[Freesurfer] Building your own fsaverage

is the pro's and con's of building your own fsaverage? All the best, Silas I searched the mailing stream and found this answer: 'make_average_subject script, but as Doug implies you probably don't need to. Our warp is high-enough dimensional that you rarely need to build average subjects from your own

[Freesurfer] Structural analysis

an idea why? If not, don't answer this. 4) What is White Matter Hypointensities comprised of in HC? 5) What is the best estimate of total white matter volume? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh

[Freesurfer] Structural analysis

1) Does these results look correct? WMV < GMV? 2) What is the difference between WMV+GMV and TIV? CSF? Ventricles? 3) I find no atrophy in the MS patients; are there reported any problems with FS and MS patients? 4) What is White Matter Hypointensities comprised of in HC?

Re: [Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

Thanks again Douglas! Your time and help is greatly appreciated! Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Thursday, August 25,

[Freesurfer] I receive an error when running recon-all with T1 and lesions from FLAIR

blem if they are placed correctly? What is the advantage of starting by running autorecon-1 and 2 and then inserting the lesions from the FLAIR? Thanks a lot for all your help! Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] Structural group analysis

to visualize the difference between two areas. I've thought about presenting each subject two times in the FSGD-file (primary motor cortex and premotor cortex), but this isn't possible and seems as a clumsy way to solve this problem. Please let me know if my problem is incomprehensible! Best, Silas

Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR

0); Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Wednesday, August 10, 2016 11:56 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [

Re: [Freesurfer] Fw: Running recon-all with T1 and FLAIR

ted with ERRORS at Mon Aug 8 15:31:32 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting' How can i solve this problem? Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>

[Freesurfer] Fw: Running recon-all with T1 and FLAIR

ing - is this preferable to using the FLAIR with manual editing? 5) How is the general strength of analysing corpus callosum structurally in MS patients using FreeSurfer? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu ht

[Freesurfer] Running recon-all with T1 and FLAIR

using FreeSurfer? Best, Silas ___ 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

Re: [Freesurfer] How to find the difference between to different fMRI datasets?

functional data sets (on the fsaverage) before starting the group analysis stream? E.g. by subtracting the files? Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Grev

[Freesurfer] How to find the difference between to different fMRI datasets?

perform this operation? Best, Silas ___ 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

Re: [Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

/... is this a necessity? How does mri_glmfit-sim recognizes that I'm investigating the label S1M1 and not cortex? Could i simply just copy-paste my results from mri_mcsim into .../S1M1_GroupAnalysis/S1M1/fsaverage/rh/cortex/ ? Best, Silas From: freesurfer-boun

[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

an following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when conf

[Freesurfer] Fw: FreeSurfer group analysis: mri_glmfit-sim

an following the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when conf

[Freesurfer] FreeSurfer group analysis: mri_glmfit-sim

ng the command-line group analysis stream in freesurfer? 2) When running mri_glmfit-sim i'm investigating the output ending with -voxel.mgh - how do i interpret the results of this file? When investigating the file in freeview what is the meaning of the units when conf

[Freesurfer] Multimodality analysis in FreeSurfer

by mapping this correlation onto the fsaverage (an one sample group mean analysis) - is this possible? Do you have an existing guide approaching this problem? Thank you! Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Multimodality analysis in FreeSurfer

study entirely in FreeSurfer - in this way I would easily be able to correlate for multiple comparisons using the standardized pipeline for FreeSurfer group analysis. Best, Silas From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-b

[Freesurfer] Smoothing of functional data mapped onto the fsaverage surface

tutorial there is a input to mri_glmfit called --wls cesvar.nii.gz which is the variance of each session at each voxel. How do i get this file? And what is the importance of doing this de-weighting of sessions with a high variance? Thanks! Best, Silas

[Freesurfer] mris_preproc -iv option

. This still requires that a subject list be supplied. Thanks again! Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information

[Freesurfer] Creating proper FSGD file

for your help, Best, Silas ___ 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

Re: [Freesurfer] How to deal with labels and structural data

to investigate e.g. cortical thickness of the labels. What command do i use? Do i have to run recon-all again with the new label (and if, which steps of recon-all is necessary to re-run?)? Thanks! Best, Silas Date: Tue, 21 Jul 2015 10:53:02 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer

[Freesurfer] How to deal with labels and structural data

and mri_label2annot?3 - Do you have an existing guide in this kind of analysis? Thanks! Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] FW: FW: Functional group analysis

Hi Bruce, I will. Thanks! Best, Silas Date: Sun, 28 Jun 2015 13:20:30 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Functional group analysis Hi Silas Doug (who normally answers this kind of question) is on vacation. Can you

[Freesurfer] FW: FW: Functional group analysis

Dear all, Can anyone help me with this question? Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 24 Jun 2015 11:35:28 +0200 Subject: [Freesurfer] FW: Functional group analysis Dear FreeSurfer team, I'm working on a functional analysis using FreeSurfer

[Freesurfer] FW: Functional group analysis

in the structural analysis in order to implement my data in the GLM. Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Functional group analysis Date: Fri, 19 Jun 2015 14:26:20 +0200 Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer

[Freesurfer] Functional group analysis

comparisons). Best, Silas ___ 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] Fsaverage template, labeling and group analysis

a label and afterwards map this label accurately to the rest of my subjects? Would you recommend to correct this label after mapping it to the subjects (for each individual subject)? Best, Silas ___ Freesurfer

[Freesurfer] Average subject

to investigate cortical thickness of this particular part of the brain by a group analysis using freesurfer tools. Do you have an thorough guide to the steps in this analysis (in addition to this guide http://freesurfer.net/fswiki/FsTutorial/GroupAnalysis)? Thank you for all your help, Best, Silas

[Freesurfer] Labeling of handknob area in primary motor cortex

Dear freesurfer, I was also wondering if you have an existing label of the handknob area located in primary motor cortex? Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Labeling of the dorsal part of BA6 (dorsal premotor cortex)

Dear freesurfer, Do you have an existing label of the dorsal part of the premotor cortex? If not, is it possible to manually label this area? Best, Silas ___ Freesurfer mailing list Freesurfer

[Freesurfer] Changing wstresh and removing wsg-atlas - consequences?

and wsgatlas in order to obtain a better fitted pial surface and white matter surface - and i was wondering if changing these parameters affect the comparability of the 3 groups (if e.g. i would like to investigate the inferior frontal gyrus)? Best, Silas

Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences?

fitting of the pial surface to the actual grey matter surface. Afterwards I've made manual editing to obtain the best possible fit. These parameter changes isn't group specific. Would you still avoid changing the parameters? Best, Silas Date: Mon, 16 Feb 2015 09:28:05 -0500 From: fis

Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences?

a talk at DRCMR - i also have some questions concerning movement artefacts. Best, Silas Date: Mon, 16 Feb 2015 15:28:46 +0100 From: ct...@dtu.dk To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Changing wstresh and removing wsg-atlas - consequences? Hi Silas

[Freesurfer] Labeling of preSMA?

to distinguish between preSMA and SMA by making a limit in y=0? Thanks, Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Brodmann Area stats to table

Hi guys! Is there an easy way to get Brodmann Area stats to table like there is for aseg and aparc stats? Thanks! Silas PS. I looked the question up and it was answered in 2011 - I was just wondering if you guys made an easy way around the problem since

[Freesurfer] Structural analysis

Hi all, I'm currently making a structural analysis on about 60 Parkinson patients and controls, and i would like to investigate specific regions in the brain - which do not seem to be included in the asegstats2table. How do i proceed from here? Best, Silas

Re: [Freesurfer] Freesurfer ROI analysis

grey matter thickness in the two groups; on and off medication (using freesurfer). Is Martin Reuther on vacation at the moment? Best, Silas Date: Fri, 25 Jul 2014 09:45:16 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer ROI analysis Hi

[Freesurfer] Freesurfer ROI analysis

differences in such specific areas in the brain? I have another question regarding movement artefacts. In a structural analysis would you remove pictures with movement artefacts if the segmentation after manual editing seems alright? Best,Silas