Re: [Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

Hi Lloyd, I dealt with the same problem at one time. My input volume was a minc volume but I imagine the procedure should work for your input as well. for native.mnc, which was your input into freesurfer, do this command: mri_info --cras native.mnc my output was -2.35588 52.7907 24.8145 Then you

Re: [Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

what are you trying to do? If you're trying to bring the surface coords into talairach (mni305) space, then you can use mri_surf2surf with the --sval-xyz-tal orig --taval-xyz options. Lloyd Elliott wrote: I am trying to overlay surface information acquired with freesurfer on to the original

[Freesurfer] cortical lesions with FS (T1+DIR sequences)

Hi all, I'm using Freesurfer to calculate cortical atrophy in patients with multiple sclerosis. These patients usually have also cortical lesions that I can see with DIR sequences. My question is: can I piece together the 2 sequences to see cortical lesions with FS? for FS we use a 3D fast-fi

[Freesurfer] What is the transformation from surfaces vertices to volume voxel coordinates?

I am trying to overlay surface information acquired with freesurfer on to the original MRI volume. I tried reading lh.orig with [vertices,faces] = freesurfer_read_surf('surf/lh.orig') and then transforming the vertices with the matrix: vertices_affine = [vertices' ; ones(1,size(vertices

Re: [Freesurfer] mris_divide_parcellation

Hi Jose, I have another tool that we haven't released that will do this more closely. You can't do that with mris_divide_parcellation since the units don't start with equal area (or multiples thereof) cheers, Bruce On Thu, 19 Feb 2009, Jose Luis Cantero Lorente wrote: Dear FS Team, I use

Re: [Freesurfer] volume changes

and how do you measure volume? Certainly the voxel count is bound to change since your voxel size is changing. The volume will certainly change as well. cheers, Bruce On Thu, 19 Feb 2009, Jeff Dewey wrote: To answer your question more completely, we're trying to compare two files with the fol

Re: [Freesurfer] about segmentation

Make sure you are selecting the 'Edit segmentation tool' on the tkmedit tools window. You can also press the 'g' key to select the tool. Sita. On Thu, 19 Feb 2009, Silvia biopanda wrote: Hi, we are making changes in the aseg.mgz and we need to know how to erase a wrong pixels. we read in

Re: [Freesurfer] control points

can you do that copy by hand? Muhammad Ayaz wrote: Yes i do have read and write permissios to these data set. I just ran another subject from the data set and it ended at different stage but again says permission denied. #...@# Fix Topology lh Thu Feb 19 11:14:14 EST 2009 cp ../surf/lh.orig.

Re: [Freesurfer] control points

Yes i do have read and write permissios to these data set. I just ran another subject from the data set and it ended at different stage but again says permission denied. #...@# Fix Topology lh Thu Feb 19 11:14:14 EST 2009 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix

Re: [Freesurfer] qdec for fMRI using categorical covariate?

Just create a race.levels file with "Black" and "White", then include "race" as a column in your qdec.table.dat. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis for more details. doug Dave Brohawn wrote: Hello, I want to generate screenshots of group activation in

Re: [Freesurfer] mris_anatomical_stats segmentation fault

are you replaceing the "?" with the actual hemisphere designation? Diana Wotruba wrote: Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) with an area threshold of 100mm2. Now I would like to get a stats file, using the following command: mris_anatomical_stats -a aparc.a

[Freesurfer] about segmentation

Hi, we are making changes in the aseg.mgz and we need to know how to erase a wrong pixels. we read in the tutorial that the button three erases, but it doesn't work.how can we do? cheers, SK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

Re: [Freesurfer] control points

Do you have read and write permissions to that file? Muhammad Ayaz wrote: Dear All, I am in phase of learning freesurfer. I added control points using tkmedit and ran recon-all -autorecon2-cp and i get the following error. " Total Number of Modified Voxels = 854 (out of 716825: 0.119136) sh: w

Re: [Freesurfer] mris_divide_parcellation

I'm surprised that the divisions are not roughly equal in area. How much different are they? You can also spec an area threshold instead of a number of subdivisions, but that just keeps dividing until all subdivisions are below that area. I don't think we have anything that will divide them int

Re: [Freesurfer] - dt_recon and coregistration of DTI to anatomy

The answer is in the help, I think: dt_recon --help doug Kjell Inge wrote: I am using Freesurfer and I am having difficulties in coregistration of a DTI volume to the anatomy image. I have been running recon-all -i -i -s 2005_anatomy followed by recon-all -autorecon1 -s 2005_anatomy a

[Freesurfer] mris_divide_parcellation

Dear FS Team, I used mris_divide_parcellation to create a new parcelation with smaller regions, but all these regions seem to have a different size. I am interested to get smaller cortical parcellated regions, but all of them with the same area. How can I get it? Could I decide the area size?

[Freesurfer] mris_anatomical_stats segmentation fault

Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) with an area threshold of 100mm2. Now I would like to get a stats file, using the following command: mris_anatomical_stats -a aparc.a2005s_100.annot -t ?h.thickness -b -f 001/stats/?h.aparc.a2005s_100.stats 001 ?h I am g

[Freesurfer] - dt_recon and coregistration of DTI to anatomy

I am using Freesurfer and I am having difficulties in coregistration of a DTI volume to the anatomy image. I have been running recon-all -i -i -s 2005_anatomy followed by recon-all -autorecon1 -s 2005_anatomy and then dt_recon --i dti/subj_539_dti.nii --b dti/aging_hds_2005_dti.bval

Re: [Freesurfer] volume changes

To answer your question more completely, we're trying to compare two files with the following headers: Freesurfer segmentation: height = 256 width = 256 depth = 256 nframe = 1 imnr0 = 1 imnr1 = 256 xnum = 256 ynum = 256 fov = 256.00 thick = 1.00 xstart = -128.00 xend = 128.0

[Freesurfer] control points

Dear All, I am in phase of learning freesurfer. I added control points using tkmedit and ran recon-all -autorecon2-cp and i get the following error. " Total Number of Modified Voxels = 854 (out of 716825: 0.119136) sh: wm.mgz: Permission denied Broken pipe Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri

[Freesurfer] qdec for fMRI analysis with categorical covariate? (continued)

as a categorical covariate? Thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] qdec for fMRI using categorical covariate?

Hello, I want to generate screenshots of group activation in an anatomical ROI on the left and right hemisphere for two different groups of subjects at a particular contrast and time point of our analysis. We want to use race as a covariate (categorical, with whites and blacks being the two racia

Re: [Freesurfer] recon-all error: libexpat.so.0

All, For Suse Enterprise ( SLED ) 10.2, the following solution seems to work ( for Narly as well ): The library libexpat.so.0 Freesurfer is looking for is actually named libexpat.so.1 - First check whether you have a libexpat.so.1 ls /usr/lib64/libexpat.so.1 - If so, create a symbolic link with

Re: [Freesurfer] volume changes

what are the voxel sizes? On Wed, 18 Feb 2009, Jared Price wrote: Dear gurus, when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz seg_edited_axial.nii to reslice from coronal to axial space we are seeing some significant volume changes in the segmentation. Anyone know why

Re: [Freesurfer] getting vertex numbers

Hi Lars, you want to do "custom fill" then click the "over statistical threshold " option. Can't remember the exact name... cheers, Bruce On Wed, 18 Feb 2009, Lars M. Rimol wrote: Hi, I've done a glm model fit comparing cortical thickness between two groups, and have certain areas ("blobs"