Hi Zeke, Thank you, we will give it a try! Caspar On Wednesday, August 5, 2015, <zkauf...@nmr.mgh.harvard.edu> wrote:
> Hello Caspar, > > I did a quick test and it appears the new dev version of mri_label2label > is still compatible with the version of 5.1 that you have. Please use the > following link to download it and also please make sure to back up the > version you already have. > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/snowleopard-i686/mri_label2label > > -Zeke > > > > Hi Bruce, Doug, and Zeke, > > just checking back regarding the dev version for mri_label2label. > > Do you have a build that works on MAC OS 10.9.5 Mavericks? > > So far, we have been using > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0. > > > > Thank you, Caspar > > > > > > 2015-08-03 6:40 GMT-04:00 Caspar M. Schwiedrzik > > <cschwie...@rockefeller.edu <javascript:;>> > > : > > > >> We are using MAC OS 10.9.5 Mavericks and freesurfer-Darwin-leopard- > >> i686-stable-pub-v5.1.0 > >> > >> > >> On Thursday, July 30, 2015, Bruce Fischl <fis...@nmr.mgh.harvard.edu > <javascript:;>> > >> wrote: > >> > >>> Hi Caspar > >>> > >>> the dev version of label2label doesn't have this problem. If you let us > >>> know your hardware/software environment Zeke can get you a new binary > >>> that > >>> should fix this issue > >>> > >>> cheers > >>> Bruce > >>> > >>> > >>> On Thu, 30 Jul 2015, Caspar M. Schwiedrzik wrote: > >>> > >>> Hi Bruce and Doug, > >>>> thanks for looking into this and sorry for the delay. > >>>> The command line we are using is: > >>>> > >>>> mri_label2label > >>>> > --srclabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p > >>>> 8.label --srcsubject y$1 > >>>> > --trglabel/Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp > >>>> 2.label --trgsubject yx$1 --regmethod surface --hemi lh > >>>> > >>>> We have several anatomies from the same subject, acquired on different > >>>> occasions. > >>>> We defined labels based on results of an fMRI experiment, and tried to > >>>> use > >>>> mri_label2label to map them within subjects from one anatomy to > >>>> another. > >>>> As a > >>>> control, we also wanted to map the Hinds V1 from one anatomy to > >>>> another, > >>>> but this > >>>> is where we ran into these holes. > >>>> We will make an example subject available for debugging later today. > >>>> > >>>> Thanks! Caspar > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> 2015-07-24 12:33 GMT-04:00 Douglas Greve <gr...@nmr.mgh.harvard.edu > <javascript:;>>: > >>>> what is your command line? What do you mean by one anatomy to > >>>> another? > >>>> > >>>> On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: > >>>> > >>>> > >>>> ---------- Forwarded message ---------- > >>>> From: Caspar M. Schwiedrzik <cschwie...@rockefeller.edu > <javascript:;>> > >>>> Date: Thursday, July 16, 2015 > >>>> Subject: problem with mri_label2label - large amount of holes > >>>> To: "Freesurfer@nmr.mgh.harvard.edu <javascript:;>" > >>>> <freesurfer@nmr.mgh.harvard.edu <javascript:;>> > >>>> > >>>> > >>>> Hi! > >>>> We are doing some analyses in which we map custom labels from one > >>>> anatomy to another, within subjects. As a control, we also tried to > >>>> map anatomically defined V1s according to the method by Hinds within > >>>> subject from one anatomy to another. However, as you can see in the > >>>> attachment, there are very many holes in the labels after using > >>>> mri_label2label. This does not happen with smaller labels. Why is > >>>> this happening and is there a solution? > >>>> Thanks, Caspar > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu <javascript:;> > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu <javascript:;> > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> The information in this e-mail is intended only for the person to whom > >>>> it > >>>> is > >>>> addressed. If you believe this e-mail was sent to you in error and the > >>>> e-mail > >>>> contains patient information, please contact the Partners Compliance > >>>> HelpLine at > >>>> http://www.partners.org/complianceline . If the e-mail was sent to > you > >>>> in > >>>> error > >>>> but does not contain patient information, please contact the sender > >>>> and > >>>> properly > >>>> dispose of the e-mail. > >>>> > >>>> > >>>> > >>>> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <javascript:;> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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