[Freesurfer] mri_watershed

We use an anatomical analysis program called Brain Image in our lab. We would like to speed up our analysis in Brain Image by replacing manual skull stripping with FreeSurfer's automated skull strip program. For this we would need to do a skull strip alone, without adjusting intensity values

[Freesurfer] process volume

hey guys, Im trying to process an orig scan from the terminal line: [EMAIL PROTECTED] orig]$ recon-all -subjid 1768-4 -segmentation INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects program versions used $Id: recon-all-nmr,v 1.72

[Freesurfer] segmentation fault during mri_convert

Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a segmentation fault. it still converts to cor format fine but i thought we were trying to get away from that. i dont know

Re: [Freesurfer] mri_watershed

Dear Sasha, mri_watershed was initially designed to skull strip orig images, without any preprocessing step, such as intensity normalization or contrast modification. So, This certainly seems like a reasonable thing to do. However, mri_watershed might normalize intensities during the

Re: [Freesurfer] process volume

It automatically tries to figure out what format you use for your analysis. It looks for mri/orig/XXX.mgz (which XXX is anything between 0-9). If it does not find that, it assumes COR. Specify -mgz to force mgz. David Soscia wrote: hey guys, Im trying to process an orig scan from the

Re: [Freesurfer] segmentation fault during mri_convert

yes, this worked. thanks so much, margaret On Fri, 19 Aug 2005, Nick Schmansky wrote: Margaret, The specified output filename needs to have .mgz at the end. In your case, it would be: $SUBJECTS_DIR/SM2C1_autoreconall/mri/orig/002.mgz I noticed that

Re: [Freesurfer] mri_watershed

Hi Sasha, If you use tkmedit to visualize the results, then the contrast change you saw may be just due to the display problem (not exactly a problem) of tkmedit. You can move the mouse around the image to actually see whether the image intensity values were changed or not. I used

Re: [Freesurfer] coregistration

You may try FLIRT from FSL. http://www.fmrib.ox.ac.uk/fsl/flirt/ -Xiao On Fri, 19 Aug 2005 [EMAIL PROTECTED] wrote: I always have a problem to coregistrate T1 images to Talairach, Is there any way to improve the accuracy of coregistration besides tkregister2? Thanks, Antao

[Freesurfer] Permission denied

Hello, Recently moved freesurfer from one system to another, but I am having trouble executing it. ./csurf: Permission denied. I have license in the right folder. Has anyone experienced the same problem. Thanks, Arvind ___ Freesurfer mailing list

Re: [Freesurfer] Permission denied

Recently moved freesurfer from one system to another, but I am having trouble executing it. ./csurf: Permission denied. I have license in the right folder. Has anyone experienced the same problem. Make sure it is executable. Try: chmod a+x csurf -- Kevin Teich

[Freesurfer] process volume again

hey guys, Now I am getting this error when trying to process the volume: [EMAIL PROTECTED] 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects program versions used $Id: recon-all-nmr,v

[Freesurfer] new freesurfer atlases for dev

For those in the NMR center using the freesurfer dev environment, there will re a change in recon-all to use "new" atlaes by default. This change will be live on Monday. The new cortical atlases are based on automatically filling ventricles and subcortical structures using the automatic

Re: [Freesurfer] mri_watershed

no, it should just strip. Is that not happening? If not, you can always use mri_mask to use the skull stripped volume as a mask to apply to whatever volume (in register with the orig) you want. cheers, Bruce On Fri, 19 Aug 2005, Sasha Wolosin wrote: We use an anatomical analysis program

Re: [Freesurfer] segmentation fault during mri_convert

you need to specify a file with the extension .mgz as the output name On Fri, 19 Aug 2005, Margaret Duff wrote: Hi, Is mri_convert setup yet to convert to mgz format? I have been trying it in both the std and dev environment from dicom format and spm format and i keep getting a

Re: [Freesurfer] mri_watershed

Alternatively, depending on what version of tkmedit you have, you can use the -mm-main min max option to specify an out-of-range min and max visible value on the command line. As Xiao said, normally the min and max visible values that determine the color scale are preset to the actual min

Re: [Freesurfer] process volume again

Not sure what's going on there. You may have gotten into a situation where some of the processing was done in COR and some im MGZ. It will assume to do things in mgz unless you specify -COR. One thing you can do to get things synched back up is to convert all your CORs to mgzs, eg, cd mri