Hello,
There was a bug in the original ConcatenateSubregionsResults.sh script. This has been fixed in the current dev version of FreeSurfer, and a patch is available herehttps://ftp.nmr.mgh.harvard.edu/pub/dist/lcnpublic/dist/ConcatenateSubregionsResults_Patch/.
There are more details in the README.md, but the main issue was that the script was looking for the .txt files that are output in the mri/ dir as an intermediate step. When it should have been looking for the final outputs in the stats/ dir. However, the values in both the .txt files in the mri/ dir and the .stats files in the stats/ dir should all have the same values.
Regarding the v21 -> v22 change, that is a version change in the stats file. The wiki hasn’t been updated yet, but v22 is the most recent version.
Best, Jackson
Jackson Nolan, BSc - Programmer Laboratory for Computational Neuroimaging (LCNhttps://www.nmr.mgh.harvard.edu/lab/lcn) Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, Mass General Hospital (413) 244-8583 | jnolan5@mgh.harvard.edumailto:jnolan5@mgh.harvard.edu From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Boa Sorte Silva, Narlon narlon.silva@ubc.ca Date: Tuesday, September 10, 2024 at 12:12 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampus Subfields Stats (FreeSurfer v7.3.2) Hi there,
I have searched the archive and couldn't find information relating to this issue.
I am running longitudinal analysis in FreeSurfer v7.3.2 in and using the segmentHA_T1_long.sh. The subfields segmentation works as expected, however the stats files are outputted to the “mri" folder instead of to the “stats" folder. Consequently, the attempts at concatenating these files using “asegstats2table” or “ConcatenateSubregionsResults.sh” won’t work. I was able to get around the issue of concatenation using a customized script.
My question is whether there are any concerns with the outputs for this version that I should be aware of? Or should I trust that the stats outputs are correct, despite being in the “mri” instead of “stats” folder? I also noticed that the Wiki shows examples with files tagged as “v21”, while the version I am using outputs “v22” text files.
Please find attached is a sample log file for a participant with details about OS etc.
These are the files listed in the “mri" folder:
Text files:
lh.amygNucVolumes-T1.long.v22.txt lh.hippoSfVolumes-T1.long.v22.txt rh.amygNucVolumes-T1.long.v22.txt rh.hippoSfVolumes-T1.long.v22.txt
Volumes:
lh.hippoAmygLabels-T1.long.v22.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.CA.mgz lh.hippoAmygLabels-T1.long.v22.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.FS60.mgz lh.hippoAmygLabels-T1.long.v22.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.HBT.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.long.v22.HBT.mgz lh.hippoAmygLabels-T1.long.v22.mgz
rh.hippoAmygLabels-T1.long.v22.CA.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.CA.mgz rh.hippoAmygLabels-T1.long.v22.FS60.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.FS60.mgz rh.hippoAmygLabels-T1.long.v22.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.HBT.FSvoxelSpace.mgz rh.hippoAmygLabels-T1.long.v22.HBT.mgz rh.hippoAmygLabels-T1.long.v22.mgz