Just add --ctab colortable On 12/4/18 9:32 AM, Winkelbeiner, Stephanie A wrote: > External Email - Use Caution > > Hi Douglas, > > I followed your advice doing the following: > > mri_annotation2label \ > --subject fsaverage \ > --hemi lh \ > --annotation new.aparc \ > --outdir ./label_new > > However, that results only in the single labels. > I couldn't find a specific flag that allows me to also extract the colortable. > > Is there one? > > Thanks, > Steph > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas > N.,Ph.D. > Sent: Monday, December 03, 2018 7:11 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [EXTERNAL] Re: [Freesurfer] create ctab from annot > > External Email. Use Caution. > > You can use mri_annotation2label to extract a color table from the annotation > > On 12/03/2018 07:06 PM, Bruce Fischl wrote: >> Hi Stephanie >> >> can you give us some details about how you generated your fine-grained >> parcellation? >> >> cheers >> Bruce >> On Mon, 3 Dec 2018, Winkelbeiner, Stephanie A wrote: >> >>> External Email - Use Caution >>> >>> Hi freesurfer-experts, >>> >>> >>> >>> I used a customized script that produces a more fine-grained >>> parcellation resulting in an .annot file. >>> >>> I don’t seem to have a look-up-table (LUT), however. >>> >>> >>> >>> I tried the following: >>> >>> - mri_annotation2label à allows me to extract the single >>> labels. But I rather need a .ctab file when I want to read out my >>> values. >>> >>> - mris_anatomical_stats with the –c flag à to output the >>> colortable as a text file I first need the .ctab file. >>> >>> >>> >>> Is there a way to get the LUT in a text file or the .ctab file just >>> from the annotation file? >>> >>> >>> >>> Thanks a lot in advance! >>> >>> Cheers, >>> >>> Stephanie >>> >>> >>> >>> Stephanie Winkelbeiner, MSc >>> >>> Research Coordinator >>> >>> Psychiatry Research >>> >>> Zucker Hillside Hospital >>> >>> 75-59 263 Street >>> >>> Glen Oaks, NY 11004 >>> >>> Tel: (718) 470-4588 >>> >>> Email: swinkel...@northwell.edu >>> >>> >>> >>> Northwell Health >>> >>> Visit us at Northwell.edu >>> >>> >>> >>> >>> The information contained in this electronic e-mail transmission and >>> any attachments are intended >>> only for the use of the individual or entity to whom or to which it >>> is addressed, and may contain >>> information that is privileged, confidential and exempt from >>> disclosure under applicable law. If the >>> reader of this communication is not the intended recipient, or the >>> employee or agent responsible for >>> delivering this communication to the intended recipient, you are >>> hereby notified that any >>> dissemination, distribution, copying or disclosure of this >>> communication and any attachment is >>> strictly prohibited. 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