hmmm, no idea. Can you send me the recon-all.log file for that subject? On Tue, 13 Oct 2009, Angel Wong wrote:
> Hi Bruce > > I have downloaded the latest version (v4.5.0) and tried again. But > unfortunately, I cannot reproduce the results same as yours. The new > generated results are similar to the results generated by the older version. > The command I used is > > recon-all -i <directory that contains COR files> -s <subjectid> -sd > <subjects_dir> -all > > and I viewed the images using > > tkmedit <subjectid> brainmask.mgz lh.white -aux-surface rh.white > > I am wondering why there is a big difference between your results and mine. > Is there any pre-setting needed before running the recon-all or additional > arguments needed during the processing? > > Cheers > Angel > > 2009/10/11 Angel Wong <angel.del...@gmail.com> > >> Hi Nick >> >> Thanks for your suggestion. I will look at it in detail later. >> >> Angel >> >> 2009/10/10 Nick Schmansky <ni...@nmr.mgh.harvard.edu> >> >> Angel, >>> >>> I noticed you have problems with some remaining dura in your images. you >>> might want to try a new utility that is being tested for inclusion in a >>> future release. Its from a group in Singapore, and does a good job >>> removing dura. Its called: >>> >>> mri_gcut >>> >>> and can be downloaded for the linux and mac platforms from here: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/ >>> >>> copy it to your $FREESURFER_HOME/bin >>> >>> usage (with reference to paper) is found in: >>> >>> mri_gcut --help >>> >>> and intended usage is: >>> >>> cd subjid/mri >>> mri_gcut -110 -mult brainmask.mgz T1.mgz brainmask.mgz >>> >>> then run: >>> >>> recon-all -s subjid -autorecon2 -autorecon3 >>> >>> but of course inspect the brainmask.mgz to see if actually helped. >>> >>> (bruce, can you point me at her image? i can run it locally) >>> >>> Nick >>> >>> On Sat, 2009-10-10 at 21:46 +0800, Angel Wong wrote: >>>> My version is 4.3.0. I will download the latest version and try again. >>>> >>>> Thank you. >>>> >>>> 2009/10/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>> I didn't do anything but run recon-all with the latest >>>> version. Remind me what version you were running? >>>> >>>> >>>> On Sat, 10 Oct 2009, Angel Wong wrote: >>>> >>>> Hi Bruce >>>> >>>> Thank you very much. The result looks much better than >>>> mine. How did you do >>>> that? Please let me know so that I can modify the >>>> other datasets if I face >>>> the same situation again. >>>> >>>> Cheers >>>> Angel >>>> >>>> 2009/10/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >>>> >>>> Hi Angel, >>>> >>>> I'm just about done running the dataset and >>>> the results actually look ok >>>> (see attached tif). I didn't intervene at all, >>>> although you would want to to >>>> get rid of some non-brain tissue that the pial >>>> surface is grabbing, but >>>> that's pretty easy. Did you minimize your TE? >>>> I don't know what your >>>> gradient set is, but usually you can get your >>>> TE down a bit more than that. >>>> You also might be better off sacrificing a bit >>>> of resolution and lengthening >>>> your TR >>>> cheers, >>>> Bruce >>>> >>>> >>>> On Thu, 8 Oct 2009, Angel Wong wrote: >>>> >>>> Thanks a lot with your help. This is because >>>> we want to perform quite a >>>> number of functional runs on the same >>>> subject at the same session. So we >>>> tried to shorten the T1 scan time to >>>> minimize the motion artifacts come >>>> from >>>> the subject. >>>> >>>> Attached please find the orig.mgz for >>>> your information. >>>> >>>> 2009/10/8 Bruce Fischl >>>> <fis...@nmr.mgh.harvard.edu> >>>> >>>> I see. Your TR is quite short and >>>> your TE relatively long, so this is >>>> probably pretty poor CNR >>>> between gray and white. If you >>>> send me the >>>> orig.mgz >>>> I'll take a look and see if >>>> it's fixable >>>> >>>> On Thu, 8 Oct 2009, Angel Wong >>>> wrote: >>>> >>>> Hi Bruce >>>> >>>> >>>> Attached please find >>>> the parameters for >>>> acquiring the T1 >>>> image. >>>> >>>> Thank you for your >>>> help. >>>> >>>> Angel >>>> >>>> 2009/10/8 Bruce Fischl >>>> < >>> fis...@nmr.mgh.harvard.edu> >>>> >>>> eek, that looks >>>> pretty bad. Can you >>>> tell us what the >>>> acquisition >>>> >>>> parameters >>>> are? >>>> >>>> On Thu, 8 Oct >>>> 2009, Angel >>>> Wong wrote: >>>> >>>> Dear all >>>> >>>> >>>> >>>> >>>> Actually >>> I would like to perform automated reconstruction for my T1 >>>> image >>>> and >>>> then >>>> obtain >>>> >>> anatomical labels after cortical parcellation. I have >>>> done >>>> fully >>>> >>> automated reconstruction using recon-all. But for my case, the >>>> white >>>> and >>>> grey >>>> matter >>>> >>> segmentation appears to be weird. The green line seems >>>> laying >>>> on the >>>> pial >>>> surface >>> rather than on the white surface, and the >>>> red >>>> line >>>> seems >>>> >>> including some non-brain structures (including small >>>> portion >>>> of >>>> CSF >>>> and >>>> skull). >>> Thus, the resultant cortical thickness appears to be >>>> very >>>> thin >>>> after >>>> the >>>> >>> segmentation. I just doubt if anything was going wrong >>>> during >>>> the >>>> >>> procedure. Or need any preprocessing to enhance the segmentation >>>> quality >>>> before >>>> >>> performing the reconstruction? If you have had similar >>>> >>> situation >>>> as >>>> mine, >>>> please >>>> let me >>>> know >>>> how to >>>> tackle >>>> the >>>> problem. >>>> >>>> Attached >>> please find the images for better illustration. >>>> >>>> >>> fs_image_brain.tiff - use brain.mgz as aux volume >>>> >>> fs_image_norm.tiff - use norm.mgz as aux volume >>>> >>> fs_image_brainmask.tiff - use brainmask.mgz as aux volume and load >>>> >>> segmentation file aseg.mgz >>>> >>>> Thanks >>>> Angel >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
