[Freesurfer] Coregister the CT image and MRI image

need to do some extra steps after the above command in order to get the correct alignment of the two images. I was hoping to get the resultant image should be well orient with the target volume image (vol2.nii image in my case). I really appreciate any help here. Hari Guragain

Re: [Freesurfer] Coregister the CT image and MRI image

you can get from here > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg > > > On 06/09/2016 01:58 PM, HARI GURAGAIN wrote: >> Dear Freesurfer community, >> >> I am relatively new to this community. >> >> I was trying to reg

Re: [Freesurfer] Coregister the CT image and MRI image

ou run it without args, it will > give you some info, but it is basically > > mri_coreg --mov vol1.nii --targ vol2.nii --reg v1to2.lta > > > On 06/09/2016 05:22 PM, HARI GURAGAIN wrote: >> Thank you Douglas. >> One more thing: Is there any syntax how to us

Re: [Freesurfer] Coregister the CT image and MRI image

reve wrote: > > try > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg.mac > > > > On 06/09/2016 06:21 PM, HARI GURAGAIN wrote: >> Dear Douglas, >> >> The executable is not working as it says ‘Library not loaded: >> @executable_path/../lib/g

Re: [Freesurfer] Coregister the CT image and MRI image

greatly appreciated. Thank you again, Hari Guragain > On Jun 9, 2016, at 5:53 PM, HARI GURAGAIN wrote: > > Dear Douglas, > > I have used the same file as you pointed, but it keeps on showing the same > error message. I copied the file to my /Applications/freesurfer/bin d

[Freesurfer] Using Freesurfer commands in matlab

Dear Freesurfer, I am using the new development version of freesurfer ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev). I am trying to call some of the freesurfer commands like: mri_coreg or some other. When I use the something like the following in Matlab: command='/Applications/freesu

[Freesurfer] Problem while using the -localGI

Dear Freesurfer experts, I am having trouble using the -localGI option to smoothen the pial surface. When I use the command like: recon-all -s ABC -localGI I got the following error: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Sta

[Freesurfer] fornix segmentation using recon-all

15.82.67. Thank you, Hari Guragain ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is

Re: [Freesurfer] fornix segmentation using recon-all

could find the volume of both left and right fornix. Thank you in advance for help. Hari Guragain, On Fri, Jul 8, 2016 at 11:38 AM, Bruce Fischl wrote: > Hi Hari > > if you include the -f flag to mri_cc it will include the fornix in the cc > segmentation. We haven't tes

[Freesurfer] Hippocampal Subfields for T2-FLAIR images

hippocampal subfields can handle the T2-FLAIR? According to the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields), it can handle the T2 but didn't say anything about the T2-FLAIR. It would be great if someone clarify this. Thank you, Hari Gur

[Freesurfer] ERROR: make_roi_paths did not complete successfully!

Hi Freesurfer experts, I was working on to conduct the local gyrification index analysis. I am getting the following error message when I used the option -localGI in recon-all. Improper assignment with rectangular empty matrix.

Re: [Freesurfer] Need Help

Thanks a lot. It helped. > On May 25, 2016, at 3:24 PM, Douglas N Greve > wrote: > > recon-all -s yoursubjectname -i /path/to/one/dicomfile.dcm > tksurfer yoursubjectname lh pial -ov > $SUBJECTS_DIR/yoursubjectname/surf/lh.thickness -fminmax .1 3 > > > On 05/24/2

[Freesurfer] ERROR: mritotal failed, see transforms/talairach.log

Hi Freesurfer Community, I was trying to run the recon-all for one of the subjects. I got following error message: "ERROR: mritotal failed, see transforms/talairach.log". The image seems to have some missing hippocampal area. I wonder If we can still run the recon-all? I checked previous archive