[Freesurfer] Re: [martinos-tech] FreeSurfer NIFTI with SPM and AFNI

OK, I think I have this sorted out now. FreeSurfer can now exchange single-file NIFTI volumes (compressed (nii.gz) and uncompressed (.nii)) with FSL and AFNI. It can exchange single-file uncompressed (.nii) with SPM (still don't know whether spm can do compressed). FreeSurfer can also read two

Re: [Freesurfer] still trouble with this motioncor problem

The problem is that one volume (001.mgz) has 158 slices, while the other volume (002.mgz) has 160 slices. Originating volumes all need to be the same size. I'll add an error-check to print a message if there is a mismatch. If you really want to use these two volumes, then you could run mri_conve

Re: [Freesurfer] --conform option

Try viewing the minc file in tkmedit to make sure it is ok. Also, you can convert to nifti gz -- afni can read that, and the dir cos will be included. Bruce Fischl wrote: thanks Bob, let us know if the problem is on our end and we'll fix it. Bruce On Thu, 23 Mar 2006, Cox, Robert W. (N

[Freesurfer] still trouble with this motioncor problem

Hi I emailed a little while ago about this, but I haven't heard any solutions yet. As a check, I re-ran recon-all again this morning on a local machine. Still crashing. Here is the output: > recon-all -s $SUBJECT -motioncor INFO: SUBJECTS_DIR is /autofs/space/megraid_043/seder/freesurfer Ac

Re: [Freesurfer] recon-all bug in -normalization2 ?

thanks Sarah, we'll check it out. Bruce On Thu, 23 Mar 2006 [EMAIL PROTECTED] wrote: hi all, i noticed this bug in the recon-all script. according to the reconAllDevTable, if recon-all is called with just the -normalization2 flag it should call both mri_normalize and mri_mask. however, in loo

Re: [Freesurfer] --conform option

thanks Bob, let us know if the problem is on our end and we'll fix it. Bruce On Thu, 23 Mar 2006, Cox, Robert W. (NIH/NIMH) [E] wrote: AFNI does read the minc orientation fields. It does not read .mgh files. If there is a problem with the minc inpiut, we'll need to get a sample file for dia

[Freesurfer] recon-all bug in -normalization2 ?

hi all, i noticed this bug in the recon-all script. according to the reconAllDevTable, if recon-all is called with just the -normalization2 flag it should call both mri_normalize and mri_mask. however, in looking at the script it seems to only call mri_normalize. so, if using that flag you should

Re: [Freesurfer] mri_convert problems

Hi Bruce and Karsten, the volume looks much better in nICE, that is why we thought it was odd. I have no idea why the log says 130 files found, there is clearly 128 files in that folder. I will process it further and see how it works out. Thanks and have a nice day Inge > The log say's that it ha

Re: [Freesurfer] Faster and Parallel recon-all

Sarah I am a little confused. Are you saying that recon-all has a bug, or that super-recon has a bug? If you are saying recon-all has a bug, you should start a new thread so others who don't care about "faster and parallel..." are aware. If super-recon is screwed up, please tell me what you thin

Re: [Freesurfer] mri_convert problems

Hi Inge, > When trying to convert some new scans with mri_convert there seems to be a > problem with the reconstruction, also the signal intensity is in the > 300-500 range. See attached image. It does not return any errors. > > Could someone please point me in the right direction here? The log

RE: [Freesurfer] --conform option

Hi Stefano, the orientation info is stored in the header, and can be accessed with mri_info. It should be propagated to AFNI, not sure why it's not. Bob and Ziad: have you had any trouble with losing the direction cosines when converting things from .mgz? cheers, Bruce On Thu, 23 Mar 2006,

RE: [Freesurfer] --conform option

thanks Bruce, actually it is ok if I view it with tkmedit. But if I try to convert it to minc format and I try to view it with AFNI (for istance), I get the wrong orientation. Is there any way to automatically know which kind of orientation I am working with, so that I can include it in a scri

Re: [Freesurfer] --conform option

Hi Stefano, the --conform does several things to the input volume to put it into a format we expect. If you bring it up in tkmedit and it properly shows you the various directions (e.g. the "coronal" view is indeed coronal) then you should be fine. Bruce On Thu, 23 Mar 2006, Pellegrini, Stef

[Freesurfer] --conform option

Hi everybody, can anybody explain to me why when I use mri_convert with the --conform option with an input volume RAS oriented (let's say it is raw_mean.mgz) I get as output a volume LIA oriented (let's say it is orig.mgz)? is that ok? thanks, -stefano _

Re: [Freesurfer] mri_convert problems

is there an error? It looks like it converted fine. The signal intensities are essentially arbitrary until the intensity normalization. The volume looks okay (the lines in it are from reslicing it into standard RAS coordinates). Did you process it further? cheers, Bruce On Thu, 23 Mar 2006 [E