Thank you for the response Lee! I was able to locate all the files now. To extract the perirhinal cortex from rh.BA_exvivo.annot, would I just use mri_annotation2label command?
On Thu, Sep 17, 2015 at 3:43 PM, Lee Tirrell <ltirr...@nmr.mgh.harvard.edu> wrote: > Hi Priyanka, > > The cortical labels are exactly the same for wmparc.mgz and the > aparc+aseg.mgz, they just differ in how they label the subcortical > structures and white matter. It should matter which you use for masking the > cortex. > > The "_exvivo" in the label names is new to the dev version of Freesurfer, > I previously answered your question based on the output from Freesurfer > 5.3. I looked at a subject processed with dev, and it seems there are are > ?h.perirhinal_exvivo.label files in the label directory and a > ?h.BA_exvivo.stats file in the stats directory. The perirhinal cortex > should also be included in the ?h.BA_exvivo.annot files. > > If the stats file is missing, you can extact them from the > ?h.BA_exvivo.annot files using the following commands: > > cd $SUBJECTS_DIR/subject_name/label > mris_anatomical_stats -mgz -f ../stats/lh.BA_exvivo.stats -b -a > ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab subject_name lh white > mris_anatomical_stats -mgz -f ../stats/rh.BA_exvivo.stats -b -a > ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab subject_name rh white > > Also, if this doesn't work, I can send you the perirhinal label from > fsaverage, and you can map this to your subject using mri_label2label. > > Best, > Lee > > > > > On Thu, 10 Sep 2015, Priyanka Mehta wrote: > > Correction in the previous message: I need to mask the functional images >> (EPI) for further analysis. >> >> On Wed, Sep 9, 2015 at 11:56 PM, Priyanka Mehta < >> priyankamehta0...@gmail.com> wrote: >> Thank you for the explanation Lee. >> I need to use the cortical labels for masking the T1 for further >> analysis. Which file should I be using then - wmparc.mgz or aparc+aseg.mgz? >> >> For the perirhinal cortex, I do not have the following files even after >> running recon-all >> <subject>/label/lh.BA.annot >> <subject>/label/rh.BA.annot >> >> <subject>/stats/lh.BA.stats >> <subject>/stats/rh.BA.stats >> >> Instead I have these files (The .stats files are missing): >> <subject>/label/lh.BA_exvivo.annot >> <subject>/label/rh.BA_exvivo.annot >> >> Your help is greatly appreciated! >> >> Priyanka Mehta >> >> >> On Thu, Sep 3, 2015 at 12:22 PM, Lee Tirrell < >> ltirr...@nmr.mgh.harvard.edu> wrote: >> Hi Priyanka, >> >> The cortical labels are the same for wmparc.mgz and aparc+aseg.mgz >> (taken from the ?h.aparc.annot files), but they differ on the way the white >> matter is labeled. The aparc+aseg uses the white matter and subcortical >> labels from the aseg.mgz, while the wmparc labels each point in the >> white matter as the nearest cortical label to that point, as well as the >> subcortical labels from the aseg. >> >> The perirhinal cortex isn't included in the aparc, so it isn't in >> either of these mgz files. However, it is included in the Brodmann area >> annotation files, and stats are computed for this region automatically when >> you run recon-all: >> >> <subject>/label/lh.BA.annot >> <subject>/label/rh.BA.annot >> >> <subject>/stats/lh.BA.stats >> <subject>/stats/rh.BA.stats >> >> >> To see this on the inflated left hemisphere, for example, you can >> run: >> >> freeview -f subject/surf/lh.inflated:annot=subject/label/lh.BA.annot >> >> Best, >> Lee >> >> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote: >> >> Hi Lee >> >> Thank you for your response. >> I have a follow up question- After running recon-all -all, I >> found the parahippocampal cortex and entorhinal cortex under two files- >> wmparc.mgz and aparc+ages.mgz. What is the difference between the two? >> Also, I haven't been able to find perirhinal cortex under any >> of the files. I wonder why? >> >> >> >> On Mon, Aug 3, 2015 at 5:22 PM, Lee Tirrell < >> ltirr...@nmr.mgh.harvard.edu> wrote: >> Hi Priyanka, >> >> These are all automatically created automatically by >> running recon-all -all. >> >> Best, >> Lee >> >> On Sat, 1 Aug 2015, Priyanka Mehta wrote: >> >> Hi >> Please excuse my extremely basic question. >> >> I would like to perform segmentation on my T1 >> image to obtain the following: >> >> a. Entorhinal Cortex >> >> b. Perirhinal Cortex >> >> c. Parahippocampal Cortex >> >> Is there a specific command I should be using in >> the 6.0 dev version? Or should I just be using recon-all -all ? >> >> Best, >> Priyanka Mehta >> >> >> >> _______________________________________________ >> 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. 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