Just to make sure, you need to run kvlQuantifyHippocampalSubfieldSegmentations.sh to collect the stats, which is the hippocampus equivalent of asegstats2table. (From what i remember that script is a bit fragile and fails if it encounters anything other than a properly structured subject in the subjects dir, so i used a bunch of symbolic links to make a clean version of the subjects dir, without the qdec folder and so on.) regards, Andreas ___ 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.
