Dear all,
I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD.
As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps?
Thanks a lot!
Katharina
Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug
On 08/14/2014 09:23 AM, Katharina Zech wrote:
Dear all,
I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD.
As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps?
Thanks a lot!
Katharina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation?
Best,
Katharina
2014-08-15 18:24 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug
On 08/14/2014 09:23 AM, Katharina Zech wrote:
Dear all,
I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD.
As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps?
Thanks a lot!
Katharina
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.
Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat
On 8/17/14 2:39 PM, Katharina Zech wrote:
Hi Doug,
I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation?
Best,
Katharina
2014-08-15 18:24 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug On 08/14/2014 09:23 AM, Katharina Zech wrote: > Dear all, > > I want to do a correlation of significant clusters found after full > monte-carlo simulation and symptom severity of patients affected with > obsessive-compulsive disorder (OCD). > The aim is as follows: > First, to see whether the severity of symptoms correlate with the > degree of structural brain alterations. > Second, whether the degree of structural brain alterations shows a > correlation with specific subtypes of OCD. > > As I run the full monte-carlo simulation, the significant clusters pop > up in tksurfer. > So could you explain to me the following steps? > > Thanks a lot! > > Katharina > > > _______________________________________________ > 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
Sorry to interrupt.
I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS?
On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat
On 8/17/14 2:39 PM, Katharina Zech wrote:
Hi Doug,
I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation?
Best,
Katharina
2014-08-15 18:24 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug
On 08/14/2014 09:23 AM, Katharina Zech wrote:
Dear all,
I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD.
As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps?
Thanks a lot!
Katharina
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
Yes, you are just getting the raw data from the ocn.dat file.
On 8/19/14 11:05 AM, yaya ya wrote:
Sorry to interrupt.
I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS?
On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat On 8/17/14 2:39 PM, Katharina Zech wrote:Hi Doug, I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation? Best, Katharina 2014-08-15 18:24 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug On 08/14/2014 09:23 AM, Katharina Zech wrote: > Dear all, > > I want to do a correlation of significant clusters found after full > monte-carlo simulation and symptom severity of patients affected with > obsessive-compulsive disorder (OCD). > The aim is as follows: > First, to see whether the severity of symptoms correlate with the > degree of structural brain alterations. > Second, whether the degree of structural brain alterations shows a > correlation with specific subtypes of OCD. > > As I run the full monte-carlo simulation, the significant clusters pop > up in tksurfer. > So could you explain to me the following steps? > > Thanks a lot! > > Katharina > > > _______________________________________________ > 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 <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 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
Dear Doug,
I am using the current version of free surfer (5.3.0). Unfortunately there isn't a file with the same/similar name. Do you think it should exist in 5.3.0?
Best
Katharina
2014-08-19 17:19 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu:
Yes, you are just getting the raw data from the ocn.dat file.
On 8/19/14 11:05 AM, yaya ya wrote:
Sorry to interrupt.
I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS?
On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat
On 8/17/14 2:39 PM, Katharina Zech wrote:
Hi Doug,
I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation?
Best,
Katharina
2014-08-15 18:24 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug
On 08/14/2014 09:23 AM, Katharina Zech wrote:
Dear all,
I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD.
As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps?
Thanks a lot!
Katharina
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
There won't be a filed called exactly that,but one of a name similar to that. Is there such a file. If you did the MC simulation in 5.3 and you had one or more significant clusters, then there should be.
On 8/25/14 7:43 AM, Katharina Zech wrote:
Dear Doug,
I am using the current version of free surfer (5.3.0). Unfortunately there isn't a file with the same/similar name. Do you think it should exist in 5.3.0?
Best
Katharina
2014-08-19 17:19 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
Yes, you are just getting the raw data from the ocn.dat file. On 8/19/14 11:05 AM, yaya ya wrote:Sorry to interrupt. I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS? On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat On 8/17/14 2:39 PM, Katharina Zech wrote:Hi Doug, I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation? Best, Katharina 2014-08-15 18:24 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug On 08/14/2014 09:23 AM, Katharina Zech wrote: > Dear all, > > I want to do a correlation of significant clusters found after full > monte-carlo simulation and symptom severity of patients affected with > obsessive-compulsive disorder (OCD). > The aim is as follows: > First, to see whether the severity of symptoms correlate with the > degree of structural brain alterations. > Second, whether the degree of structural brain alterations shows a > correlation with specific subtypes of OCD. > > As I run the full monte-carlo simulation, the significant clusters pop > up in tksurfer. > So could you explain to me the following steps? > > Thanks a lot! > > Katharina > > > _______________________________________________ > 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 <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 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_______________________________________________ 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
Also in case of a full mc simulation? I know that ocn files exist for precomputed mc simulations in qdec. Yes, I got version 5.3.0 and significant clusters.
2014-08-25 16:07 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu:
There won't be a filed called exactly that,but one of a name similar to that. Is there such a file. If you did the MC simulation in 5.3 and you had one or more significant clusters, then there should be.
On 8/25/14 7:43 AM, Katharina Zech wrote:
Dear Doug,
I am using the current version of free surfer (5.3.0). Unfortunately there isn't a file with the same/similar name. Do you think it should exist in 5.3.0?
Best
Katharina
2014-08-19 17:19 GMT+02:00 Douglas Greve greve@nmr.mgh.harvard.edu:
Yes, you are just getting the raw data from the ocn.dat file.
On 8/19/14 11:05 AM, yaya ya wrote:
Sorry to interrupt.
I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS?
On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat
On 8/17/14 2:39 PM, Katharina Zech wrote:
Hi Doug,
I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation?
Best,
Katharina
2014-08-15 18:24 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug
On 08/14/2014 09:23 AM, Katharina Zech wrote:
Dear all,
I want to do a correlation of significant clusters found after full monte-carlo simulation and symptom severity of patients affected with obsessive-compulsive disorder (OCD). The aim is as follows: First, to see whether the severity of symptoms correlate with the degree of structural brain alterations. Second, whether the degree of structural brain alterations shows a correlation with specific subtypes of OCD.
As I run the full monte-carlo simulation, the significant clusters pop up in tksurfer. So could you explain to me the following steps?
Thanks a lot!
Katharina
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. Do you have significant clusters?
On 08/25/2014 10:41 AM, Katharina Zech wrote:
Also in case of a full mc simulation? I know that ocn files exist for precomputed mc simulations in qdec. Yes, I got version 5.3.0 and significant clusters.
2014-08-25 16:07 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
There won't be a filed called exactly that,but one of a name similar to that. Is there such a file. If you did the MC simulation in 5.3 and you had one or more significant clusters, then there should be. On 8/25/14 7:43 AM, Katharina Zech wrote:Dear Doug, I am using the current version of free surfer (5.3.0). Unfortunately there isn't a file with the same/similar name. Do you think it should exist in 5.3.0? Best Katharina 2014-08-19 17:19 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Yes, you are just getting the raw data from the ocn.dat file. On 8/19/14 11:05 AM, yaya ya wrote:Sorry to interrupt. I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS? On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat On 8/17/14 2:39 PM, Katharina Zech wrote:Hi Doug, I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation? Best, Katharina 2014-08-15 18:24 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug On 08/14/2014 09:23 AM, Katharina Zech wrote: > Dear all, > > I want to do a correlation of significant clusters found after full > monte-carlo simulation and symptom severity of patients affected with > obsessive-compulsive disorder (OCD). > The aim is as follows: > First, to see whether the severity of symptoms correlate with the > degree of structural brain alterations. > Second, whether the degree of structural brain alterations shows a > correlation with specific subtypes of OCD. > > As I run the full monte-carlo simulation, the significant clusters pop > up in tksurfer. > So could you explain to me the following steps? > > Thanks a lot! > > Katharina > > > _______________________________________________ > 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 <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 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_______________________________________________ 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 <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 The information in this e-mail is intended only for the person to whom it is addressed. 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Yes, i got several ones.
Am Montag, 25. August 2014 schrieb Douglas N Greve :
yes. Do you have significant clusters?
On 08/25/2014 10:41 AM, Katharina Zech wrote:
Also in case of a full mc simulation? I know that ocn files exist for precomputed mc simulations in qdec. Yes, I got version 5.3.0 and significant clusters.
2014-08-25 16:07 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu javascript:;>>:
There won't be a filed called exactly that,but one of a name similar to that. Is there such a file. If you did the MC simulation in 5.3 and you had one or more significant clusters, then there should be. On 8/25/14 7:43 AM, Katharina Zech wrote:Dear Doug, I am using the current version of free surfer (5.3.0). Unfortunately there isn't a file with the same/similar name. Do you think it should exist in 5.3.0? Best Katharina 2014-08-19 17:19 GMT+02:00 Douglas Greve <greve@nmr.mgh.harvard.edu <javascript:;> <mailto:greve@nmr.mgh.harvard.edu javascript:;>>:
Yes, you are just getting the raw data from the ocn.dat file. On 8/19/14 11:05 AM, yaya ya wrote:Sorry to interrupt. I have a relevant question about the correlation analysis. If the age has been controlled for when surface-based analysis is done, do we need to controll for age again when we do subsequent correlational analysis in SPSS? On Tue, Aug 19, 2014 at 5:01 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <javascript:;> <mailto:greve@nmr.mgh.harvard.edu <javascript:;>>> wrote: Depending on the version of FS that you are using, the data you want may already be part of the MC simulation output in a file called something like csdbase.y.ocn.dat On 8/17/14 2:39 PM, Katharina Zech wrote:Hi Doug, I did a full monte-carlo simulation. And now I am trying to do a ROI extraction of my significant clusters on tksurfer (for the purpose of a further correlation). And it is not working. Do you see the error in the attachment? I cannot choose "Graph marked vertices avg". Do you see any other possibility to get the values of my clusters for further analysis, i.e. correlation? Best, Katharina 2014-08-15 18:24 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <javascript:;> <mailto:greve@nmr.mgh.harvard.edu <javascript:;>>>: Hi Katharina, I don't understand from your description what you are trying to do. Can you clarify? doug On 08/14/2014 09:23 AM, Katharina Zech wrote: > Dear all, > > I want to do a correlation of significant clusters found after full > monte-carlo simulation and symptom severity of patients affected with > obsessive-compulsive disorder (OCD). > The aim is as follows: > First, to see whether the severity of symptoms correlate with the > degree of structural brain alterations. > Second, whether the degree of structural brain alterations shows a > correlation with specific subtypes of OCD. > > As I run the full monte-carlo simulation, the significant clusters pop > up in tksurfer. > So could you explain to me the following steps? > > Thanks a lot! > > Katharina > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <javascript:;> <mailto:Freesurfer@nmr.mgh.harvard.edu <javascript:;>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <javascript:;> <mailto:greve@nmr.mgh.harvard.edu <javascript:;>> 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%3E
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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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Douglas Greve -
Douglas N Greve
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Katharina Zech -
yaya ya