Re: [Freesurfer] -autorecon2-cp

Hi Jaiashre as long as they are in unpartial-volumed, healthy white matter you should be ok cheers Bruce On Mon, 14 Mar 2016, Jaiashre Sridhar wrote: > > Bruce, > Thanks! Apart from the control points on the lesions, I have control points > that were placed on consequent slices on the coron

Re: [Freesurfer] -autorecon2-cp

Bruce, Thanks! Apart from the control points on the lesions, I have control points that were placed on consequent slices on the coronal view but they look stacked upon one another from a different view. But these control points are placed on voxels that are definitely white matter. Does placing

[Freesurfer] error while running dt-recon all

Dear Freesurfer experts, FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.5.0 x86_64 I received the following error while running the dt_recon --i 00010001 --s 40 --o /Users/jasminalves/Desktop/data/FREESURFER/40. The parti

Re: [Freesurfer] -autorecon2-cp

if you can really remove them all then you can do so without starting from scratch, but make sure you get every one. Any control point in a lesion will mess everything up I would think cheers Bruce On Mon, 14 Mar 2016, Jaiashre Sridhar wrote: Hi,  I have a general question about control poin

Re: [Freesurfer] Editing Lesions in FreeSurfer 5.1

Hi Allison you need to tell us what kind of lesion and what the reconstruction issues are cheers Bruce On Mon, 14 Mar 2016, Allison Rainford wrote: > Hi Freesurfer Team, > > In FSTutorial, it states that control points should not be placed on lesions > to try to normalize the intensity there a

[Freesurfer] -autorecon2-cp

Hi, I have a general question about control points. I have added control points to fix the white matter boundary errors throughout the brain. I think that some of these control points that were placed in brain lesions (lower intensity voxels or black spots that are supposedly white matter) have

[Freesurfer] Editing Lesions in FreeSurfer 5.1

Hi Freesurfer Team, In FSTutorial, it states that control points should not be placed on lesions to try to normalize the intensity there and only white matter edits should be made. What should be done in the case that white matter edits alone do not resolve reconstruction issues at the site of

[Freesurfer] voxel vs surface based morphometric analysis

Hi Doug, I ran voxel based analysis in FSL to check the differnce in PET signal between two groups. The results are totally differnt than surface based analysis in Freesurfer.  I this real or I am doing something wrong? I tried to do the same but using FA maps and also I got totally differnt resul

[Freesurfer] Extremely small numbers of extracted pial surace area

Dear FS team: I want to ask for some advice on how to extract the values of pial surface area. I use QDEC to perform a surface-based F-test. The measurement is area.pial and the smoothing is 10 in QDEC. After correction, there is one significant cluster with size of ~760 mm^2. The problem comes

Re: [Freesurfer] group analysis all measures same results

I don't know what happened. I cannot replicate it here. Can you re-run the recon-all -s -qcache command and verify that the files are still the same? On 3/14/16 11:11 AM, Kaiming Yin wrote: Dear Douglas, Yes, both of the two pairs of files are the same. i.e. mri_diff rh.ad_hv.thick.10.mgh rh

[Freesurfer] Volumes of individual subject based on 001.mgz or nu.mgz?

Dear guys, Could I ask in the process of each individual data, are the volumes in the aseg.stat file or other files in the stats/ folder based on the 001.mgz data or the nu.mgz data, or others? It seems there is a bit transformation from the 001.mgz to the nu.mgz, is this true? And will this trans

[Freesurfer] Fw: mri_glmfit-sim

  Hi FS experts, I am trying to correct the results of groups analysis using mri_glmfit-sim the command is :   mri_glmfit-sim --glmdir lh_10mm --cache 3 pos --cwpvalthresh .0166   I receive the follwoing error :   ERROR: cannot find /usr/local/freesurfer/stable6/average/mult-comp-cor/

Re: [Freesurfer] group analysis all measures same results

Dear Douglas, Yes, both of the two pairs of files are the same. i.e. mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh diffcount 0 mri_diff rh.thickness.fwhm10.fsaverage.mgh rh.area.fwhm10.fsaverage.mgh diffcount 0 Does this mean I run the "-qcache" wrongly? I just run "recon-all -s XX -q

Re: [Freesurfer] group analysis all measures same results

Check whether rh.ad_hv.thick.10.mgh and rh.ad_hv.area.10.mgh are the same, ie, mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh If those are the same, then check whether thickness.fwhm10.fsaverage and area.fwhm10.fsaverage are the same in each subject On 3/14/16 10:53 AM, Kaiming Yin wr

Re: [Freesurfer] mris_anatomical_stats -th3

Without -th3, it will compute cortical volume using thickness*surface area. With -th3 it computes volume using truncated tetrahedra. -th3 will become the default in v6 (requiring -no-th3 to revert back to thickness*area) On 3/14/16 10:49 AM, Kaiming Yin wrote: Dear Douglas, I saw the previou

Re: [Freesurfer] group analysis all measures same results

Dear Douglas, My command lines were, e.g. right thickness and right white surface (using the same ad_hv.fsgd and group_diff.mtx files in the command lines): ad_hv.fsgd GroupDescriptorFile 1 Title AD_HV_GroupAnalysis Class AD Class HV Input AD_003 AD Input AD_005 AD ... Input HV_AB HV Input HV_A

Re: [Freesurfer] unknown option in new brainstem segmentation

Hi Douglas, I downloaded the current version of Freesurfer 6.0 and now recon-all with brainstem option works! Thanks a lot Claudia Da: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] per conto di Douglas N Greve [gr...@n

Re: [Freesurfer] mris_anatomical_stats -th3

Dear Douglas, I saw the previous tutorials didn't include this "-th3" flag, is there any difference between the following two command lines? mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subje

[Freesurfer] Anterior to Posterior Length

Good morning, I would like to use anterior to posterior length as a covariate in my DTI analysis. Is there an easy way to obtain this information for each subject? Thank you, Heather Acuff ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

[Freesurfer] aparc stats volume outputting area instead

Hi, I am trying to pull out the volumes from the aparc stats file but when I input the following (below) it produces a file identical to the area instead: aparcstats2table --subjects 001 002 003 --hemi rh --meas volume --tablefile aparc_stats_volume_rh.txt It works fine for thickness and area

[Freesurfer] Problems with file un qdec analysis

Hello everyone, I've got some problems with qdec. I have .levels with more than 2 factors. For example a "grpe.levels" with three factors : children (enfant), adults (adultes) and nothing (rien). But if I want to exclude some subjects like children qdec doesn't work anymore (attachment : error mes

Re: [Freesurfer] hippocampal subfields - multispectral segmentation with FLAIR

Ciao Eugenio, thanks a lot for the support. We made some tests and clearly the high res T2 gives the best subfields contrast. We will proceed with the ADNI like parameters. Have a nice day, Luigi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] error - mri_nu_correct.mni

Hi Douglas, I have done this and I got the following message: “cd /data/PDE10_PD_DENOVO/Freesurfer/DENOVO/subjects/PD1/mri hwilson@nig05 mri]$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale ERROR: must specify an input volume hwilson@nig05 mri]$ --i orig.mgz --o orig_n