Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

2013-02-12 Thread Douglas N Greve
Anyone know how to reset the LOCAL? Even if temporarily to see if this 
is the problem?
doug


On 02/12/2013 08:23 AM, Richter, Julia wrote:
 It says the same even if I put 1.3 in quotes. :( Any other possibility to get 
 access to the data?


 -Ursprüngliche Nachricht-
 Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Gesendet: Montag, 11. Februar 2013 19:04
 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: AW: AW: AW: [Freesurfer] mean cortical thickness of significant 
 clusters in qdec


 It may be a German operating system replacing 1.3 with 1,3. Maybe put it in 
 quotes, ie, 1.3

 On 02/11/2013 04:17 AM, Richter, Julia wrote:
 Dear Doug,

 this is what appears when I type my command in the command window:

 mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99
 ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0

 That's it...Any ideas why this is happening?

 Many thanks in advance!

 Best, Julia

 -Ursprüngliche Nachricht-
 Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Gesendet: Donnerstag, 7. Februar 2013 17:32
 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of
 significant clusters in qdec

 it does not look like you changed the command line. Also, please cut and 
 paste the info into the email instead of taking a snapshot.
 thanks
 doug

 On 02/04/2013 07:26 AM, Richter, Julia wrote:
 This doesn't work either (see attachment)  :(

 -Ursprüngliche Nachricht-
 Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Gesendet: Donnerstag, 31. Januar 2013 20:29
 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant
 clusters in qdec

 The threshold must be in the form of -log10(pthreshold). So, if you
 want pthreshold=.05, then use 1.3 doug



 On 01/31/2013 07:37 AM, Richter, Julia wrote:
 Dear Doug,

 thanks for your reply. I tried the command you suggested, but I always get 
 an error message that there is something wrong with my threshold. I took a 
 screenshot of the command window and attached it to this mail. I will be 
 very happy if you have a look at it.

 Looking forward to your answer,

 Best, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
 Douglas Greve
 Gesendet: Mittwoch, 30. Januar 2013 17:16
 An: Richter, Julia; free surfer
 Betreff: Re: [Freesurfer] mean cortical thickness of significant
 clusters in qdec

 Oh, sorry, I thought you said you were using mri_glmfit-sim (which
 does not have an FDR option). Are you using the FDR in QDEC? If so,
 it will display the voxel-wise threshold that realizes the FDR
 threshold. You can then run mri_glmfit-sim --cache threshold sign
 --cwpvalthresh .99 where threshold is the voxelwise threshold from
 FDR and sign is either abs (absolute), pos, or neg. Setting
 cwpvalthresh=.99 tell it to report all clusters

 doug

 On 1/30/13 8:09 AM, Richter, Julia wrote:
 No it is not...or I just do not find it.

 Might it be that I only get the xxx.y.ocn.dat if I correct for multiple 
 comparisons with Monte Carlo? If yes, is there any possibility that I get 
 this xxx.y.ocn.dat when correcting with FDR?

 Many thanks, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
 Douglas N Greve
 Gesendet: Dienstag, 29. Januar 2013 18:46
 An: freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] mean cortical thickness of significant
 clusters in qdec

 Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
 doug


 On 01/29/2013 11:03 AM, Richter, Julia wrote:
 Dear FreeSurfer experts,

 I did a group analysis in qdec, found several significant clusters
 and would now like to extract the mean cortical thickness of each
 significant cluster. I know that I have to run mri_glmfit-sim to
 do this, but I do not understand which commands I need to get the
 xxx.y.ocn.dat as output by running mri_glmfit-sim.

 Any ideas? Any help is appreciated. J

 Best wishes, Julia



 ___
 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
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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 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

Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

2013-02-11 Thread Douglas N Greve

It may be a German operating system replacing 1.3 with 1,3. Maybe put it 
in quotes, ie, 1.3

On 02/11/2013 04:17 AM, Richter, Julia wrote:
 Dear Doug,

 this is what appears when I type my command in the command window:

 mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99
 ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0

 That's it...Any ideas why this is happening?

 Many thanks in advance!

 Best, Julia

 -Ursprüngliche Nachricht-
 Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Gesendet: Donnerstag, 7. Februar 2013 17:32
 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of significant 
 clusters in qdec

 it does not look like you changed the command line. Also, please cut and 
 paste the info into the email instead of taking a snapshot.
 thanks
 doug

 On 02/04/2013 07:26 AM, Richter, Julia wrote:
 This doesn't work either (see attachment)  :(

 -Ursprüngliche Nachricht-
 Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Gesendet: Donnerstag, 31. Januar 2013 20:29
 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant
 clusters in qdec

 The threshold must be in the form of -log10(pthreshold). So, if you
 want pthreshold=.05, then use 1.3 doug



 On 01/31/2013 07:37 AM, Richter, Julia wrote:
 Dear Doug,

 thanks for your reply. I tried the command you suggested, but I always get 
 an error message that there is something wrong with my threshold. I took a 
 screenshot of the command window and attached it to this mail. I will be 
 very happy if you have a look at it.

 Looking forward to your answer,

 Best, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
 Douglas Greve
 Gesendet: Mittwoch, 30. Januar 2013 17:16
 An: Richter, Julia; free surfer
 Betreff: Re: [Freesurfer] mean cortical thickness of significant
 clusters in qdec

 Oh, sorry, I thought you said you were using mri_glmfit-sim (which
 does not have an FDR option). Are you using the FDR in QDEC? If so,
 it will display the voxel-wise threshold that realizes the FDR
 threshold. You can then run mri_glmfit-sim --cache threshold sign
 --cwpvalthresh .99 where threshold is the voxelwise threshold from
 FDR and sign is either abs (absolute), pos, or neg. Setting
 cwpvalthresh=.99 tell it to report all clusters

 doug

 On 1/30/13 8:09 AM, Richter, Julia wrote:
 No it is not...or I just do not find it.

 Might it be that I only get the xxx.y.ocn.dat if I correct for multiple 
 comparisons with Monte Carlo? If yes, is there any possibility that I get 
 this xxx.y.ocn.dat when correcting with FDR?

 Many thanks, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von
 Douglas N Greve
 Gesendet: Dienstag, 29. Januar 2013 18:46
 An: freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] mean cortical thickness of significant
 clusters in qdec

 Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
 doug


 On 01/29/2013 11:03 AM, Richter, Julia wrote:
 Dear FreeSurfer experts,

 I did a group analysis in qdec, found several significant clusters
 and would now like to extract the mean cortical thickness of each
 significant cluster. I know that I have to run mri_glmfit-sim to do
 this, but I do not understand which commands I need to get the
 xxx.y.ocn.dat as output by running mri_glmfit-sim.

 Any ideas? Any help is appreciated. J

 Best wishes, Julia



 ___
 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
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 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 list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617

Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

2013-02-07 Thread Douglas N Greve
it does not look like you changed the command line. Also, please cut and 
paste the info into the email instead of taking a snapshot.
thanks
doug

On 02/04/2013 07:26 AM, Richter, Julia wrote:
 This doesn't work either (see attachment)  :(

 -Ursprüngliche Nachricht-
 Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
 Gesendet: Donnerstag, 31. Januar 2013 20:29
 An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant clusters 
 in qdec

 The threshold must be in the form of -log10(pthreshold). So, if you want 
 pthreshold=.05, then use 1.3 doug



 On 01/31/2013 07:37 AM, Richter, Julia wrote:
 Dear Doug,

 thanks for your reply. I tried the command you suggested, but I always get 
 an error message that there is something wrong with my threshold. I took a 
 screenshot of the command window and attached it to this mail. I will be 
 very happy if you have a look at it.

 Looking forward to your answer,

 Best, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
 Gesendet: Mittwoch, 30. Januar 2013 17:16
 An: Richter, Julia; free surfer
 Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in 
 qdec

 Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not 
 have an FDR option). Are you using the FDR in QDEC? If so, it will display 
 the voxel-wise threshold that realizes the FDR threshold. You can then run 
 mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is 
 the voxelwise threshold from FDR and sign is either abs (absolute), pos, or 
 neg. Setting cwpvalthresh=.99 tell it to report all clusters

 doug

 On 1/30/13 8:09 AM, Richter, Julia wrote:
 No it is not...or I just do not find it.

 Might it be that I only get the xxx.y.ocn.dat if I correct for multiple 
 comparisons with Monte Carlo? If yes, is there any possibility that I get 
 this xxx.y.ocn.dat when correcting with FDR?

 Many thanks, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N 
 Greve
 Gesendet: Dienstag, 29. Januar 2013 18:46
 An: freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters 
 in qdec

 Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
 doug


 On 01/29/2013 11:03 AM, Richter, Julia wrote:
 Dear FreeSurfer experts,

 I did a group analysis in qdec, found several significant clusters and
 would now like to extract the mean cortical thickness of each
 significant cluster. I know that I have to run mri_glmfit-sim to do
 this, but I do not understand which commands I need to get the
 xxx.y.ocn.dat as output by running mri_glmfit-sim.

 Any ideas? Any help is appreciated. J

 Best wishes, Julia



 ___
 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
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 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 list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

2013-01-31 Thread Douglas N Greve
The threshold must be in the form of -log10(pthreshold). So, if you want 
pthreshold=.05, then use 1.3
doug



On 01/31/2013 07:37 AM, Richter, Julia wrote:
 Dear Doug,

 thanks for your reply. I tried the command you suggested, but I always get an 
 error message that there is something wrong with my threshold. I took a 
 screenshot of the command window and attached it to this mail. I will be very 
 happy if you have a look at it.

 Looking forward to your answer,

 Best, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
 Gesendet: Mittwoch, 30. Januar 2013 17:16
 An: Richter, Julia; free surfer
 Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in 
 qdec

 Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not 
 have an FDR option). Are you using the FDR in QDEC? If so, it will display 
 the voxel-wise threshold that realizes the FDR threshold. You can then run 
 mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is 
 the voxelwise threshold from FDR and sign is either abs (absolute), pos, or 
 neg. Setting cwpvalthresh=.99 tell it to report all clusters

 doug

 On 1/30/13 8:09 AM, Richter, Julia wrote:
 No it is not...or I just do not find it.

 Might it be that I only get the xxx.y.ocn.dat if I correct for multiple 
 comparisons with Monte Carlo? If yes, is there any possibility that I get 
 this xxx.y.ocn.dat when correcting with FDR?

 Many thanks, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N 
 Greve
 Gesendet: Dienstag, 29. Januar 2013 18:46
 An: freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in 
 qdec

 Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
 doug


 On 01/29/2013 11:03 AM, Richter, Julia wrote:
 Dear FreeSurfer experts,

 I did a group analysis in qdec, found several significant clusters and
 would now like to extract the mean cortical thickness of each
 significant cluster. I know that I have to run mri_glmfit-sim to do
 this, but I do not understand which commands I need to get the
 xxx.y.ocn.dat as output by running mri_glmfit-sim.

 Any ideas? Any help is appreciated. J

 Best wishes, Julia



 ___
 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
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 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 list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

2013-01-30 Thread Douglas Greve
Oh, sorry, I thought you said you were using mri_glmfit-sim (which does 
not have an FDR option). Are you using the FDR in QDEC? If so, it will 
display the voxel-wise threshold that realizes the FDR threshold. You 
can then run mri_glmfit-sim --cache threshold sign --cwpvalthresh .99
where threshold is the voxelwise threshold from FDR and sign is either 
abs (absolute), pos, or neg. Setting cwpvalthresh=.99 tell it to report 
all clusters

doug

On 1/30/13 8:09 AM, Richter, Julia wrote:
 No it is not...or I just do not find it.

 Might it be that I only get the xxx.y.ocn.dat if I correct for multiple 
 comparisons with Monte Carlo? If yes, is there any possibility that I get 
 this xxx.y.ocn.dat when correcting with FDR?

 Many thanks, Julia

 -Ursprüngliche Nachricht-
 Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
 Gesendet: Dienstag, 29. Januar 2013 18:46
 An: freesurfer@nmr.mgh.harvard.edu
 Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in 
 qdec

 Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
 doug


 On 01/29/2013 11:03 AM, Richter, Julia wrote:
 Dear FreeSurfer experts,

 I did a group analysis in qdec, found several significant clusters and
 would now like to extract the mean cortical thickness of each
 significant cluster. I know that I have to run mri_glmfit-sim to do
 this, but I do not understand which commands I need to get the
 xxx.y.ocn.dat as output by running mri_glmfit-sim.

 Any ideas? Any help is appreciated. J

 Best wishes, Julia



 ___
 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
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: 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.




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[Freesurfer] mean cortical thickness of significant clusters in qdec

2013-01-29 Thread Richter, Julia
Dear FreeSurfer experts,

I did a group analysis in qdec, found several significant clusters and would 
now like to extract the mean cortical thickness of each significant cluster. I 
know that I have to run mri_glmfit-sim to do this, but I do not understand 
which commands I need to get the xxx.y.ocn.dat as output by running 
mri_glmfit-sim.

Any ideas? Any help is appreciated. :)

Best wishes, Julia
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


Re: [Freesurfer] mean cortical thickness of significant clusters in qdec

2013-01-29 Thread Douglas N Greve
Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
doug


On 01/29/2013 11:03 AM, Richter, Julia wrote:

 Dear FreeSurfer experts,

 I did a group analysis in qdec, found several significant clusters and 
 would now like to extract the mean cortical thickness of each 
 significant cluster. I know that I have to run mri_glmfit-sim to do 
 this, but I do not understand which commands I need to get the 
 xxx.y.ocn.dat as output by running mri_glmfit-sim.

 Any ideas? Any help is appreciated. J

 Best wishes, Julia



 ___
 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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