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
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
Hi Yoon, when you run the script kvlQuantifyHippocampalSubfieldSegmentations.sh, it goes along the volumeStats_left.txt and volumeStats_right.txt to build a large table with all the volumes. The output files (nonPartialVolumeStatsLeft.txt/nonPartialVolumeStatsRight.txt) should be in your subjects directory $subject. Regarding the partial volume segmentation, it's not fully implemented / tested yet. Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Yoonho Chung" yoonho.chung@yale.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, August 15, 2014 10:33:19 PM Subject: [Freesurfer] Hippocampal Subfields missing nonPartialVolumeStatsRight.txt file
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
_______________________________________________ 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@nmr.mgh.harvard.edu
-
Andreas Berger -
Chung, Yoonho -
Eugenio Iglesias