Re: [Freesurfer] Segmentation in dev version
cd $SUBJECTS_DIR/$subject/mri
set hemi=lh
mri_label2vol --labe ${hemi}.perirhinal_exvivo.thresh.label \
--regheader \
../mri/norm.mgz \
--fill-ribbon \
--subject $subject \
--hemi $hemi \
--o ${hemi}.peri.nii.gz
should do the trick
cheers
Bruce
On Thu, 24 Sep 2015,
Priyanka Mehta wrote:
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
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
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 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
/label/lh.BA.annot
/label/rh.BA.annot
/stats/lh.BA.stats
/stats/rh.BA.stats
Instead I have these files (The .stats
files are missing):
/label/lh.BA_exvivo.annot
/label/rh.BA_exvivo.annot
Your help is greatly appreciated!
Priyanka Mehta
On Thu, Sep 3, 2015 at 12:22 PM, Lee
Tirrell 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 subc
Re: [Freesurfer] Segmentation in dev version
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 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 >> /label/lh.BA.annot >> /label/rh.BA.annot >> >> /stats/lh.BA.stats >> /stats/rh.BA.stats >> >> Instead I have these files (The .stats files are missing): >> /label/lh.BA_exvivo.annot >> /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: >> >> /label/lh.BA.annot >> /label/rh.BA.annot >> >> /stats/lh.BA.stats >> /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- Afte
Re: [Freesurfer] Segmentation in dev version
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 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 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 /label/lh.BA.annot /label/rh.BA.annot /stats/lh.BA.stats /stats/rh.BA.stats Instead I have these files (The .stats files are missing): /label/lh.BA_exvivo.annot /label/rh.BA_exvivo.annot Your help is greatly appreciated! Priyanka Mehta On Thu, Sep 3, 2015 at 12:22 PM, Lee Tirrell 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: /label/lh.BA.annot /label/rh.BA.annot /stats/lh.BA.stats /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 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 Ple
Re: [Freesurfer] Segmentation in dev version
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 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 >> /label/lh.BA.annot >> /label/rh.BA.annot >> >> /stats/lh.BA.stats >> /stats/rh.BA.stats >> >> Instead I have these files (The .stats files are missing): >> /label/lh.BA_exvivo.annot >> /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: >> >> /label/lh.BA.annot >> /label/rh.BA.annot >> >> /stats/lh.BA.stats >> /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.ha
Re: [Freesurfer] Segmentation in dev version
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 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 /label/lh.BA.annot /label/rh.BA.annot /stats/lh.BA.stats /stats/rh.BA.stats Instead I have these files (The .stats files are missing): /label/lh.BA_exvivo.annot /label/rh.BA_exvivo.annot Your help is greatly appreciated! Priyanka Mehta On Thu, Sep 3, 2015 at 12:22 PM, Lee Tirrell 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: /label/lh.BA.annot /label/rh.BA.annot /stats/lh.BA.stats /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 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. 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.
Re: [Freesurfer] Segmentation in dev version
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 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 > /label/lh.BA.annot > /label/rh.BA.annot > > /stats/lh.BA.stats > /stats/rh.BA.stats > > Instead I have these files (The .stats files are missing): > /label/lh.BA_exvivo.annot > /label/rh.BA_exvivo.annot > > Your help is greatly appreciated! > > Priyanka Mehta > > > On Thu, Sep 3, 2015 at 12:22 PM, Lee Tirrell > 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: >> >> /label/lh.BA.annot >> /label/rh.BA.annot >> >> /stats/lh.BA.stats >> /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. 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. >>> >>> >>> >>> >> ___ >> 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. 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. >> >> > ___ 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. 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.
Re: [Freesurfer] Segmentation in dev version
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 /label/lh.BA.annot /label/rh.BA.annot /stats/lh.BA.stats /stats/rh.BA.stats Instead I have these files (The .stats files are missing): /label/lh.BA_exvivo.annot /label/rh.BA_exvivo.annot Your help is greatly appreciated! Priyanka Mehta On Thu, Sep 3, 2015 at 12:22 PM, Lee Tirrell 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: > > /label/lh.BA.annot > /label/rh.BA.annot > > /stats/lh.BA.stats > /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 >> 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. 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. >> >> >> >> > ___ > 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. 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. > > ___ 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. 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.
Re: [Freesurfer] Segmentation in dev version
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: /label/lh.BA.annot /label/rh.BA.annot /stats/lh.BA.stats /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 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. 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. ___ 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. 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.
Re: [Freesurfer] Segmentation in dev version
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 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. 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. > > ___ 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. 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.
Re: [Freesurfer] Segmentation in dev version
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. 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.
[Freesurfer] Segmentation in dev version
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. 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.
