Dear freesurfer experts,
I am working on a project on cortical asymmetry and I have analyzed vertex-wise cortical thickness/surface area asymmetry. However, I noticed that Freesurfer doesn't not seem to facilitate such analysis for gray matter volume, as after running surfreg -xhemi there is no ?h.volume file in subject/xhemi/surf. I searched the literature and found studies on gray matter density asymmetry with VBM and ROI-based volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise volume asymmetry analysis? And may I know the rationale?
Thanks, Cherry
There should be a ?h.volume file. Are you sure there is not? You can specify -meas volume when you run mris_preproc doug
On 04/27/2014 08:35 PM, Yizhou Ma wrote:
Dear freesurfer experts,
I am working on a project on cortical asymmetry and I have analyzed vertex-wise cortical thickness/surface area asymmetry. However, I noticed that Freesurfer doesn't not seem to facilitate such analysis for gray matter volume, as after running surfreg -xhemi there is no ?h.volume file in subject/xhemi/surf. I searched the literature and found studies on gray matter density asymmetry with VBM and ROI-based volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise volume asymmetry analysis? And may I know the rationale?
Thanks, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug. I have ?h.volume in subject/surf but not in subject/xhemi/surf. I followed this page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem with surfreg rather than mris_preproc. Can I just copy the ?h.volume from subject/surf to subject/xhemi/surf?
Best, Cherry
On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
There should be a ?h.volume file. Are you sure there is not? You can specify -meas volume when you run mris_preproc doug
On 04/27/2014 08:35 PM, Yizhou Ma wrote:
Dear freesurfer experts,
I am working on a project on cortical asymmetry and I have analyzed vertex-wise cortical thickness/surface area asymmetry. However, I noticed that Freesurfer doesn't not seem to facilitate such analysis for gray matter volume, as after running surfreg -xhemi there is no ?h.volume file in subject/xhemi/surf. I searched the literature and found studies on gray matter density asymmetry with VBM and ROI-based volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise volume asymmetry analysis? And may I know the rationale?
Thanks, Cherry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
Then something went wrong along the way. Check the xhemi/xhemireg.?h.log to see if there is an error. If not, send the log file to me
On 04/28/2014 04:14 PM, Yizhou Ma wrote:
Thanks Doug. I have ?h.volume in subject/surf but not in subject/xhemi/surf. I followed this page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem with surfreg rather than mris_preproc. Can I just copy the ?h.volume from subject/surf to subject/xhemi/surf?
Best, Cherry
On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
There should be a ?h.volume file. Are you sure there is not? You can specify -meas volume when you run mris_preproc doug On 04/27/2014 08:35 PM, Yizhou Ma wrote: > Dear freesurfer experts, > > I am working on a project on cortical asymmetry and I have analyzed > vertex-wise cortical thickness/surface area asymmetry. However, I > noticed that Freesurfer doesn't not seem to facilitate such analysis > for gray matter volume, as after running surfreg -xhemi there is no > ?h.volume file in subject/xhemi/surf. I searched the literature and > found studies on gray matter density asymmetry with VBM and ROI-based > volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise > volume asymmetry analysis? And may I know the rationale? > > Thanks, > Cherry > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please see attached for the files.
On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Then something went wrong along the way. Check the xhemi/xhemireg.?h.log to see if there is an error. If not, send the log file to me
On 04/28/2014 04:14 PM, Yizhou Ma wrote:
Thanks Doug. I have ?h.volume in subject/surf but not in subject/xhemi/surf. I followed this page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem with surfreg rather than mris_preproc. Can I just copy the ?h.volume from subject/surf to subject/xhemi/surf?
Best, Cherry
On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
There should be a ?h.volume file. Are you sure there is not? You can specify -meas volume when you run mris_preproc doug On 04/27/2014 08:35 PM, Yizhou Ma wrote: > Dear freesurfer experts, > > I am working on a project on cortical asymmetry and I have analyzed > vertex-wise cortical thickness/surface area asymmetry. However, I > noticed that Freesurfer doesn't not seem to facilitate suchanalysis
> for gray matter volume, as after running surfreg -xhemi there is no > ?h.volume file in subject/xhemi/surf. I searched the literature and > found studies on gray matter density asymmetry with VBM and ROI-based > volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise > volume asymmetry analysis? And may I know the rationale? > > Thanks, > Cherry > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I just read from the .log files that the lh.thickness/area/pial/... files in subject/xhemi/surf are copied from subject/surf at the end of the command. Thus it seems that I can just copy lh.volume, too?
Thanks, Cherry
On Mon, Apr 28, 2014 at 6:25 PM, Yizhou Ma ym850@nyu.edu wrote:
Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please see attached for the files.
On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Then something went wrong along the way. Check the xhemi/xhemireg.?h.log to see if there is an error. If not, send the log file to me
On 04/28/2014 04:14 PM, Yizhou Ma wrote:
Thanks Doug. I have ?h.volume in subject/surf but not in subject/xhemi/surf. I followed this page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem with surfreg rather than mris_preproc. Can I just copy the ?h.volume from subject/surf to subject/xhemi/surf?
Best, Cherry
On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
There should be a ?h.volume file. Are you sure there is not? You can specify -meas volume when you run mris_preproc doug On 04/27/2014 08:35 PM, Yizhou Ma wrote: > Dear freesurfer experts, > > I am working on a project on cortical asymmetry and I haveanalyzed
> vertex-wise cortical thickness/surface area asymmetry. However, I > noticed that Freesurfer doesn't not seem to facilitate suchanalysis
> for gray matter volume, as after running surfreg -xhemi there isno
> ?h.volume file in subject/xhemi/surf. I searched the literatureand
> found studies on gray matter density asymmetry with VBM and ROI-based > volume asymmetry. Is it true that Freesurfer doesn't offer vertex-wise > volume asymmetry analysis? And may I know the rationale? > > Thanks, > Cherry > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
OK, you're using an older version that did not copy the volume. You can just do this
cp subject/surf/lh.volume subject/surf/rh.volume
Note the change from lh to rh!
doug
On 04/28/2014 06:25 PM, Yizhou Ma wrote:
Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please see attached for the files.
On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Then something went wrong along the way. Check the xhemi/xhemireg.?h.log to see if there is an error. If not, send the log file to me On 04/28/2014 04:14 PM, Yizhou Ma wrote: > Thanks Doug. I have ?h.volume in subject/surf but not in > subject/xhemi/surf. I followed this page > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a > problem with surfreg rather than mris_preproc. Can I just copy the > ?h.volume from subject/surf to subject/xhemi/surf? > > Best, > Cherry > > > On Mon, Apr 28, 2014 at 4:01 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > > There should be a ?h.volume file. Are you sure there is not? You can > specify -meas volume when you run mris_preproc > doug > > On 04/27/2014 08:35 PM, Yizhou Ma wrote: > > Dear freesurfer experts, > > > > I am working on a project on cortical asymmetry and I have analyzed > > vertex-wise cortical thickness/surface area asymmetry. However, I > > noticed that Freesurfer doesn't not seem to facilitate such analysis > > for gray matter volume, as after running surfreg -xhemi there is no > > ?h.volume file in subject/xhemi/surf. I searched the literature and > > found studies on gray matter density asymmetry with VBM and > ROI-based > > volume asymmetry. Is it true that Freesurfer doesn't offer > vertex-wise > > volume asymmetry analysis? And may I know the rationale? > > > > Thanks, > > Cherry > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: 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> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel: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 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Douglas N Greve -
Yizhou Ma