Hi Sal, when you run kvlQuantifyHippocampalSubfieldSegmentations.sh, two things happen: 1. First, the script goes subject by subject and creates the files you mentioned (volumeStats_X.txt). 2. Goes along those files and combines the outputs into a single table which you can find in two files: "nonPartialVolumeStatsLeft.txt" and "nonPartialVolumeStatsRight.txt" If you're sure that those files haven't been written, please send me the output from kvlQuantifyHippocampalSubfieldSegmentations.sh and I'll take a look Cheers, /Eugenio
On 08/06/2013 04:12 PM, Douglas N Greve wrote:
I actually have not used the hipposubfields yet, so I'm not familiar with the output. If it is the same format as the aseg.stats file, then you can use asegstats2table. Maybe Eugenio knows. doug
On 08/06/2013 03:33 PM, Salil Soman wrote:
Hi Doug,
I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh
It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group?
Thank you for all your help.
Sal
On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, you are right. I had thought that they generated a single file with the segmentations. In this case, you will need to threshold at some value of the posterior probability. Alternatively, you could generate a segmentation file by selecting the seg at a voxel that has the highest post prob using mri_concat with the --max-index-prune option. You'd then create your own LUT and run mri_segstats using the seg volume and the LUT doug On 08/06/2013 03:09 PM, Salil Soman wrote: On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: mri/hippsubfieldseg.mgz Thank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields: posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-Cortex.mgz posterior_Right-Cerebral-White-Matter.mgz posterior_Right-Hippocampus.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_fissure.mgz posterior_left_presubiculum.mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_fissure.mgz posterior_right_presubiculum.mgz posterior_right_subiculum.mgz If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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.-- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System