[Freesurfer] PROBLEMS WITH SEGMENTATION

Hi, I'm Leonardo an italian student of Pisa. I'm writing to you to ask if there's any way to correct this problem: we have a 3.0T machine with a 8 channels head coil to acquire the volumetric image. we have found a big inhomogeneity in the contrast of the image particularly in the frontal lob

[Freesurfer] recon-all with nifti

Hi, I'd like to launch recon-all with a nifti input file and get a nifti file in output... Do you know how can I do that? Thanks in advance! Chris' ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

Re: [Freesurfer] recon-all with nifti

Hi Chris, you can use nifit as input with no problem, and you can convert any of the output volumes to nifti using mri_convert. cheers, Bruce On Wed, 14 Apr 2010, Christophe Chênes wrote: Hi, I'd like to launch recon-all with a nifti input file and get a nifti file in output... Do you kno

Re: [Freesurfer] PROBLEMS WITH SEGMENTATION

Hi Leonardo, we need more details about your acquisition. What sequence with what parameters? What type of scanner? Was there any prescan normalization? Which 8 channel coil did you use and do you have access to other coils? cheers Bruce On Wed, 14 Apr 2010 chesi.leona...@alice.it wrote: > Hi

Re: [Freesurfer] mris_make_face_parcellation

yes, you can use the talairach.xfm file to get MNI coords of whatever you want. Not sure if it is reported anywhere by default though. Doug? On Wed, 14 Apr 2010, Diana Wotruba wrote: > Hi Bruce > Thank you for the quick answer. We already considered using > mris_divide_parcellation. Unfortunatel

[Freesurfer] recon-all with nifti

For the input,I try using this command: # recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning It returns the following error: # ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force ... __

Re: [Freesurfer] recon-all with nifti

that means the subject already exists, probably from a previous run that failed. Did you try running it with -force? On Wed, 14 Apr 2010, Christophe Chênes wrote: For the input,I try using this command: # recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -nota

Re: [Freesurfer] Problem with tkmedit Edit Voxels Tool on Intel Mac

Hi Ed, What do you exactly mean? The right click and drag doesn't remove the voxels and the middle click and drag doesn't add the voxels? I tried it and it works for me. I've copied the nightly build to ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/intel-mac/tkmedit.bin

[Freesurfer] 3d slicer view only the post-central gyros

hello, How can i use 3d slicer to only view the post-central gyros without the other areas, than you Asaf ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] displaying time course for blocked-design

Dear Freesurfer users, Is there a way to display time course information for blocked-design experiments? I have used the command tkmedit-sess, which displays time course information for event-related designs. However, it does not display anything like that for blocked design. Is it possible to cha