Hi again, I do have the following files in the label directory:
lh.perirhinal_exvivo.label lh.perirhinal_exvivo.thresh.label rh.perirhinal_exvivo.label rh.perirhinal_exvivo.thresh.label I want to get the right perirhinal cortex in the .nii format for further analysis. How can I get that? Thanks, Priyanka On Thu, Sep 24, 2015 at 11:54 AM, Lee Tirrell <ltirr...@nmr.mgh.harvard.edu> wrote: > Hi Priyanka, > > I believe there should already be a perirhinal label created (the > ?h.BA_exvivo.annot is created by combining together a few labels). > > Try seeing if these files exist with this command (replacing subject_name > with your subject): > ls $SUBJECTS_DIR/subject_name/label/*perirhinal*.label > > If no files exist, I can send you the command or files necessary. > > Best, > Lee > > > On Thu, 24 Sep 2015, Priyanka Mehta wrote: > > 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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