Hi Alex, I am using the same method, I created a Python script to automate it for multiple users.

Basically, if you give it a file with all the subject ID-s, it maps labels with mri_label2label, obtains statistics with mris_anatomical_stats and writes all the stats in a single file. You also have to give the source brain (usually fsaverage, but I am using Colin27 for example since I exported ROI-s in that space), the hemi you are working with and the name of the ROI (the custom labels in <sourcebrain>/labels/<hemi>.<ROI>.label must exist before running this script)

The output is a file with a name similar to lh.ROIIFG.from_Colin27.txt, and it has values organized like in this example:

SubjectID StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd 004 lh.ROIIFG.label 9347 6391 17824 2.431 0.608 0.151 0.060 136 22.2 008 lh.ROIIFG.label 7031 4860 12730 2.194 0.603 0.152 0.065 143 18.2 017 lh.ROIIFG.label 8751 6127 18744 2.676 0.653 0.143 0.051 140 18.4 021 lh.ROIIFG.label 9891 6696 20523 2.641 0.617 0.138 0.048 155 19.2 032 lh.ROIIFG.label 9604 6448 15500 2.126 0.552 0.146 0.055 155 21.1 039 lh.ROIIFG.label 6658 4644 12752 2.403 0.601 0.144 0.053 94 14.2 040 lh.ROIIFG.label 6280 4274 13779 2.723 0.717 0.131 0.043 80 10.4 045 lh.ROIIFG.label 6694 4555 11482 2.252 0.678 0.141 0.055 157 15.7 049 lh.ROIIFG.label 8782 6029 17528 2.482 0.629 0.148 0.061 146 19.7 067 lh.ROIIFG.label 7738 5326 14518 2.367 0.573 0.141 0.057 154 16.2

If you are interested in the Python script I can send it to you by email (or I don't know if another method is preferred in the mailing list, as attachment or Dropbox style)

best, Gari

On 2012-09-05, at 17:43, Alexandra Tanner atanner@nmr.mgh.harvard.edu wrote:

Hi again,

This is a follow-up question to my previous email -- the method I used may not be the most efficient or the correct way to extract cortical thickness from manually created ROIs. I'm unfamiliar with how to obtain thickness data from a label, so I'm not sure if what I did is correct or if first I must convert my label to volume or to an annotation file. If anyone knows a better or more accurate way to measure thickness from the ROI I'd really appreciate your advice!

Best, Alex

...

Hi Doug and Freesurfers,

I'm currently working on extracting thickness measurements from an ROI I

manually created. I created my ROI label in tksurfer and applied the label

...

to each subject I'd like to extract thickness data from using mri_label2label. I then used the following command to generate a stats

file, with the thickness measurement, from my label:

...

mris_anatomical_stats -f something.stats -l something.label subjid

?h

...

(http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit).

This generated a stats file that gave me the average thickness for my

ROI

...

in my subject. I was wondering if there is a way to run the same

command,

...

but on multiple subjects at once, so as not to have to run this command

on

...

each individual subject. Any suggestions would be greatly appreciated!

Best, Alex _______________________________________________ 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.