[Freesurfer] Unsupported slice timing problem

We recently ran into an issue with Freesurfer's mri_convert tool where it gives an error of "unsupported slice timing pattern". We have some NIFTI MPRAGE files that have a "slice_code" with a value of NIFTI_SLICE_ALT_INC2 (=5). Issue arises in utils/mriio.c (line 9549 of rev:stable5), two slice

Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences

Hello Bruce, Thank you for your reply. I used recon-all -make all -s subject. Thanks, Jeff On Thu, Jun 16, 2011 at 3:11 PM, Bruce Fischl wrote: > Hi Jeff > > what command did you run to run them over? > > cheers > Bruce > > On Thu, 16 Jun 2011, Jeff Sadino wrote: > > Hello, >> >> When FS5 cam

Re: [Freesurfer] interpolation during conform step of oblique acquisitions

Hi Mike, the intent was to be independent of the prescription of the slices so that we could always depend on voxel coordinates having some anatomical meaning, regardless of what crazy slice orientation was prescribed. Not sure if Doug has some easier work around for you to prevent the rotation

Re: [Freesurfer] Name of the atlas

it's the version of Christophe Destrieux's atlas he updated in 2009 cheers Bruce On Thu, 16 Jun 2011, Dalwani, Manish wrote: > What atlas does aparc2009 represent? > > Regards, > Manish Dalwani > Sr. PRA > Dept. of Psychiatry > University of Colorado > __

Re: [Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences

Hi Jeff what command did you run to run them over? cheers Bruce On Thu, 16 Jun 2011, Jeff Sadino wrote: > Hello, > > When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects > Directory, and then reran them using the FS5 recon-all stream. This updated > their subject folders

[Freesurfer] Name of the atlas

What atlas does aparc2009 represent? Regards, Manish Dalwani Sr. PRA Dept. of Psychiatry University of Colorado ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in t

[Freesurfer] interpolation during conform step of oblique acquisitions

Hi guys, I'm curious why the conform step of mri_convert (in generating mri/orig.mgz) automatically interpolates oblique acquisitions. Is this a historical legacy? Something mandated by other elements of the FS pipeline? As a consequence of this behavior, if you have an oblique acquisition tha

[Freesurfer] ReRunning Subjects in Newer FreeSurfer Versions and ICV Differences

Hello, When FS5 came out, I copied over my FS4 reconstructions to my FS5 Subjects Directory, and then reran them using the FS5 recon-all stream. This updated their subject folders with the FS5 changes, but not in as many places as I would have thought. For example, on 6 test subjects, I created

Re: [Freesurfer] Overlay issues on freeview

Are you running the latest release version? Would it be possible to send us the surface file and the overlay file that crashes? Best, Ruopeng On 6/16/2011 3:34 PM, iac...@nmr.mgh.harvard.edu wrote: > Hi all, > I am trying to overlay a map on a specific subcortical structure (the > caudate). > >

[Freesurfer] Overlay issues on freeview

Hi all, I am trying to overlay a map on a specific subcortical structure (the caudate). -I obtained the surface of the structure using the command: mri_tessellate structure.nii.gz 1 lh.structure.surf -then I projected my map on the surface using: mri_vol2surf --mov map.nii --regheader structure

Re: [Freesurfer] Whole brain parcellation contd..

Thank you. I just found this: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ 1) Is it better to extract the masks from the .mgz file (as explained on this site) as opposed to converting the aparc+aseg-inhighres.mgz file to .nii.gz

Re: [Freesurfer] mri_annotation2labels

Hi Actually, its the opposite. I'm trying to get a volume from the label aka http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ On 06/16/11, Douglas N Greve wrote: > > If you're trying to create a label from a volume then use mri_cor2

Re: [Freesurfer] mri_annotation2labels

If you're trying to create a label from a volume then use mri_cor2label. doug Sudhin A. Shah wrote: > Hi, > > I am trying to use this for the aparc+aseg-in-highres.mgz file instead > of the default aparc > > mri_annotation2label --subject AY --hemi lh --outdir > $fsfolder/AY/labels this works >

Re: [Freesurfer] pre-bedposted data in tracula

Hi Scott, You can do trac-all -prep first, to make sure you generate all the files needed for path reconstruction (including generating priors and masks from freesurfer recons), then move all your bedpostx files to the dmri.bedpostX as Anastasia mentioned and then do trac-all -path (for tract reco

Re: [Freesurfer] Custom color table overlay for ROI analysis

Hi Shashwath you can load a color table from the file menu in tksurfer. We almost never do this, so I'm not positive it works. The other thing you could do is read the annotation into matlab and change the color table that is stored in it, then write it back out. cheers Bruce On Thu, 16 Jun 20

Re: [Freesurfer] Custom color table overlay for ROI analysis

Hi Alan - I dont see the instructions on how QDEC handles this? Could you point me out to the wiki page that has this info. Again I dont want to draw manual ROIs instead i want to assign my own value to the color tables corresponding to the aparc labels in FS. On Wed, Jun 15, 2011 at 4:28 PM, Alan

Re: [Freesurfer] mri_cc error

Hi Vanessa, it looks like the error must have occurred earlier in the process as the input to mri_cc can't be read. Can you send the whole recon-all.log? cheers Bruce On Thu, 16 Jun 2011, Vanessa Lim wrote: > Hi, > > > > does anyone know what to do here please? I can see it in file manager. >