Re: [Freesurfer] mris_anatomical_stats

Hi Bruce, Thank you so much for this suggestion. In case anyone searches for this thread in the future, I am writing back to report that it worked and thickness indices remain the same (although other indices, which are of no interest to me for this analysis, did change). Best, Arkadiy

Re: [Freesurfer] overlapping area question

Hi Doug, Thank you for the information about the matlab method. Since asking the question, I found a way to do this with the help of tksurfer and freesurfer commands, and wanted to share with the community, in case someone will find this useful in the future. Basically, after the desired

[Freesurfer] mris_anatomical_stats

Dear Freesurfer Experts, I am trying to run mris_anatomical_stats in order to extra thickness data from my participants' label files. However, I only have access to a subj_recon data (without wm.mgz in that folder). Does anyone know if there is a way to extract the thickness measures for every

[Freesurfer] overlapping area question

Hello Freesurfers, I was wondering if someone might have information for how I can measure overlapping areas between a cluster that was generated as a results of a cortical thickness analysis, with a portion of a Yeo Network atlas. Specifically, I would like to calculate the percentage that the

[Freesurfer] cache.th13.neg.sig.cluster.mgh directionality

Hello, I apologize if the questions are trivial- I have checked the archives, but could not find anything on this. I have run a t-test between two groups on cortical thickness, and used mri_glmfit-sim for pos, neg, and abs versions. 1. If my FSGD is organized as: Group 1 Group 2 and my matrix

[Freesurfer] Mri_glmfit-sim hemisphere correction

Hi Everyone, I was wondering if someone might know whether it is necessary to use the flag "2spaces" on both the left and the right hemisphere? If I am understanding correctly, this flag corrects for a specific multiple comparison of two hemispheres. Thus, it seems like it would only be

Re: [Freesurfer] controlling for total gray matter volume (Clara K?hn)

Hi Clara, Yes- my apologies. I misunderstood your initial analyses description. Sounds right to me as well. - Arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] controlling for total gray matter volume

Hi Clara, If I am understanding your question correctly, you don't need to control for brain volume when looking at thickness analyses. See quote below from this link: http://www.freesurfer.net/fswiki/eTIV "Note that this correction is only useful in situations where the structure scales with

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Thank you for catching this. Really appreciate your help. - Arkadiiy ___ 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

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

Thank you!! ___ 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

[Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

Hello, Hello, I am getting the following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 Command line: mri_glmfit --y lh.BD_SD.thickness.10B.mgh --fsgd FSGD_Collapsed_Across_Smokers_demeaned.fsgd dods --C BDvsSD1.mtx --surf fsaverage

Re: [Freesurfer] Freesurfer Digest, Vol 148, Issue 28

mgh.harvard.edu > Message-ID: <5765c30a.5080...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > try now > > On 6/16/16 11:50 PM, Arkadiy Maksimovskiy wrote: > > Hi Freesurfers, > > > > I am having a similar problem with

Re: [Freesurfer] GLM_Fit Question

Hi Freesurfers, I am having a similar problem with the FSGD file as the user indicated at this thread: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40599.html I am trying to access the script that Doug wrote in order to fix it, however, the link to download the script does not

Re: [Freesurfer] tutorial data

Hi Everyone, I have found a solution and wanted to update this thread in case anyone runs into the same problem. I was able to download the tutorial data directly from this link: http://ftp.nmr.mgh.harvard.edu/pub/data/ - Arkadiy On Wed, Jun 8, 2016 at 7:44 PM, Arkadiy Maksimovskiy <ar

[Freesurfer] tutorial data

Hello, I am trying to download the light tutorial dataset from this page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data The file link is titled: tutorial_data.tar.gz I have tried clicking on the link as well as using