[Freesurfer] FS 6.0 dev for Mac?

Hi Freesurfer team! I wonder if the newest FS version (6.0) is available for a more recent MacOs Version than Lion... Best wishes, Luke___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Hi Bruce! I am working on a Mac, OS 10.10.1, FS version: freesurfer-Darwin-lion-stable-pub-v5.3.0 Many thanks in advance! Lukas > Hi Luke > > what software/hardware version do you need? > Bruce > On Wed, 17 Dec 2014, lukas.sch...@ukb.uni-bonn.de wrote: > > Hi Bruce! > > I just would like to

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Hi Bruce! I just would like to come back to your offer to post the current version of mri_tessellate. Would you mind to send me the file? Sincerely yours, Luke > Hi Bruce! > I am working on a Mac, OS 10.10.1, FS version: > freesurfer-Darwin-lion-stable-pub-v5.3.0 > > All the best, > > Luke

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Hi Bruce! I am working on a Mac, OS 10.10.1, FS version: freesurfer-Darwin-lion-stable-pub-v5.3.0 All the best, Luke > Re: [Freesurfer] use of high res T1 for subcortical segmentation > Bruce Fischl Thu, 11 Dec 2014 05:36:52 -0800 > > if you tell us what hardware/software platform you want it

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Dear Remi! Would you mind to send me the new mri_tessellate? Best wishes, Luke > Re: [Freesurfer] use of high res T1 for subcortical segmentation > Remi Gau Wed, 10 Dec 2014 06:29:04 -0800 > > Hey, > > Someone corrects me if I am wrong, but it seems that the number of > vertices currently all

Re: [Freesurfer] subcortical segmentation only

Dear Bruce! Thanks a lot for the response. I try to get an idea about the minimal time needed to get the subcortical volumes. Best wishes, Luke > Re: [Freesurfer] subcortical segmentation only > Bruce Fischl Wed, 10 Dec 2014 05:22:18 -0800 > > Hi Luke > > you can run -autorecon1 and -autoreco

Re: [Freesurfer] use of high res T1 for subcortical segmentation

Dear Remi! Thanks a lot for the fast response. Could comment further on your point that I might need a different version of mri_tesselate ... The spatial resolution I am talking about is 0.5x0.5x0.8 mm3. Best wihes, Luke > Yup. > > http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon > > Depend

[Freesurfer] use of high res T1 for subcortical segmentation

Hi folks! Is there any way to convince FS to make use of a high spatial resolution (better than 1 x 1 x 1 mm3) for subcortical segmentation? Best wishes, Luke___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

[Freesurfer] subcortical segmentation only

Hi FS-folks! I would like to perform a subcortical segmentation only and I am not sure which preprocessing steps I would have to perform to achieve this goal. So far I did always the full monty using reconall -all. Which reconall stages are needed if only the subcortical segmentation is of intere

Re: [Freesurfer] using multiple cores

Hi Zeke!Thanks a lot for the response. Better a late response than none :o)! Do you have any vague estimate when a new release will be available? So far I did not try to compile it from the sources, because it is not my daily business and for an inexperienced it most likely ends up with pure frust

Re: [Freesurfer] When/What to edit?

Hi Andrew!Your mail hit the point! I would love to hear some response of the experienced guys... Best wishes,Luke ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information i

Re: [Freesurfer] using multiple cores

Hi Bruce and others!I am still puzzeling how to speed up the process... I tried 4 prarallel sessions running exactly the same dataset as before. With 4 cores and 32 GB RAM I expected that I won't loose time / session. However, it was about 50% slower. Shell 1:recon-all -s ernie1  -i  /Applicatio

Re: [Freesurfer] using multiple cores

Hi Bruce!I just run: recon-all -s ernie2  -autorecon2 -openmp 4 mri_ca_register  uses 100.9% CPU at most ... Any idea?  Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes,Lukas>Hi Bruce!

Re: [Freesurfer] using multiple cores

Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas > Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 > > Hi Luke > > what version of FS are you running? We see s

[Freesurfer] using multiple cores

Hi folks! I try to use -openmp option on an iMAC with 4 cores. Unfortunately, I do not see any accelartion when processing a single data set with or without the flag -openmp flag set. recon-all -s ernie_1 -all leads to ~6,4h processing time. Unfortunately recon

[Freesurfer] Problems with hippocampus subfields segmentation

Hi FreeSurfer Experts! I try to run the hippocampus subfield reconstructions. Because I already run reconall -all on my subjects (without errors, all necessary manual edits were done) I try to reconstruct only the hippo-subfields: recon-all -s my_subjects -hippo-subfields The shell output is

[Freesurfer] awk issues on MacOS and RegionSettings

Hi folks! I just like to send some information regarding "awk" problems under MacOs which occurs at least on "German" systems. I am not quite sure if FS uses awk at any point - but it might help when processing FS results: With the Region Setting "Germany" in the general settings of MacOs ( sys

Re: [Freesurfer] version 5.3 coming out soon

Hi Bruce, Thanks a lot for the info. Would it mean we have to completely reprocess the data processed with 5.2? Or at which point of the preprocessing pipeline we should step in to fix the problems of 5.2...? I just have finished to process about 200 data sets with 5.2... Best wishes, Luke Am

Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

Dear Matt! Many thanks for your help! I will try it... All the best, Luke Matt Glasser

Re: [Freesurfer] Advice on integrating FSL\'s BET with recon-all

Hi Matt! Refering to an older mail from 06 Mar 2013 I would be also interested to integrate BET-results for the initial registration step. Using the -B option in BET I get very robust results. You recommend: "... using the BET extracted image instead of the image with skull for the initial

Re: [Freesurfer] convert phillips PAr/Rec files

You might use dcm2nii written by Chris Rorden http://www.nitrc.org/projects/mricron It is part of the MriCron package. For Windows, you can directly use the gui by dragging the files on the GUI. For MAC or Linux use the command line. Beste wishes, Luke Am 24.04.2013 um 21:56 schrieb "Douglas N

[Freesurfer] Set up data for longitudinal processing

Hi folks, sorry it's me again with a very basic question. What is the best way to import longitudinal data? recon-all -i /path/T1A.nii -i /path/T1B.nii FIRSTSUBJECT or recon-all -i /path/T1A.nii FIRSTSUBJECT_A recon-all -i /path/T1A.nii FIRSTSUBJECT_B I tend to use the second choice because

[Freesurfer] Antwort: Re: Incorporating (high resolution) T2- and FLAIR volumes

Dear Matt! Thanks a lot. We do have both FLAIR and T2 -> so I could use the FLAIR for the clean-up procedure and use the T2 volumes for myelin part... Best wishes, Luke Matt Glasser

[Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes

Hi FreeSurfer experts! We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions: 1) How do I incorporate T2/Flair volumes

[Freesurfer] Question regarding the subject directory

Hi folks! I would like to use a different subject dirctory (setenv SUBJECTS_DIR ). Does freesurfer still finds the folders which are located in the default subjects directory of the FS installation? Or are they simply not needed for the recon-all process ? I refer to cvs_avg35 etc. not to the te