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 <[email protected]>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 >> <[email protected]<mailto: >> [email protected].**edu <[email protected]>>> 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 > [email protected] > Phone Number: 617-724-2358 > Fax: 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<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/ <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<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
_______________________________________________ Freesurfer mailing list [email protected] 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.
