Hello,

I am attempting to run hippocampal segmentation with freesurfer 7.3.1, using the segmentHA_T2.sh script with a high-resolution hippocampus T2 sequence as additional scan input. The code runs fine, but oddly it places the outputs into the mri subfolder rather than into stats (output file names shown below). 

mri/

rh.amygNucVolumes-T2HighResHippo.v22.txt

rh.hippoSfVolumes-T2HighResHippo.v22.txt

rh.hippoAmygLabels-T2HighResHippo.v22.mgz

The stats folder also contains output .stats files for hippocampus and amygdala, but they only have one sentence in them: " # Amygdala nuclei volumes as created by segmentHA_T2.sh "

These are the names of the files in the stats directory:

stats/

amygdalar-nuclei.lh.T2.v22.T2HighResHippo.stats

amygdalar-nuclei.rh.T2.v22.T2HighResHippo.stats

hipposubfields.lh.T2.v22.T2HighResHippo.stats
hipposubfields.rh.T2.v22.T2HighResHippo.stats

It seems to me that the output files are initialized in the stats directory, but the values themselves get written to files in the mri directory. 

When I go to compile the data across subjects, the ConcatenateSubregionsResults script is missing from the installation (I have confirmed this both for 7.3.1 and 7.4.1 installations). I found the following thread in archive with a similar issue of this file missing:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg76908.html

In this thread Antoine shared a direct download for the ConcatenateSubregionsResults, then Jackson shares a batched version of the script to resolve an issue with it looking for files in the /mri directory (which is where those files are written in my case anyways).

Either by using the unbatched script or using the batched script and manually moving the files from the mri to the stats, I am able to run the script but run into another issue. The output file contains in the first row the values for the first subject and then for all subsequent subject rows it has region labels. I looked at each subject's output and it looks like this:

Hippocampal_tail 547.477135

Whole_hippocampus 2906.119003

My guess is that the labels are being incorrectly pulled from the second column and the values from the first column. 

Doe anyone have any insight on how to resolve this? I could always pull what I need manually, but if this is an issue with the code it would be nice to see it resolved.

Many thanks! 

Jenya C. 

Indiana University School of Medicine