updating ashs description

docs/mri_analysis.md

@@ -1,6 +1,6 @@
-# MRI Analysis
+# Overview
 
-Included here are resource and tips for best practices within the lab. There are many great resources available online for MRI analysis, check the links below!
+Included here are resources and tips for best practices within the lab. There are many general-purpose resources available online for MRI analysis, check the links below!
 
 ## Lab-specific resources
 * [MRI quality control](mri_qc.md)

docs/mri_ashs.md

@@ -4,11 +4,36 @@
 
 ## ASHS on ix
 
-Running ASHS on ix is simple. First, activate the `mri-preproc` conda environment:
+Running ASHS on ix is simple. First, navigate to your project's BIDS directory. Then, activate the `mri-preproc` conda environment:
 
-'''sh
-> conda activate mri-preproc
-'''
+```
+$ conda activate mri-preproc
+```
+
+Next, set an environment variable to the path of the ASHS binaries:
+
+```
+$ export ASHS_ROOT=/data/software/ashs/ashs
+```
+
+Finally, you can run ASHS on your participant. To do so, you will need the path to their T1 and T2 volumes and the path to the Princeton Young Adult atlas. Here, I'll use an example participant from the gardener project:
+
+```
+$ ${ASHS_ROOT}/bin/ashs_main.sh \
+    -I sub-028 \
+    -a /data/software/ashs/atlases/ashs_atlas_princeton \
+    -g /data2/gardener/sub-028/anat/sub-028_T1w_crop.nii.gz \
+    -f /data2/gardener/sub-028/anat/sub-028_T2w.nii.gz \
+    -w /data2/gardener/derivatives/ashs/sub-028
+```
+
+In the above command, `-I` is the subject code, `-a` sets the path to the atlas (this is fixed, you won't change this!), `-g` and `-f` are the paths to the participant's T1 and T2 volumes, and `-w` is the output directory. 
+
+ASHS takes 10-15 minutes to finish a segmentation. The output directory will contain all the files ASHS generates including measures of ICV and subfield volumes. The final segmentations and measures are in the `final` directory, look for the *_left_lfseg_corr_usegray.nii.gz and *_right_lfseg_corr_usegray.nii.gz volumes. The two hemispheres are segmented separately and will be in the same space as the T2 volume. They can be quickly combined with the following fslmaths command:
+
+```
+$ fslmaths sub-028_left_lfseg_corr_usegray.nii.gz -add sub-028_right_lfseg_corr_usegray.nii.gz sub-028_ashs.nii.gz
+```
 
 ## ASHS via DSS