Hi Doug, Turns out the kvlQuantifyHippocampalSubfieldSegmentations.sh was crashing before it got a chance to write the summary files. It crashed after trying to go into fsaverage/mri. I edited the file to specifically only go into my current study folders (they all have a common prefix), and then the script worked and generated the 2 summary files.
Best wishes, Sal On Tue, Aug 6, 2013 at 12:40 PM, Salil Soman <[email protected]> wrote: > I can add that after running "kvlQuantifyHippocampalSubfield > Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt > and nonPartialVolumeStatsRigt.txt files mentioned on the tutorial page: > > http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation > > I only have the volumeStats_left.txt and volumeStats_right.txt files in > the mri subdirectory. > > Again, any pointers on how to generate group stats into a table would be a > great help. > > Best wishes, > > Sal > > > On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman <[email protected]>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 < >> [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 >> > > > > -- > 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 > -- 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
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