Re: [Freesurfer] create ctab from annot
External Email - Use Caution Oh! I thought with that flag I have to provide a colortable. That worked perfectly now!! Thanks so much! -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: Tuesday, December 04, 2018 10:45 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] create ctab from annot External Email. Use Caution. 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. If you have received this transmission in error, please >>> notify the sender immediately by telephone and electronic mail, and >>> delete the original communication and any attachment from any >>> computer, server or other electronic recording or storage device or >>> medium. >>> Receipt by anyone other than the intended recipient is not a waiver >>> of any attorney-client, physician-patient or other privilege. >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.har >> vard.edu_mailman_listinfo_freesurfer=DwIGaQ=v
Re: [Freesurfer] create ctab from annot
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. If you have received this transmission in error, >>> please notify the sender >>> immediately by telephone and electronic mail, and delete the original >>> communication and any >>> attachment from any computer, server or other electronic recording or >>> storage device or medium. >>> Receipt by anyone other than the intended recipient is not a waiver >>> of any attorney-client, >>> physician-patient or other privilege. >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=vq5m7Kktb9l80A_wDJ5D-g=ycrYUdKGMCyTnsIy5TvOdBwS8HE5ZtmVMesLULEN8xE=QPv8K_5wpyhJr_LRmZsTwvapZlVEurTkAES4Y6HMm3o=VYUpTK7eYnYVq1m1PpzlUbOWPHHR-IaxQF7Ubuqp-lU= > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=vq5m7Kktb9l80A_wDJ5D-g=ycrYUdKGMCyTnsIy5TvOdBwS8HE5ZtmVMesLULEN8xE=
Re: [Freesurfer] create ctab from annot
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. If you have received this transmission in error, >> please notify the sender >> immediately by telephone and electronic mail, and delete the original >> communication and any >> attachment from any computer, server or other electronic recording or >> storage device or medium. >> Receipt by anyone other than the intended recipient is not a waiver >> of any attorney-client, >> physician-patient or other privilege. >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=vq5m7Kktb9l80A_wDJ5D-g=ycrYUdKGMCyTnsIy5TvOdBwS8HE5ZtmVMesLULEN8xE=QPv8K_5wpyhJr_LRmZsTwvapZlVEurTkAES4Y6HMm3o=VYUpTK7eYnYVq1m1PpzlUbOWPHHR-IaxQF7Ubuqp-lU= ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIGaQ=vq5m7Kktb9l80A_wDJ5D-g=ycrYUdKGMCyTnsIy5TvOdBwS8HE5ZtmVMesLULEN8xE=QPv8K_5wpyhJr_LRmZsTwvapZlVEurTkAES4Y6HMm3o=VYUpTK7eYnYVq1m1PpzlUbOWPHHR-IaxQF7Ubuqp-lU= 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, distributio
Re: [Freesurfer] create ctab from annot
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. If you have received this transmission in error, >> please notify the sender >> immediately by telephone and electronic mail, and delete the original >> communication and any >> attachment from any computer, server or other electronic recording or >> storage device or medium. >> Receipt by anyone other than the intended recipient is not a waiver >> of any attorney-client, >> physician-patient or other privilege. >> > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] create ctab from annot
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. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
