Hello,
I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though.
1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is larger"?
2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions?
3) I've noticed from the archives that some people are performing laterality indices. How would I calculate laterality indices?
Thanks! Krista
Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2
doug
On 12/08/2013 08:45 PM, krista kelly wrote:
Hello,
I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though.
- When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?
- I have no idea how to view the results in tksurfer AFTER performing
the step of correcting for multiple comparisons. Any suggestions?
- I've noticed from the archives that some people are performing
laterality indices. How would I calculate laterality indices?
Thanks! Krista
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug! I'll try that instead.
Also, do you or anyone else happen to have the answers to my other questions (reposted below):
1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is larger"?
2) I have no idea how to view the results in tksurfer AFTER performing the step of correcting for multiple comparisons. Any suggestions?
Thanks! Krista
On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2
doug
On 12/08/2013 08:45 PM, krista kelly wrote:
Hello,
I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though.
- When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?
- I have no idea how to view the results in tksurfer AFTER performing
the step of correcting for multiple comparisons. Any suggestions?
- I've noticed from the archives that some people are performing
laterality indices. How would I calculate laterality indices?
Thanks! Krista
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
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.
On 12/09/2013 11:53 AM, krista kelly wrote:
Thanks Doug! I'll try that instead.
Also, do you or anyone else happen to have the answers to my other questions (reposted below):
- When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?
If you are just doing a simple interhemispheric difference, then yellow/red will be left>right and blue left<right
- I have no idea how to view the results in tksurfer AFTER performing
the step of correcting for multiple comparisons. Any suggestions?
If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh )
doug
Thanks! Krista
On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: > Hello, > > I'm analysing interhemispheric differences using xhemi. I have > followed the instructions on the webpage with no problems. I do have a > few questions though. > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which represents "right hemisphere is larger"? > > 2) I have no idea how to view the results in tksurfer AFTER performing > the step of correcting for multiple comparisons. Any suggestions? > > 3) I've noticed from the archives that some people are performing > laterality indices. How would I calculate laterality indices? > > Thanks! > Krista > > > > > _______________________________________________ > 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
Great Thanks!
On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
On 12/09/2013 11:53 AM, krista kelly wrote:
Thanks Doug! I'll try that instead.
Also, do you or anyone else happen to have the answers to my other questions (reposted below):
- When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?
If you are just doing a simple interhemispheric difference, then yellow/red will be left>right and blue left<right
- I have no idea how to view the results in tksurfer AFTER performing
the step of correcting for multiple comparisons. Any suggestions?
If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh )
doug
Thanks! Krista
On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: > Hello, > > I'm analysing interhemispheric differences using xhemi. I have > followed the instructions on the webpage with no problems. I do have a > few questions though. > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which represents "right hemisphere is larger"? > > 2) I have no idea how to view the results in tksurfer AFTER performing > the step of correcting for multiple comparisons. Any suggestions? > > 3) I've noticed from the archives that some people are performing > laterality indices. How would I calculate laterality indices? > > Thanks! > Krista > > > > > _______________________________________________ > 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 again,
I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache..... Are these the files I should be overlaying? Or should I be using different commands for my analyses?
here is the command line I used:
mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs
Prior to mri_glmfit, I conducted the "create a stack of subjects" using paired-diff-norm in place of paired-diff
Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately.
I would also like to see if laterality indices differ between groups. Is this possible?
Thanks! Krista
On Mon, Dec 9, 2013 at 4:00 PM, krista kelly krista.kelly16@gmail.comwrote:
Great Thanks!
On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
On 12/09/2013 11:53 AM, krista kelly wrote:
Thanks Doug! I'll try that instead.
Also, do you or anyone else happen to have the answers to my other questions (reposted below):
- When viewing the results in tksurfer, which color represents "left
hemisphere is larger" and which represents "right hemisphere is larger"?
If you are just doing a simple interhemispheric difference, then yellow/red will be left>right and blue left<right
- I have no idea how to view the results in tksurfer AFTER performing
the step of correcting for multiple comparisons. Any suggestions?
If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh )
doug
Thanks! Krista
On Mon, Dec 9, 2013 at 11:09 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: > Hello, > > I'm analysing interhemispheric differences using xhemi. I have > followed the instructions on the webpage with no problems. I do have a > few questions though. > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which represents "right hemisphere is larger"? > > 2) I have no idea how to view the results in tksurfer AFTER performing > the step of correcting for multiple comparisons. Any suggestions? > > 3) I've noticed from the archives that some people are performing > laterality indices. How would I calculate laterality indices? > > Thanks! > Krista > > > > > _______________________________________________ > 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
Yes, use the cache files. When "--cache" is used, the csdbase="cache"
On 12/10/2013 12:20 PM, krista kelly wrote:
Hi again,
I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache..... Are these the files I should be overlaying? Or should I be using different commands for my analyses?
here is the command line I used:
mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs
Prior to mri_glmfit, I conducted the "create a stack of subjects" using paired-diff-norm in place of paired-diff
Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately.
I would also like to see if laterality indices differ between groups. Is this possible?
Thanks! Krista
On Mon, Dec 9, 2013 at 4:00 PM, krista kelly <krista.kelly16@gmail.com mailto:krista.kelly16@gmail.com> wrote:
Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 12/09/2013 11:53 AM, krista kelly wrote: > Thanks Doug! I'll try that instead. > > Also, do you or anyone else happen to have the answers to my other > questions (reposted below): > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which represents "right hemisphere is larger"? If you are just doing a simple interhemispheric difference, then yellow/red will be left>right and blue left<right > > 2) I have no idea how to view the results in tksurfer AFTER performing > the step of correcting for multiple comparisons. Any suggestions? If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh ) doug > > Thanks! > Krista > > > > > On Mon, Dec 9, 2013 at 11:09 AM, 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: > > Run mris_preproc with --paired-diff-norm which will then compute > LI = (L-R)/(.5*(L+R)) > Note that some people use > LI = (L-R)/(L+R) > If that is what you want, then divide the mris_preproc result by 2 > > doug > > On 12/08/2013 08:45 PM, krista kelly wrote: > > Hello, > > > > I'm analysing interhemispheric differences using xhemi. I have > > followed the instructions on the webpage with no problems. I do > have a > > few questions though. > > > > 1) When viewing the results in tksurfer, which color represents > "left > > hemisphere is larger" and which represents "right hemisphere is > larger"? > > > > 2) I have no idea how to view the results in tksurfer AFTER > performing > > the step of correcting for multiple comparisons. Any suggestions? > > > > 3) I've noticed from the archives that some people are performing > > laterality indices. How would I calculate laterality indices? > > > > Thanks! > > Krista > > > > > > > > > > _______________________________________________ > > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
great thanks Doug!
Is there any way to analyze group differences with xhemi? I can get the laterality indices per group, but I'd like to do a whole brain analyses looking at group differences in laterality indices.
Thanks, Krista
On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Yes, use the cache files. When "--cache" is used, the csdbase="cache"
On 12/10/2013 12:20 PM, krista kelly wrote:
Hi again,
I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache..... Are these the files I should be overlaying? Or should I be using different commands for my analyses?
here is the command line I used:
mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs
Prior to mri_glmfit, I conducted the "create a stack of subjects" using paired-diff-norm in place of paired-diff
Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately.
I would also like to see if laterality indices differ between groups. Is this possible?
Thanks! Krista
On Mon, Dec 9, 2013 at 4:00 PM, krista kelly <krista.kelly16@gmail.com mailto:krista.kelly16@gmail.com> wrote:
Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
On 12/09/2013 11:53 AM, krista kelly wrote: > Thanks Doug! I'll try that instead. > > Also, do you or anyone else happen to have the answers to my other > questions (reposted below): > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which represents "right hemisphere is larger"? If you are just doing a simple interhemispheric difference, then yellow/red will be left>right and blue left<right > > 2) I have no idea how to view the results in tksurfer AFTER performing > the step of correcting for multiple comparisons. Any suggestions? If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh ) doug > > Thanks! > Krista > > > > > On Mon, Dec 9, 2013 at 11:09 AM, 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: > > Run mris_preproc with --paired-diff-norm which will then compute > LI = (L-R)/(.5*(L+R)) > Note that some people use > LI = (L-R)/(L+R) > If that is what you want, then divide the mris_preproc result by 2 > > doug > > On 12/08/2013 08:45 PM, krista kelly wrote: > > Hello, > > > > I'm analysing interhemispheric differences using xhemi. I have > > followed the instructions on the webpage with no problems. I do > have a > > few questions though. > > > > 1) When viewing the results in tksurfer, which color represents > "left > > hemisphere is larger" and which represents "right hemisphere is > larger"? > > > > 2) I have no idea how to view the results in tksurfer AFTER > performing > > the step of correcting for multiple comparisons. Any suggestions? > > > > 3) I've noticed from the archives that some people are performing > > laterality indices. How would I calculate laterality indices? > > > > Thanks! > > Krista > > > > > > > > > > _______________________________________________ > > 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 contactthe
> 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, 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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Just wanted to repost this in case anyone else can give some advice. Thanks!
Is there any way to analyze group differences with xhemi? I can get the laterality indices per group, but I'd like to do a whole brain analyses looking at group differences in laterality indices.
Thanks, Krista
On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Yes, use the cache files. When "--cache" is used, the csdbase="cache"
On 12/10/2013 12:20 PM, krista kelly wrote:
Hi again,
I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones that begin with cache..... Are these the files I should be overlaying? Or should I be using different commands for my analyses?
here is the command line I used:
mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ --cwpvalthresh .5 --cache 2 abs
Prior to mri_glmfit, I conducted the "create a stack of subjects" using paired-diff-norm in place of paired-diff
Ultimately, I want to look at hemisphere asymmetries (preferably in terms of laterality indices) in two different groups separately.
I would also like to see if laterality indices differ between groups. Is this possible?
Thanks! Krista
On Mon, Dec 9, 2013 at 4:00 PM, krista kelly <krista.kelly16@gmail.com mailto:krista.kelly16@gmail.com> wrote:
Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
On 12/09/2013 11:53 AM, krista kelly wrote: > Thanks Doug! I'll try that instead. > > Also, do you or anyone else happen to have the answers to my other > questions (reposted below): > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which represents "right hemisphere is larger"? If you are just doing a simple interhemispheric difference, then yellow/red will be left>right and blue left<right > > 2) I have no idea how to view the results in tksurfer AFTER performing > the step of correcting for multiple comparisons. Any suggestions? If you run mri_glmfit-sim with --help you will see a list of output files with descriptions for each. Choose the one you want and run tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc -overlay csdbase.sig.cluster.mgh ) doug > > Thanks! > Krista > > > > > On Mon, Dec 9, 2013 at 11:09 AM, 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: > > Run mris_preproc with --paired-diff-norm which will then compute > LI = (L-R)/(.5*(L+R)) > Note that some people use > LI = (L-R)/(L+R) > If that is what you want, then divide the mris_preproc result by 2 > > doug > > On 12/08/2013 08:45 PM, krista kelly wrote: > > Hello, > > > > I'm analysing interhemispheric differences using xhemi. I have > > followed the instructions on the webpage with no problems. I do > have a > > few questions though. > > > > 1) When viewing the results in tksurfer, which color represents > "left > > hemisphere is larger" and which represents "right hemisphere is > larger"? > > > > 2) I have no idea how to view the results in tksurfer AFTER > performing > > the step of correcting for multiple comparisons. Any suggestions? > > > > 3) I've noticed from the archives that some people are performing > > laterality indices. How would I calculate laterality indices? > > > > Thanks! > > Krista > > > > > > > > > > _______________________________________________ > > 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 contactthe
> 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
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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yes, it is just like a "normal" group analysis. You create a stack of LI maps, one for each subject, create an FSGD file, run mri_glmfit, then mri_glmfit-sim.
doug
On 01/13/2014 06:22 PM, krista kelly wrote:
Just wanted to repost this in case anyone else can give some advice. Thanks!
Is there any way to analyze group differences with xhemi? I can get the laterality indices per group, but I'd like to do a whole brain analyses looking at group differences in laterality indices.
Thanks, Krista
On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes, use the cache files. When "--cache" is used, the csdbase="cache" On 12/10/2013 12:20 PM, krista kelly wrote: > Hi again, > > I've looked into mri_glmfit-sim --help to figure out which files I > could overlay in tkurfer after correcting for multiple comparisons > using the instructions for xhemi on the freesurfer wiki. However, I do > not see any of these files (csd.base...) in the glmdir/osgm folder. I > only see ones that begin with cache..... Are these the files I should > be overlaying? Or should I be using different commands for my analyses? > > here is the command line I used: > > mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ > --cwpvalthresh .5 --cache 2 abs > > Prior to mri_glmfit, I conducted the "create a stack of subjects" > using paired-diff-norm in place of paired-diff > > Ultimately, I want to look at hemisphere asymmetries (preferably in > terms of laterality indices) in two different groups separately. > > I would also like to see if laterality indices differ between groups. > Is this possible? > > Thanks! > Krista > > > On Mon, Dec 9, 2013 at 4:00 PM, krista kelly <krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com> > <mailto:krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com>>> wrote: > > Great Thanks! > > > > > On Mon, Dec 9, 2013 at 11:57 AM, 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: > > > On 12/09/2013 11:53 AM, krista kelly wrote: > > Thanks Doug! I'll try that instead. > > > > Also, do you or anyone else happen to have the answers to my > other > > questions (reposted below): > > > > 1) When viewing the results in tksurfer, which color > represents "left > > hemisphere is larger" and which represents "right hemisphere > is larger"? > If you are just doing a simple interhemispheric difference, then > yellow/red will be left>right and blue left<right > > > > 2) I have no idea how to view the results in tksurfer AFTER > performing > > the step of correcting for multiple comparisons. Any > suggestions? > > If you run mri_glmfit-sim with --help you will see a list of > output > files with descriptions for each. Choose the one you want and run > tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc > -overlay > csdbase.sig.cluster.mgh ) > > doug > > > > > Thanks! > > Krista > > > > > > > > > > On Mon, Dec 9, 2013 at 11:09 AM, 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > Run mris_preproc with --paired-diff-norm which will then > compute > > LI = (L-R)/(.5*(L+R)) > > Note that some people use > > LI = (L-R)/(L+R) > > If that is what you want, then divide the mris_preproc > result by 2 > > > > doug > > > > On 12/08/2013 08:45 PM, krista kelly wrote: > > > Hello, > > > > > > I'm analysing interhemispheric differences using > xhemi. I have > > > followed the instructions on the webpage with no > problems. I do > > have a > > > few questions though. > > > > > > 1) When viewing the results in tksurfer, which color > represents > > "left > > > hemisphere is larger" and which represents "right > hemisphere is > > larger"? > > > > > > 2) I have no idea how to view the results in tksurfer > AFTER > > performing > > > the step of correcting for multiple comparisons. Any > suggestions? > > > > > > 3) I've noticed from the archives that some people are > performing > > > laterality indices. How would I calculate laterality > indices? > > > > > > Thanks! > > > Krista > > > > > > > > > > > > > > > _______________________________________________ > > > 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>> > > <mailto: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>> > <mailto: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>> > <tel: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>> <tel: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> > > <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> > > > <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>> > <mailto: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> > <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 > > > > > > _______________________________________________ > 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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Hi Doug,
Sorry I should have specified BETWEEN groups analyses. I have two groups (control, patient) and I wanted to see if the hemisphere asymmetries (or laterality indices) differed between groups. Is there a way to do that?
Thanks for all you help! Krista
On Mon, Jan 13, 2014 at 6:25 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
yes, it is just like a "normal" group analysis. You create a stack of LI maps, one for each subject, create an FSGD file, run mri_glmfit, then mri_glmfit-sim.
doug
On 01/13/2014 06:22 PM, krista kelly wrote:
Just wanted to repost this in case anyone else can give some advice. Thanks!
Is there any way to analyze group differences with xhemi? I can get the laterality indices per group, but I'd like to do a whole brain analyses looking at group differences in laterality indices.
Thanks, Krista
On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Yes, use the cache files. When "--cache" is used, the csdbase="cache" On 12/10/2013 12:20 PM, krista kelly wrote: > Hi again, > > I've looked into mri_glmfit-sim --help to figure out which files I > could overlay in tkurfer after correcting for multiple comparisons > using the instructions for xhemi on the freesurfer wiki. However, I do > not see any of these files (csd.base...) in the glmdir/osgm folder. I > only see ones that begin with cache..... Are these the files I should > be overlaying? Or should I be using different commands for my analyses? > > here is the command line I used: > > mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ > --cwpvalthresh .5 --cache 2 abs > > Prior to mri_glmfit, I conducted the "create a stack of subjects" > using paired-diff-norm in place of paired-diff > > Ultimately, I want to look at hemisphere asymmetries (preferably in > terms of laterality indices) in two different groups separately. > > I would also like to see if laterality indices differ between groups. > Is this possible? > > Thanks! > Krista > > > On Mon, Dec 9, 2013 at 4:00 PM, krista kelly <krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com> > <mailto:krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com>>> wrote: > > Great Thanks! > > > > > On Mon, Dec 9, 2013 at 11:57 AM, 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: > > > On 12/09/2013 11:53 AM, krista kelly wrote: > > Thanks Doug! I'll try that instead. > > > > Also, do you or anyone else happen to have the answers to my > other > > questions (reposted below): > > > > 1) When viewing the results in tksurfer, which color > represents "left > > hemisphere is larger" and which represents "right hemisphere > is larger"? > If you are just doing a simple interhemispheric difference, then > yellow/red will be left>right and blue left<right > > > > 2) I have no idea how to view the results in tksurfer AFTER > performing > > the step of correcting for multiple comparisons. Any > suggestions? > > If you run mri_glmfit-sim with --help you will see a listof
> output > files with descriptions for each. Choose the one you want and run > tksurfer on it (eg, tksurfer fsaverage_sym lh inflated -aparc > -overlay > csdbase.sig.cluster.mgh ) > > doug > > > > > Thanks! > > Krista > > > > > > > > > > On Mon, Dec 9, 2013 at 11:09 AM, 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > Run mris_preproc with --paired-diff-norm which will then > compute > > LI = (L-R)/(.5*(L+R)) > > Note that some people use > > LI = (L-R)/(L+R) > > If that is what you want, then divide themris_preproc
> result by 2 > > > > doug > > > > On 12/08/2013 08:45 PM, krista kelly wrote: > > > Hello, > > > > > > I'm analysing interhemispheric differences using > xhemi. I have > > > followed the instructions on the webpage with no > problems. I do > > have a > > > few questions though. > > > > > > 1) When viewing the results in tksurfer, whichcolor
> represents > > "left > > > hemisphere is larger" and which represents "right > hemisphere is > > larger"? > > > > > > 2) I have no idea how to view the results in tksurfer > AFTER > > performing > > > the step of correcting for multiple comparisons.Any
> suggestions? > > > > > > 3) I've noticed from the archives that some people are > performing > > > laterality indices. How would I calculatelaterality
> indices? > > > > > > Thanks! > > > Krista > > > > > > > > > > > > > > > _______________________________________________ > > > 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>> > > <mailto: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> <mailto: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>> > <tel: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>> <tel: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> > > <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> > > > <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>> > <mailto: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-mailwas
> 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> > <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 > > > > > > _______________________________________________ > 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
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
There is still no difference between that and doing a regular thickness study with two groups. Were are you getting stuck? doug
On 01/17/2014 12:35 PM, krista kelly wrote:
Hi Doug,
Sorry I should have specified BETWEEN groups analyses. I have two groups (control, patient) and I wanted to see if the hemisphere asymmetries (or laterality indices) differed between groups. Is there a way to do that?
Thanks for all you help! Krista
On Mon, Jan 13, 2014 at 6:25 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
yes, it is just like a "normal" group analysis. You create a stack of LI maps, one for each subject, create an FSGD file, run mri_glmfit, then mri_glmfit-sim. doug On 01/13/2014 06:22 PM, krista kelly wrote: > > Just wanted to repost this in case anyone else can give some advice. > Thanks! > > Is there any way to analyze group differences with xhemi? I can get > the laterality indices per group, but I'd like to do a whole brain > analyses looking at group differences in laterality indices. > > Thanks, > Krista > > > On Tue, Dec 10, 2013 at 2:01 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: > > > Yes, use the cache files. When "--cache" is used, the csdbase="cache" > > On 12/10/2013 12:20 PM, krista kelly wrote: > > Hi again, > > > > I've looked into mri_glmfit-sim --help to figure out which files I > > could overlay in tkurfer after correcting for multiple comparisons > > using the instructions for xhemi on the freesurfer wiki. > However, I do > > not see any of these files (csd.base...) in the glmdir/osgm > folder. I > > only see ones that begin with cache..... Are these the files I > should > > be overlaying? Or should I be using different commands for my > analyses? > > > > here is the command line I used: > > > > mri_glmfit-sim --glmdir glm.lh.lh-rh.area.pial.sm05 \ > > --cwpvalthresh .5 --cache 2 abs > > > > Prior to mri_glmfit, I conducted the "create a stack of subjects" > > using paired-diff-norm in place of paired-diff > > > > Ultimately, I want to look at hemisphere asymmetries (preferably in > > terms of laterality indices) in two different groups separately. > > > > I would also like to see if laterality indices differ between > groups. > > Is this possible? > > > > Thanks! > > Krista > > > > > > On Mon, Dec 9, 2013 at 4:00 PM, krista kelly > <krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com> <mailto:krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com>> > > <mailto:krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com> > <mailto:krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com>>>> wrote: > > > > Great Thanks! > > > > > > > > > > On Mon, Dec 9, 2013 at 11:57 AM, 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > On 12/09/2013 11:53 AM, krista kelly wrote: > > > Thanks Doug! I'll try that instead. > > > > > > Also, do you or anyone else happen to have the answers > to my > > other > > > questions (reposted below): > > > > > > 1) When viewing the results in tksurfer, which color > > represents "left > > > hemisphere is larger" and which represents "right > hemisphere > > is larger"? > > If you are just doing a simple interhemispheric > difference, then > > yellow/red will be left>right and blue left<right > > > > > > 2) I have no idea how to view the results in tksurfer > AFTER > > performing > > > the step of correcting for multiple comparisons. Any > > suggestions? > > > > If you run mri_glmfit-sim with --help you will see a list of > > output > > files with descriptions for each. Choose the one you > want and run > > tksurfer on it (eg, tksurfer fsaverage_sym lh inflated > -aparc > > -overlay > > csdbase.sig.cluster.mgh ) > > > > doug > > > > > > > > Thanks! > > > Krista > > > > > > > > > > > > > > > On Mon, Dec 9, 2013 at 11:09 AM, 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>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > Run mris_preproc with --paired-diff-norm which > will then > > compute > > > LI = (L-R)/(.5*(L+R)) > > > Note that some people use > > > LI = (L-R)/(L+R) > > > If that is what you want, then divide the mris_preproc > > result by 2 > > > > > > doug > > > > > > On 12/08/2013 08:45 PM, krista kelly wrote: > > > > Hello, > > > > > > > > I'm analysing interhemispheric differences using > > xhemi. I have > > > > followed the instructions on the webpage with no > > problems. I do > > > have a > > > > few questions though. > > > > > > > > 1) When viewing the results in tksurfer, which color > > represents > > > "left > > > > hemisphere is larger" and which represents "right > > hemisphere is > > > larger"? > > > > > > > > 2) I have no idea how to view the results in > tksurfer > > AFTER > > > performing > > > > the step of correcting for multiple comparisons. Any > > suggestions? > > > > > > > > 3) I've noticed from the archives that some > people are > > performing > > > > laterality indices. How would I calculate laterality > > indices? > > > > > > > > Thanks! > > > > Krista > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto: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>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> <tel: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>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>>> <tel: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> > > <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> > > > <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>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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>> > <mailto: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> > > <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> > > > <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>> > > <mailto: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 > > > > > > > > > > > > _______________________________________________ > > 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> > Fax: 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 > > > > > > _______________________________________________ > 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 Fax: 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
krista kelly