[Freesurfer] Hippocampal volume estimation

Hello, I have to segment out hippocampus only and calculate its volume. Since FreeSurfer segments out many sub-cortical structures and their respective volumes, it takes a lot of time ( more than 10 hours ). Is there any way to extract a particular sub-cortical structure only from brain ( hippoca

[Freesurfer] TRACULA error: pre-processing

Hi, I have a problem running TRACULA in the pre-processing stage. The error message is the following; Loading streamline start ROI from /usr/local/freesurfer/subjects/tracula/tutorialdata/diffusion_tutorial/Diff001/dlabel/mni/lh.cst_AS_roi1.flt.nii.gz niiRead(): error opening file /usr/local/fre

Re: [Freesurfer] Problems converting MNC to NII

Hi Doug, your suggestion to go via Matlab with loadminc worked perfectly. Thank you very much! Caspar 2014/1/22 Douglas N Greve > > I've looked at the volume you sent. One problem may be that the minc file > might have a scale factor which we are not properly reading. When I use > mnc2nii it pr

Re: [Freesurfer] Hippocampal volume estimation

no, sorry. The contextual information from segmenting everything helps a lot in improving accuracy, so there is no way to only segment a single structure. cheers Bruce On Thu, 23 Jan 2014, Tanya Verma wrote: > Hello, > I have to segment out hippocampus only and calculate its volume. Since > Fre

[Freesurfer] Time taken by Freesurfer for processing

Hi, I would like to ask that why does the Freesurfer takes so much time for processing particularly autorecon2 ? Knowing that Freesurfer takes a lot of time for processing, why is it still used widely by researchers ? For segmentation followed by volume calculation , does one has to really wait f

Re: [Freesurfer] Time taken by Freesurfer for processing

Hi Tanya we have always preferenced minimizing manual interactions over computer time. It takes so long because of its level of automation and its completeness. This is also why it is so widely used I assume - because it generates a comprehensive, accurate and automated morphometric assay of th

Re: [Freesurfer] Time taken by Freesurfer for processing

Newer versions also have the ability to run some stages on multiple CPU cores (with the -openmp flag) which speeds certain stages (e.g. in autorecon2) up considerably. I'm also sure Bruce wouldn't turn down more resources to hire the programmers needed to make it faster either! Peace, Matt. On

[Freesurfer] mri_surfcluster

Hi all, I have obtained laterality indices using xhemi analyses and would like to use FDR instead of the mri_glmfit-sim suggested in the xhemi instructions. I know to get the FDR threshold from tksurfer, but I want to restrict the clusters to a certain cluster size. Based on a previous thread ( ht

Re: [Freesurfer] mri_surfcluster

just add "--subject fsaverage_sym" btw, that command does not perform FDR doug On 01/23/2014 01:41 PM, krista kelly wrote: > Hi all, > > I have obtained laterality indices using xhemi analyses and would like > to use FDR instead of the mri_glmfit-sim suggested in the xhemi > instructions. I kn

[Freesurfer] poor grey/white distinction in superior part of scan

Hello, I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from grey.

Re: [Freesurfer] poor grey/white distinction in superior part of scan

Some pictures would probably be helpful to know what the issue is. Peace, Matt. From: Christine Smith Date: Thursday, January 23, 2014 1:05 PM To: Subject: [Freesurfer] poor grey/white distinction in superior part of scan Hello, I am emailing to inquire about whether poor grey/white cont

[Freesurfer] Help Thickness Reproducibility

Dear FreeSurfers I am having some troubles to run step 4 of protocol to thickness reproducibility. The error message is below: nf04:~> mris_surface_stats -nsmooth 100 -surf_name /home/nf04/subjects/t_pac01/su > > rf/lh.white -out_name > > /home/nf04/subjects/groupstudy/lh_std_60.mg

Re: [Freesurfer] mri_surfcluster

Thanks Doug! I realize this doesn't do FDR but I've gotten the FDR threshold from tksurfer and will use that as my -thmin. One last thing, how would I view the results of mri_surfclluster in tksurfer? Would I load the ocn.mgh file? If so, I can't seem to find it. On Thu, Jan 23, 2014 at 2:02 PM

Re: [Freesurfer] mri_surfcluster

there are lots of output. You can create an annotation (--oannot), labels (--olab), copy the input and set nonclusters to 0 (--o), map of corrected voxel-wise significances (--vwsig), or map of cluster-wise significances (--cwsig). Of course you can get a simple table of the output too (--sum

Re: [Freesurfer] Help Thickness Reproducibility

The dimension mismatch means that the input data does not match the surface. It looks like the surface is from an individual but the input data is from a group analysis (which means fsaverage subject) On 01/23/2014 02:35 PM, Thiago Junqueira wrote: > Dear FreeSurfers > I am having some trouble

[Freesurfer] converting binary cortical GM ribbon mask to mative T1 space

Hi, We'd like to map the cortical GM ribbon on our original single volume native space anatomical T1. The dataset has been run through recon-all -all. The 'rawavg.mgz' or '001.mgz' is the native space T1 and 'ribbon.mgz' is the cortical GM mask in freesurfer space, correct? I converted the ribb

Re: [Freesurfer] Corrections to the segmentation lead to giant defects

Hi Thomas when you say errors in the hippocampus do you mean the aseg or the surfaces? If the surfaces, don't worry about them as they are not used in the hippocampal region. You are probably connecting the temporal lobe to the main body of the white matter creating a giant defect. cheers Br

Re: [Freesurfer] -qcache / fsaverage / number of vertices errors

Hi Mihaela usually that means the subject was partially but not completely rerun. You can try using recon-all -s -make all and see if it fixes it cheers Bruce On Thu, 23 Jan 2014, Mihaela Stefan wrote: Hello FreeSurfers, I am trying to run a group analysis with Qdec following thistutorial

[Freesurfer] Fwd: QDEC error

-- Forwarded message -- From: Wanda Truong Date: 23 January 2014 16:57 Subject: QDEC error To: freesurfer@nmr.mgh.harvard.edu Hello, I am having trouble with my group analysis using QDEC. I have 3 groups, 72 subjects, and 4 covariates. This is the error I get: Loading data tabl

Re: [Freesurfer] Fwd: QDEC error

there is something wrong with the format. did you make your qdec table on a windows machine? If so, convert it to linux format or recreate it on a linux/mac machine doug On 01/23/2014 07:02 PM, Wanda Truong wrote: > > > -- Forwarded message -- > From: *Wanda Truong*

[Freesurfer] FW: poor grey/white distinction in superior part of scan

From: Christine Smith Date: Thursday, January 23, 2014 3:58 PM To: Matt Glasser Subject: Re: [Freesurfer] poor grey/white distinction in superior part of scan Please note that the left and right sides of the brain are flipped for freesurfer vs the dicom picture. Please find attached a dico

[Freesurfer] (no subject)

Hi freesurfer crew, I found some details through this website http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm about cortical thickness maps with freesurfer. I have done some reading but can't really make much sense of how I might do this for a single subject thr

[Freesurfer] defect_labels to volume

Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red? Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Fleming