[Freesurfer] Admin: Please unsubscribe this email address

Hello Admin, Please unsubscribe this email address. Regards, Manish ___ 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

[Freesurfer] Admin please unsubscribe this email!

Admin please unsubscribe this email address Thanks, Manish Dalwani ___ 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

[Freesurfer] How to load specific color label for rois

Hi Freesurfer's, How can I load color labels for specific for display purposes? Regards, Manish Dalwani Instructor Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] What is MNI coordinates

Hi BOBO, There are 2 popular atlases the Talairach (which was developed from a single female brain) and the MNI (which has been developed on an average of several adult brains). MNI coordinates is basically co-ordinates of the MNI space and extremely popular and well-used in the neuroimaging mo

[Freesurfer] Vertex size and vertex value export

Hello Freesurfer's, What is the size of a vertex? Also, how do you define a vertex? Also, in the Qdec analyses, once you get a cluster and the maximum vertex, is there a way to export individual vertex value (for each subject)? Regards, Manish Dalwani Instructor Dept. of Psychiatry University o

Re: [Freesurfer] QDEC question

Nevermind, I figured out both my questions! I just have to read the instructions carefully :) Manish On 2/2/12 3:02 PM, "Manish Dalwani" wrote: Ok I figured that it is ctrl and mouse click on the co-ordinate of interest. How can I get the cluster size out? Thanks, Manish On 2/2/12 2:47 PM

Re: [Freesurfer] QDEC question

Ok I figured that it is ctrl and mouse click on the co-ordinate of interest. How can I get the cluster size out? Thanks, Manish On 2/2/12 2:47 PM, "Manish Dalwani" wrote: Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and p

[Freesurfer] QDEC question

Hi Freesurfer users, I ran a QDEC analysis and loaded annotation. Is there a way to click on the activated cluster and print the region with co-ordinates? Thanks, Manish Dalwani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] Algorithm for cluster-wise simulation

Hello folks, We are in the processing of writing a paper on cortical thickness. The cluster-wise simulation that we use is it similar to alphasim monte-carlo simulation by afni? Do you have any paper on it? Best Regards, Manish Dalwani Instructor Dept. of Psychiatry Univ. of CO

Re: [Freesurfer] QDEC analyses

Ok thanks so much Nick! On 9/27/11 2:08 PM, "Nick Schmansky" wrote: its possible to have different versions installed, just install it in another directory. qdec will not change any of the existing data processed with another version. n. On Tue, 2011-09-27 at 14:05 -0600, Dalwa

Re: [Freesurfer] QDEC analyses

. it will include the necessary libs that qdec is built against. n. On Tue, 2011-09-27 at 11:13 -0600, Dalwani, Manish wrote: > Hello Freesurfer's, > > I posted this last week. Does someone have any insights? Kindly > advise! > > Manish > -- Forwarded Message > From

[Freesurfer] QDEC analyses

Hello Freesurfer's, I posted this last week. Does someone have any insights? Kindly advise! Manish -- Forwarded Message From: , Manish Dalwani Date: Fri, 23 Sep 2011 14:25:42 -0600 To: Conversation: QDEC analyses Subject: QDEC analyses Hello Freesurfer's I want to set up (thanks to Nick'

[Freesurfer] QDEC analyses

Hello Freesurfer's I want to set up (thanks to Nick's advice) a model with 2 covariates and one nuisance variable in QDEC. I am using the Freesurfer Version 4.5 but the QDEC version I am running is 1.2. I did not see any option for nuisance variables in it? I therefore went to this link ftp:/

[Freesurfer] How can I include 3 covariates in my GLM model

Hello Freesurfer's, I am using QDEC and I have created and FSGD descriptor file with 2 groups (pts and ctrls) and three continuous variables: age, IQ and mean thickness. I have 2 questions: 1. I can only choose 2 covariates at one time? How can I choose all three covariates in one model in

[Freesurfer] Laterality Issue!

Hello Freesurfer's If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice! Regards, Manish Dalwani P.s. I sent this email out earlier with the wrong subject name... _

Re: [Freesurfer] mris_calc problem

Hello Freesurfer's If tkmedit shows the T1 image in radiological convention, then what convention does the surface reconstruction follow? Please advice! Regards, Manish Dalwani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nm

[Freesurfer] Name of the atlas

What atlas does aparc2009 represent? Regards, Manish Dalwani Sr. PRA Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in t

[Freesurfer] Vertex-by-vertex analyses within ROIS?

Hello Freesurfers, I am happy to find out that it is possible to carry out vertex-by-vertex analyses for specific ROIs. Can someone help me understand, 1. How to run such a vertex-by-vertex analyses for certain ROI or ROIs? 2. Can we apply cluster-wise correction or FDR to the ROI to correc

[Freesurfer] Vertex-by-vertex analyses within ROIS?

Hello Freesurfers, We are interested in comparing cortical thickness in 2 groups. Due to small sample size (and thus less power), we are swaying away from whole-brain vertex analyses. Instead we would like to compare specific ROIs between two groups. We understand that we can get an estimate

[Freesurfer] how to check the version of freesurfer?

Sorry for this lame question but how can I check the current version of freesurfer? Regards, Manish Dalwani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in thi

[Freesurfer] Destrieux Atlas (aparc.a2009s.annot)

Hi Freesurfers, Where can I find documentation and labels for Destrieux Atlas? How can I download this new atlas? My stats folders for each subject has aparc.a2005s.stats. Can I generate the stats for the new atlas? Sincerely, Manish Dalwani Sr. PRA Univ. of CO

[Freesurfer] GLM model for cortical thickness!

Hi All, If you don't have a linear trend in the Cortical thickness vs age correlation, is there a way to use a polynomial (quadratic, cubic) regression model to best fit the cortical thickness vs age using the GLM mechanism of freesurfer? Regards, Manish Dalwani Sr. PRA Univ. of CO

[Freesurfer] cluster simulation script error!

Hi All, I am getting the following error after running the simulation script generated by QDEC. ERROR: dimension mismatch between X and contrast /usr/local/freesurfer/subjects/ qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has 2 cols, C has 6 cols Kindly advise! Regar

[Freesurfer] (no subject)

Hi All, I am getting the following error after running the simulation script generated by QDEC. ERROR: dimension mismatch between X and contrast /usr/local/freesurfer/subjects/ qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has 2 cols, C has 6 cols Kindly advise!

[Freesurfer] (no subject)

Hi All, I am getting the following error after running the simulation script generated by QDEC. ERROR: dimension mismatch between X and contrast /usr/local/freesurfer/subjects/ qdec/Untitled/tmp.mri_glmfit-sim-15306/lh-Avg-Intercept-volume.mtx X has 2 cols, C has 6 cols Kindly advise!