[Freesurfer] Number of pixel count

Hello Free surfer Expert , I am kooking for the exact value of voxel / pixel which represent White ,Grey and CSF fluid matter in brain. I am trying to draw contour, and to measure the count...or How to count the pixel for particular region...? Thanks in advance for your timely advise. cheers Sa

[Freesurfer] Compute DTI metrics in NAWM in Tracula

Hi Anastasia and freesurfer experts, I am trying to get DTI values along the tracts as in the pathstatbyvoxel file, but excluding inflammatory WM lesions. I have masks of the WM lesions that I could apply on the DTI maps, but then how could I compute the DTI metrics along the tract with the exclusi

Re: [Freesurfer] Hemispherectomy Surgery

Hi Kristian Can you send us an image to illustrate what you mean? Thanks Bruce > On Feb 11, 2014, at 8:31 PM, Kristian Eschenburg > wrote: > > Hi > > I have a dataset of children who have had hemispherectomy surgery to treat > epilepsy. I want to be able to run recon-all on these children.

[Freesurfer] Hemispherectomy Surgery

Hi I have a dataset of children who have had hemispherectomy surgery to treat epilepsy. I want to be able to run recon-all on these children. I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere t

Re: [Freesurfer] Cortical Thickness values

Look in the QDEC output folder. In each contrast folder, you should see a summary file. I think the info you want is in that file. doug On 02/11/2014 03:08 PM, Natasha Haris wrote: > Dear Freesurfers, > > Is there anyway to get a compiled list of all the significant clusters > with information

[Freesurfer] Cortical Thickness values

Dear Freesurfers, Is there anyway to get a compiled list of all the significant clusters with information about their maximum thickness value, x/y/z vertices, t statistic etc on QDEC? Does this have anything to do with a SaveClusterFile command? All of this information must be stored somewhere for

[Freesurfer] dt_recon error for Siemens mosaics image

HI! All, I got an error when I ran dt_recon WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass

Re: [Freesurfer] FreeSurferWiki RecentChanges

There may be an easier wqay to do this but a simple hack that appears to work is to use the "max_days" parameter in the url. For example: https://surfer.nmr.mgh.harvard.edu/fswiki/RecentChanges?max_days=100 -Zeke On 02/11/2014 12:57 PM, Kaiming Yin wrote: > Dear guys, > > Is there some way to h

[Freesurfer] FreeSurferWiki RecentChanges

Dear guys, Is there some way to have a more detailed look of the recent changes on the FreeSurfer Wiki page? I click on the recent changes option but can only see the latest 13 updates within around 10 days. Could I have a check of that from further past days? Thanks a lot, Kaiming __

[Freesurfer] Program Director job opening at the NINDS (fwd)

FYI -- Forwarded message -- Date: Tue, 11 Feb 2014 16:50:15 + From: "Babcock, Debra (NIH/NINDS) [E]" To: "Babcock, Debra (NIH/NINDS) [E]" Subject: Program Director job opening at the NINDS Dear Colleagues,   The NINDS is currently seeking to hire several program directo

Re: [Freesurfer] creating specific files

you shouldn't On Tue, 11 Feb 2014, Borzello, Mia wrote: > Another question- will I need to re-coregister if I rerun a reconstruction? > > Thanks, > m > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of B

Re: [Freesurfer] creating specific files

Hi Mia I don't know where that file comes from - I don't think it's one we typically generate, but I would imagine it does need the ?h.pial surface as input cheers Bruce On Tue, 11 Feb 2014, Borzello, Mia wrote: > woops- sorry meant to include everyone. The name of the file I use to plot is

Re: [Freesurfer] FDR question

Hi Doug and Martin, Thanks both for your replies! Doug, I would normally set the FDR to something close to .05 but when this value didn't give me any significant clusters for my analysis, I was trying to find which value was the min one that gave significant clusters just out of curiosity, and th

Re: [Freesurfer] creating specific files

Hi Mia, while that is possible, it may be smarter to re-run those subjects from scratch. It is unclear why those files are empty. Maybe there are files that have been partially written etc. Those would not be re-created. I'd be very reluctant re-using data even partially that I know has been

[Freesurfer] Variability in bedpostx output

Hello all, I have run bedpostx on a series of DTI scans over ~1 year, the earlier ones in stable 5.1 and later ones in 5.3. I'm seeing quite a lot of variability in intensity from the earlier to later versions - re-running bedpostx in 5.3 on an older scan and comparing with 5.1 yields up to 10%

Re: [Freesurfer] FDR question

Hi Panos, also the LME tools (matlab) have tools for FDR correction: /lme_mass_FDR/ (Original Benjamini and Hochberg FDR procedure) /lme_mass_FDR2/ (A more powerful two-stage FDR procedure: "Adaptive Linear Step-up Procedures that control the False Discovery Rate" Benjamini, Krieger, Yekutiel

Re: [Freesurfer] FDR question

Sorry, for the delay... 1. You can use mri_surfcluster with the --fdr option. 2. I'm not sure I understand. Are you really setting the FDR to .88? Usually it is some thing like .05 doug On 02/10/2014 03:28 PM, pfot...@nmr.mgh.harvard.edu wrote: > Hi FS community, > > I was wondering if anyon

Re: [Freesurfer] How to caulculate the differences in subcortical volumes and display it?

What is in lh.volume.average.fwhm10.mgh? It is named as if it is a file with surface data in it. On 02/11/2014 11:04 AM, Wang, Guoying wrote: > > Dear freesurfer experts, > > I am trying to compute the differences in subcortical volumes between > two groups. I have read previous mail, > https

Re: [Freesurfer] creating specific files

Another question- will I need to re-coregister if I rerun a reconstruction? Thanks, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Tuesday, February 11, 2014 11:05 AM To: Bruce Fisc

Re: [Freesurfer] creating specific files

woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? From: Bruce Fischl [fis...@nm

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Hi again Anastasia, I tried also to convert my three row bvecs file in a three column one but I still got the same "bvecs and bvals don't have the same number of entries" error. I then tried also to change the dot to comma as the decimal separator but still nothing Francesco Baldacchini 2014-02

[Freesurfer] How to caulculate the differences in subcortical volumes and display it?

Dear freesurfer experts, I am trying to compute the differences in subcortical volumes between two groups. I have read previous mail, https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17597.html , and in this mail, your answer was 'you can do a subcortical volume analysi

Re: [Freesurfer] creating specific files

what kind of plotting do you mean? On Tue, 11 Feb 2014, Borzello, Mia wrote: > Okay and is there a way to check if the files I currently have are sufficient > to plot with? > > Thanks, > m > > > >> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" >> wrote: >> >> if they are zero length there is noth

[Freesurfer] wmparc

Hi All, I have a few questions about wmparc: What rule is used to determine what grey matter structure corresponds to a white matter point? What exactly has to be the case when UnsegmentedWhiteMatter is reported? Is there a reference you could point me to? Thanks, Sujith __

Re: [Freesurfer] creating specific files

Okay and is there a way to check if the files I currently have are sufficient to plot with? Thanks, m > On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" > wrote: > > if they are zero length there is nothing there now >> On Tue, 11 Feb 2014, Borzello, Mia wrote: >> >> Is this okay to do even i

[Freesurfer] combining FS commands

Dear Freesurfers, I want to run: mri_normalize gentle, And mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80 in MY recon-all script. I understand that I have to put the flag -expert to do this - but I seem to make errors in my command It would be greatly apprecia

Re: [Freesurfer] creating specific files

if they are zero length there is nothing there now On Tue, 11 Feb 2014, Borzello, Mia wrote: > Is this okay to do even if I've done a coregistration, nothing will be > deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if > I can just use the files that I have to create

Re: [Freesurfer] creating specific files

Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything. Thanks, Mia > On Feb 10, 2014, at 4:31 PM, "Bruce F

Re: [Freesurfer] Fwd: Tracula Error: bvecs and bvals don't have the same number of entries

Ciao Anastasia, I checked and I'm using the latest version of Freesurfer, version 5.3.0. It seems like that the command trac-all path while working on the bvecs table and doing the corrections makes some errors and you can see it from the bvecs file I found in the dmri directory which is only 4 row

Re: [Freesurfer] Combining FS commands

Hi Erik you can do this with the expert options in recon-all. Run recon-all -help and see if it is clear, otherwise post and someone here who has used it can walk you through it. cheers Bruce On Tue, 11 Feb 2014, Erik Lindberg wrote: Dear Freesufers, I want to run: mri_normalize gentle,

[Freesurfer] Combining FS commands

Dear Freesufers, I want to run: mri_normalize gentle, And mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80 In as few steps as possible as I will run around 800 images. So far I only managed to this by braking up the process several subparts (like doing autorecon1 before m