[Freesurfer] glm without class variable
Hi, Does anyone know how to run a glm with only one continous variable and without a class variable? I would like to run mri_glmfit with age as the only variable, but I can't figure out how to do this without including and controlling for a class variable such as gender. I have run the command: mri_glmfir --glmdir ../glm/dev_age_rh --y preproc/rh-thick15.mgz --fsgd fsgd_age.txt doss --surf average rh --C contrast_age The fsgd file contains gender as a class variable (F or M) and age as a continous variable. The contrast is: 0 0 1 Any tips would be appreciated. best regards, Christian -- Christian K. Tamnes Center for the Study of Human Cognition Department of Psychology, University of Oslo PB 1094 Blindern, 0317 Oslo, Norway Cell ph: (+47) 97572410 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] prenatal - cortical thickness
dear support , we are currently interesting in measuring cortical thickness and voulume in prenatals. do you think it can be done in freesurfer? thank you Asaf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] glm without class variable
Christian, The .fsgd file would look like this: GroupDescriptorFile 1 Title Untitled MeasurementName thickness Class Main Variables age Input 030815_4882 Main 15.00 Input 030713_1197 Main 18.00 Input 000803_vc4829 Main 20.00 Input 010728_vc7352 Main 20.00 Input 010819_vc7505 Main 21.00 . . . and the contrast is: 0 1 The 'qdec' app might work well for you in this sort of analysis. At the very least it will generate the .fsgd and contrast matrices for you, which you can then manually input to mri_glmfit. Nick On Mon, 2008-10-27 at 09:17 +0100, [EMAIL PROTECTED] wrote: Hi, Does anyone know how to run a glm with only one continous variable and without a class variable? I would like to run mri_glmfit with age as the only variable, but I can't figure out how to do this without including and controlling for a class variable such as gender. I have run the command: mri_glmfir --glmdir ../glm/dev_age_rh --y preproc/rh-thick15.mgz --fsgd fsgd_age.txt doss --surf average rh --C contrast_age The fsgd file contains gender as a class variable (F or M) and age as a continous variable. The contrast is: 0 0 1 Any tips would be appreciated. best regards, Christian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec questions
Martin, To answer question 1, the fsaverage surface is used as a target surface to which the data (ie thickness) of each subject in the group is sampled and then smoothed, so the accuracy of the recon of the fsaverage subject itself is not relevant to accuracy of the group analysis. For 2., unfortunately, the only way to get qdec to recognize ?h.pial_lgi is via the 'hack' that you mention: renaming the files as 'thickness'. A feature to be added to qdec is the reading of a text configuration file to allow selection of arbitrary surface data files into the qdec menu. Actually, I think I might implement that feature this week, as I hate that hack, and can post this version of qdec for you if you want. To create the smoothed ?h.pial_lgi files, you would do this: recon-all -s subjid -qcache -measure pial_lgi and it will create the fsaverage sampled and smoothed data for each subject. For 3., I think you are in new territory here, the first to do this, so you will have to experiment. Although 0mm smoothing, as you suggest, seems reasonable. Nick On Sun, 2008-10-26 at 21:41 +0100, Martin Kavec wrote: Hello all, I have started with a group analysis using qdec and have some questions: 1. loading fsaverage into tkmedit along with rh.white and lh.white surprised me that the pial surfaces do not run under the skull, as I see it on a single subject but copy the white matter. It is also correct, but it looks a bit odd. I suppose that this is a result of averaged out WM, but my concern is whether it can anyhow affect the analysis 2. I am interested in group analysis of LGI. I do not see however ?h.pial_lgi in fsaverage. Also when I run qdec, lgi is not among the parameters available for testing. I could backup say the thickness files and than rename my lgi results as thickness, but if there is a more straightforward solution I would like to avoid this trouble 3. Since lgi is for each vertex calculated over a certain diameter, thus has inherent smoothing. Therefore I would tend to use 0 smoothing in GLM. What do you think about this idea? Thanks, Martin ___ Freesurfer mailing list 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
Re: [Freesurfer] prenatal - cortical thickness
Hi Asaf, not easily, as the gray/white contrast is reversed and quite spatially inhomogeneous. It's something we're interested in, but have only done a bit of. cehers, Bruce On Mon, 27 Oct 2008, asaf achiron wrote: dear support , we are currently interesting in measuring cortical thickness and voulume in prenatals. do you think it can be done in freesurfer? thank you Asaf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Qdec, group analysis, and p-values
Hi all. I have a few group analysis questions: 1. After running QDEC I find several significant regions that have a p-value associated with them. (This is obtained by clicking on the most significant vertex) However, if I change the threshold from the default to 1.3, 2, 3, to show all vertices with p.05 then the p-value associated with the significant regions stays this same as it was during the default display. The threshold bar appears to only have affect on the visualization not on finding significant regions. So, is there a default p-value that is in qdec to find signicant regions? 2. How would one go about reporting these regions in a manuscript? Would they be called uncorrected at blank with a value of blank? 3. I thought that mri_glmfit, which is what QDEC does, is essentially an F-test. If so, where is the F value? 4. After running a full monte-carlo simulation I have many regions close to 0.99 and therefore are not significant. However, they were significant enough to be generated on the simulation table. How would one go about reporting these clusters in a manuscript? 5. Are the CWP values, from the simulations, p-values? Any help or input from anyone would be greatly appreciated. Thanks, Judith ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Qdec questions
Thanks for the replay, Nick! On Monday 27 October 2008 16:48:26 Nick Schmansky wrote: Martin, To answer question 1, the fsaverage surface is used as a target surface to which the data (ie thickness) of each subject in the group is sampled and then smoothed, so the accuracy of the recon of the fsaverage subject itself is not relevant to accuracy of the group analysis. Thanks, it's clear now. For 2., unfortunately, the only way to get qdec to recognize ?h.pial_lgi is via the 'hack' that you mention: renaming the files as 'thickness'. A feature to be added to qdec is the reading of a text configuration file to allow selection of arbitrary surface data files into the qdec menu. Actually, I think I might implement that feature this week, as I hate that hack Sorry, I could not come up with something more pleasant. :D , and can post this version of qdec for you if you want. That would be great, though I do not want to press you! For 3., I think you are in new territory here, the first to do this, so you will have to experiment. Although 0mm smoothing, as you suggest, seems reasonable. OK. I'll give it a try! Thanks, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Making Binary Masks
Hello- Can somebody point me towards the best way to make a thresholded binary mask out of a sig.mgh file that comes out of qdec/mri_glmfit? I'd like to take the sig.mgh file and use all values above threshold as a mask for another mri_glmfit analysis. I'm used to functional data in FSL, and could do this lickety-split with fslmaths or fslroi. Does FreeSurfer have a similar set of utilities to be used in manipulating .mgh files? I've tried to run thresholding within tksurfer, then Save Overlay As but that doesn't cut off the sub-threshold values. I'm sure I could draw on the surface to trace my supra-threshold areas and create a mask that way, but I'd prefer to just do it mathematically if possible. Thanks! -- - Jim Porter Graduate Student Clinical Science Psychopathology Research University of Minnesota ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness
Dear FreeSurfer Experts, I was trying to run freesurfer on one of my MPRAGEs that was acquired on 7T scanner with isotropic resolution of 0.5mm. I have got two different errors below. Could you please suggest something for me? [EMAIL PROTECTED] Talairach Failure Detection Tue Sep 9 16:02:41 BST 2008 /data_local/ali/freesurfer/subjects/MPRAGE/MS_PC/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0090, pval=0. threshold=0.0050) Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 10 16:12:41 BST 2008 *WATERSHED** Sorting... first estimation of the COG coord: x=208 y=168 z=180 r=51 first estimation of the main basin volume: 562273 voxels mean intensity too low ! Modification of the image: intensity*0.50 first estimation of the COG coord: x=208 y=168 z=179 r=51 first estimation of the main basin volume: 559292 voxels mean intensity too low ! Modification of the image: intensity*3.72 first estimation of the COG coord: x=208 y=168 z=180 r=51 first estimation of the main basin volume: 569632 voxels mri_watershed Error: Interpolation problem in the white matter curve analysis Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 14 18:44:05 BST 2008 Many thanks in advance Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] cortical thickness
Hi Ali, you're better off acquiring a 1mm isotropic dataset in addition and running recon-all on it. It's pretty tough to get uniform contrast at 7T due to the dielectric effects though. cheers, Bruce On Mon, 27 Oct 2008, Al-Radaideh Ali wrote: Dear FreeSurfer Experts, I was trying to run freesurfer on one of my MPRAGEs that was acquired on 7T scanner with isotropic resolution of 0.5mm. I have got two different errors below. Could you please suggest something for me? [EMAIL PROTECTED] Talairach Failure Detection Tue Sep 9 16:02:41 BST 2008 /data_local/ali/freesurfer/subjects/MPRAGE/MS_PC/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0090, pval=0. threshold=0.0050) Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 10 16:12:41 BST 2008 *WATERSHED** Sorting... first estimation of the COG coord: x=208 y=168 z=180 r=51 first estimation of the main basin volume: 562273 voxels mean intensity too low ! Modification of the image: intensity*0.50 first estimation of the COG coord: x=208 y=168 z=179 r=51 first estimation of the main basin volume: 559292 voxels mean intensity too low ! Modification of the image: intensity*3.72 first estimation of the COG coord: x=208 y=168 z=180 r=51 first estimation of the main basin volume: 569632 voxels mri_watershed Error: Interpolation problem in the white matter curve analysis Linux morgana 2.6.11.4-21.11-smp #1 SMP Thu Feb 2 20:54:26 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Tue Oct 14 18:44:05 BST 2008 Many thanks in advance Ali This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
