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:greve@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:greve@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:greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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 greve@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 greve@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/
-- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve