Re: [Freesurfer] Converting a cluster to a ROI without manually drawing

Hi all, I figured it out. This is easily doable using TkSurfer. Thanks, Nasim On Sep 13, 2011, at 12:37 PM, Nasim Maleki wrote: > Hi all, > > In qdec, is there a way to convert a cluster to an ROI without > manually drawing the ROI? I'm talking about selecting clusters o

[Freesurfer] Converting a cluster to a ROI without manually drawing

Hi all, In qdec, is there a way to convert a cluster to an ROI without manually drawing the ROI? I'm talking about selecting clusters on the mc-z maps. Thanks, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

Re: [Freesurfer] Recon-all Error: _FindFacePath

On 15 February 2011 09:55, Bruce Fischl wrote: > Hi Nasim, > > can you tar and gzip the entire subject dir and send it to us? I'll try > to track it down. In the mean time if you just rerun with the old topo > fixer it should work. Nick can post the appropriate flags >

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hello, I'm facing the same problem for one of my subjects. Is there a general solution for this problem or would you solve this problem on a case by case basis? I saw posts from others with the same problem. Thanks for your help, Nasim On Nov 29, 2010, at 7:55 AM, Bruce Fischl wrote: > Hi Jenn

Re: [Freesurfer] Recon-all Error: _FindFacePath

Hello, I'm facing the same problem for one of my subjects. Is there a general solution for this problem or would you solve this problem on a case by case basis? I saw posts from others with the same problem. Thanks for your help, Nasim On Dec 2, 2010, at 9:18 AM, Jennifer Addicks wrote: > Hell

[Freesurfer] Demeaning TIV

Hi all, I have a question with regards to using the TIV as a covariate in comparing the subcortical volumes between the two cohorts. In particular I'm wondering: 1-Should you demean the TIV at all or not? 2-1-If you are using both age and TIV as your covariates, will it make sense to demean th

[Freesurfer] recon-all: Stages 6-11 only

Hi all, Is there a flag that you could run stages 6-11 ONLY of the autorecon process stages (after running the stages 1-5) instead of doing the whole 6-23 with -autorecon2 flag? Thank you, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.

[Freesurfer] --fsl flag in bbregister

Hello Doug, I get an error message when using --fsl flag with bbregister: "ERROR: Flag --fsl unrecognized." I'm using: bbregister,v 1.14.2.12 2009/08/07 22:21:00 greve Is this version of the bbregister that I'm using the latest? Thank you, Nasim _

[Freesurfer] FreeSurferColorLUT for FSL

Dear all, I would like to view the aparc.a2009s+aseg files in FSL and therefore I need to make LUTs for FSL from the FreeSurferColorLUT. I was just curious to know if any of you has ever done this and if there is an easy way around it. Thanks for your help in advance, Nasim ___

[Freesurfer] Labels for the auditory cortex

Dear developers, I was wondering if you would have labels for the Broadman areas corresponding to the auditory cortex for the fsaverage subject. Thank you, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard

[Freesurfer] Measuring the Volume of a 3D Mask

Dear all, I have 3D masks defined in MNI space using FSL. I would like to transform these masks to each subjects anatomical space in FreeSurfer and measure the volumes corresponding to these masks. Should I just count the number of voxels in each mask after transformation to the structural

[Freesurfer] mc-z, the same CWP for all clusters?

Hi all, I did the correction for multiple comparisons using mc-z with 1 iterations (sign=abs, Threshold=1.3). Now for all the clusters (30 clusters) on one of the hemispheres I find the same CWP (0.00140), CWPLow (0.00090) and CWPHi(0.00190) for all of them. For the other hemisphere h

[Freesurfer] Partial Volume Correction and wmparc.stats

Dear Freesurfer developers, I'm wondering whether the wmparc.stats is computed with a partial volume correction at the boundaries of the structures. Thank you, Nasim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.har

[Freesurfer] (repost) viewing sig.mgh files on the image volumes

Dear Freesurfers! I'm trying to transform and overlay the sig.mgh files on the 3D volumetric data. I use mri_surf2vol to convert sig.mgh and everything works fine up to the point that I try to view the overlay with tkmedit. There is no overlay on top of the main volume although it is succ

[Freesurfer] Problem viewing sig overlay?

Dear FreeSurfers, I'm trying to transform and overlay the sig.mgh files on the 3D volumetric data. I use mri_surf2vol to convert sig.mgh and everything works fine up to the point that I try to view the overlay with tkmedit. There is no overlay on top of the main volume although it is suc

[Freesurfer] Thalamus Segments

Dear Freesurfers, What would be the best approach to sub-segment the subcortical structures (using mri_divide_parcellation) to anatomically relevant sub-segments similar to Thalamus sub-segments in FreeSurferColorLUT.txt (SegID 8001 to 80014). Thank you, Nasim

[Freesurfer] Qdec and error with ?h.aparc.a2005s.thickness

Dear Freesurfers, I get the following error message in Qdec (1.1) when I choose ? h.aparc.a2005s.thickness on the tutorial data: Loading data table /Applications/freesurfer/subjects/qdec/ stats_tables//lh.aparc.a2005s.thickness.stats.dat... Number of columns: 79 fsid column:1 Number

Re: [Freesurfer] wm edits

scan, it'll probably take an hour or less. Sita. On Tue, 3 Mar 2009, Nasim Maleki wrote: Dear Freesurfers, I have a question on manual white matter edits: I have cases where a considerable amount of gray matter is classified as white in my wm.mgz and therefore the original surface

[Freesurfer] wm edits

Dear Freesurfers, I have a question on manual white matter edits: I have cases where a considerable amount of gray matter is classified as white in my wm.mgz and therefore the original surface (green) is not accurate but then that is fixed in the next steps and the wm surface (yellow) is a