[Freesurfer] $SUBJECTS_DIR

HI,1-I'm working with FreeSurfer that is on a server.  I don't have permission to create files under the $SUBJECTS_DIR.  Is there any way I can specify -subject to be in a directory for which I do have permission? for example: recon-all -subject /location of the file or my own subject_dir locati

Re: [Freesurfer] $SUBJECTS_DIR

Thanks, any thoughts about Q#2:2-Also, Is there a way to segment the cortices as a whole, like left and right frontal cx, parietal cx, temporal cx, occipital cx? Thanks aj On Saturday, August 20, 2016 9:21 PM, "sha...@nmr.mgh.harvard.edu" wrote: Hi Adil,   My understanding is that, you

[Freesurfer] structure volume

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of structures for the same brain. Just trying to understand why that is? best, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mg

[Freesurfer] structure volume dti_recon vs recon_all

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of various structures for the same brain. Just trying to understand why that is? best, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail

[Freesurfer] T1 lesions

Hi, Is there any way in tkmedit or freeview to set T1 lesions to background value or to exclude them before recon-all is run so that these lesions do not get misclassified? Thanks, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] freeview

Hi, is there any way to overlay only certain regions of interest from the LUT table and not all of them in freeview or tkmedit over a T1 image?  I want to just display certain areas or ROIs. thanks, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.har

[Freesurfer] subtracting segmented volumes

Hi, Is there a way to subtract segmented files in freesurfer?  For example, aparc+aseg.mgz - aseg.mgz= aparc.mgz only?  I am interested in looking only at the cortex.  I find that label to volume conversion doesn't give me a nice segmented cortex, with some patchy areas of intensities lost. tha

[Freesurfer] segment lobes

Hi, This may be complicated, but ... I would like to segment various brain lobes, save them as mask files, convert them to NIFTI format, feed them to FSL for tractography. Can anyone tell me if it is possible to segment brain lobes in freesurfer and then feed them to fsl? many thanks in advan

[Freesurfer] label to volume

Hi, I am a bit new to freesurfer. I want to convert rh.V1.label to volume. I have read the wiki for it but still having some problems. All I want is just a volume in the native space. Can someone just detail the script for me. Thanks. AJ ___

[Freesurfer] MRI book

Hi, Is there any good MRI book that teaches the basics of MRI acquisition and various types of sequences or maybe another that teaches basics of image analysis? Thanks, AJ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m