[Freesurfer] Issues with transferring edits from v6.0dev into v7.1

subject.tar.gz. Kind regards, Melanie -- Yours sincerely Melanie Ganz-Benjaminsen Forsker Direct: + 45 35 45 67 18 Mail: melanie.g...@nru.dk Neurobiology Research Unit Rigshospitalet, building 6931 Juliane Maries Vej 28, 3rd floor DK-2100 Copenhagen, Denmark Phone: +45 3545 6712 Fax: +45 3545

[Freesurfer] Issues with transferring edits from v6.0dev into v7.1

subject.tar.gz. Kind regards, Melanie -- Yours sincerely Melanie Ganz-Benjaminsen Forsker Direct: + 45 35 45 67 18 Mail: melanie.g...@nru.dk Neurobiology Research Unit Rigshospitalet, building 6931 Juliane Maries Vej 28, 3rd floor DK-2100 Copenhagen, Denmark Phone: +45 3545 6712 Fax: +45 3545

[Freesurfer] FSdev compilation error

Dear list, In order to use a brandnew Nvidia GPU we downloaded FSdev and are trying to compile it locally with a new CUDA version. We get all the way to the configure command described on http://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page which is: ./configure

[Freesurfer] Cuda version > 5.0

gotten it to work with 8.0 (see e.g. here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-May/052047.html). Has anyone gotten FS version 6 compiled with cuda 9.1? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen

[Freesurfer] 7 T analysis - does GPU help?

Dear list, especially Bruce and Jon, We are starting to acquire images on the local 7T Philips scanner and would like to run them through FS. We did some pilot runs following what's described on http://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon and in

Re: [Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Thanks, Zheng At 2017-10-30 16:33:02, "Melanie Ganz" < <mailto:melanie.g...@nru.dk> melanie.g...@nru.dk> wrote: Hi, So here’s the Wiki page for the human Allen brain data recons: <https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas> https://surfer.nmr.mgh.

[Freesurfer] Recons for Allen Brain Institute T1 images with v5.3 online

Hi, So here’s the Wiki page for the human Allen brain data recons: https://surfer.nmr.mgh.harvard.edu/fswiki/AllenBrainAtlas Right now there’s only the v5.3 recons, but the v6 recons are coming asap. Cheers, Melanie ___ Freesurfer mailing

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

Yes, I will write an email out once they are done.On Oct 20, 2017 10:49 PM, Sean Froudist Walsh wrote:That would be great Melanie, thank you very much. And thanks to Bruce and Satra for the quick responses.How will I be able to find the processed files? Will it be announced

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

quite straightforward to rerun with freesurfer 6. any chance you can run it through? otherwise i can send you a filedrop link off the list.cheers,satraOn Thu, Oct 19, 2017 at 4:13 PM, Melanie Ganz <melanie.ganz@nru.dk> wrote:Hi Sean, Satra and Bruce,We just recently ran them all with v5.3 and did

Re: [Freesurfer] Recon-all for Allen Brain Institute T1 image

Hi Sean, Satra and Bruce,We just recently ran them all with v5.3 and did quite a few edits, especially to the subject ending in 10. Remember, we asked you for help, Bruce? 5I had asked before if someone was interested in us uploading the work since we took quite some care in doing it, but there

[Freesurfer] Consistent volume increases for some regions when using longitudinal stream

Dear list and especially Martin, we have used Freesurfers crosssectional as well as the longitudinal stream and are inspecting the outcomes at the moment. We have as quality assurance been inspecting regions where the difference between initial CROSS results and the corresponding LONG

Re: [Freesurfer] Creating an illustration on what Freesurfer has considered to be intracranial volume

contact the sender and properly dispose of the e-mail. -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: melanie.g...@nru.dk web

[Freesurfer] eTIV estimation on same subject over time

the single eTIV value for volume correction, but for comparison in case of the cross-sectional stream we want to use the single time point values of eTIV. Any ideas what else I can check or is this simply noise transferred from the linear estimation of eTIV? Cheers, Mel -- Melanie Ganz

[Freesurfer] mri_vol2vol --mni152reg flips volume

$SUBJECTS_DIR/fsaverage/mri/orig.mgz --mni152reg --o fsaverage.orig.MNI152.nii.gz ends up yielding the attached image (red is the output file and background is FSL MNI152 template). Anything obvious he's doing wrong? Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology

Re: [Freesurfer] Strange wm error

. Does that make any sense to you why that helps? Cheers, Mel On 27-02-2017 5:23, Douglas Greve wrote: Hi Mel, how does the orig or orig.nofix look? On 2/24/17 9:21 AM, Melanie Ganz wrote: Dear list, we are experiencing a strange wm surface error that we are not quite sure about how

[Freesurfer] Writing FSL compatible ascii files

easier? Cheers from Copenhagen, Mel -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: melanie.g...@nru.dk web: http

[Freesurfer] QATools FreeView

/QATools#FutureDirections. Cheers, Melanie -- Melanie Ganz-Benjaminsen, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: melanie.g...@nru.dk web: http

[Freesurfer] Rat model in FreeSurfer

Hi, one of our lab mates who works with small animal models would also like to try FreeSurfer. I know from the mail archive that people have used it like this before. Could any people that have used it on rats please give some info on what they have tried? Cheers, Melanie -- Melanie Ganz

[Freesurfer] Announcing the Copenhagen FreeSurfer Course 2016

​​We are pleased to announce a European FreeSurfer Course that will be held  from August 10th to 12th, 2016 in Copenhagen, Denmark. The course will be  organized by the Neurobiology Research Unit, Copenhagen University  Hospital in cooperation with the Laboratory for Computational Neuroimaging  of

[Freesurfer] QAtools - tkmedit snapshots all black (X server issue?)

am suspecting that it is an x server issue with how I log into our Linux cluster here, but has anyone had the same problem before? Cheers, Mel -- Melanie Ganz, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100

[Freesurfer] Fwd: Re: success and failure of wm surfaces in (almost) identical structural image

']); disp(vol{n}); sum(img1.vol(:)10e-4) end Original Message Subject: Re: [Freesurfer] success and failure of wm surfaces in (almost) identical structural image Date: Tue, 26 Aug 2014 14:05:19 +0200 (CEST) From: Eugenio Iglesias e.igles...@bcbl.eu To: Melanie Ganz