Re: [Freesurfer] Pial surface editing

Hi Michelle the wm segmentation is kind of irrelevant - it's the ?h.white surfaces that matter (and maybe not even those if you only care about subcortical things) cheers Bruce On Fri, 25 Aug 2017, Michelle VanTieghem wrote: Hi Bruce,  I got this to work, but we are still having the same

Re: [Freesurfer] Pial surface editing

Hi, As a related question, we have been using FSL 5.3. I would like to use LME methods. I noticed that FSL 5.3 "Allows processing of subjects with single time point through the longitudinal stream to include them without bias into statistical analysis (LME)." but the Matlabs LME tools are only

Re: [Freesurfer] Pial surface editing

Hi Bruce, I got this to work, but we are still having the same problem wth over-inclusion of pial matter in the white matter segmentations even when using skullstrip from other packages (AFNI , FSL, ANTs). I am mainly interested in the subcortical volumes, and I want to do a longitudinal

Re: [Freesurfer] [SpamVerdacht!] Re: cudadetect fails: wrong amount of memory and number of cores detected

On 25 August 2017 at 07:10, wrote: > thank you for that hint. I will try to download all required packages and to > compile FreeSurfer myself. Make sure that you install the latest NVIDIA SDK - and that the Freesurfer compile is picking it up. Richard

Re: [Freesurfer] dividing cortex into equal patches

Also I tried using both lh.sphere and lh.sphere.reg and in both cases, the patches arent equal in surface area. There is a lot of variablility in surface area and the number of vertices. Please see below. Is there a way to generate roughly equal size patches ? Thank you, Ani USING lh.sphere in

Re: [Freesurfer] dividing cortex into equal patches

you can't specify the exact number - it has to be one of the icosahedral superparcellations (one of the ic?.tri files) On Fri, 25 Aug 2017, Aniqa Dalowr wrote: Thank you for your quick reply. This is dividing the cortex into 642 patches. Is there a way to divide it into say 50 patches ? Can

Re: [Freesurfer] dividing cortex into equal patches

Thank you for your quick reply. This is dividing the cortex into 642 patches. Is there a way to divide it into say 50 patches ? Can I specify the number ? Thank you, Ani On Fri, Aug 25, 2017 at 2:56 PM, Bruce Fischl wrote: > mris_make_face_parcellation should be

Re: [Freesurfer] dividing cortex into equal patches

mris_make_face_parcellation should be able to do this On Fri, 25 Aug 2017, Aniqa Dalowr wrote: Hi All, I want to divide the cortex into patches that have the ~ same surface area. Is there a quick way to do that ? Please let me know, Thanks Ani 

[Freesurfer] dividing cortex into equal patches

Hi All, I want to divide the cortex into patches that have the ~ same surface area. Is there a quick way to do that ? Please let me know, Thanks Ani ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Please unsubscribe me

Sure, you should be unsubscribed now. best, Andrew > On Aug 25, 2017, at 11:29 AM, Micah Rhodes wrote: > > Please unsubscribe me to this email list. > > Thanks. > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Please unsubscribe me

Please unsubscribe me to this email list. Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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

Re: [Freesurfer] nuiterations question

Hi Floris yes, taht is strange. We must have lost that option somewhere along the way. I think if you specify -3T it will set niterations to 1 (and also a couple of other things). We'll add it back in, but for no you could just edit the recon-all script to change nuiterations to be 1 by

[Freesurfer] Cortical Thickness of Hippocampus subfields

Dear Sir, I have performed Subfield segmentation of Hippocampus subfields, I would like to how i can calculate thickness of each subfield post segmentation, are the values in the text files *[lr]h.hippoSfVolumes--.v10.txt*: indicate estimated volume of each subfield , Is there any way i can

[Freesurfer] nuiterations question

Dear Freesurfer developers and community, I am using recon-all as part of a pipeline and I am wondering about how to control the non-uniform intensity correction. When I run `recon-all -help` I get: -nuiterations Number of iterations in the non-uniform intensity correction. Default is 1.

Re: [Freesurfer] recon-all

yes, it's fine On Fri, 25 Aug 2017, John Anderson wrote: Hi Dr Bruce, Yes it is in the blue circle. I point into it and I checked the other sections. Kindly see attached. Thank you for the advice Original Message Subject: Re: [Freesurfer] recon-all Local Time: August

Re: [Freesurfer] recon-all

Hi John I'm not entirely certain what you mean, but the figure you sent looked fine. If you are thinking that the circled area is a detached piece of wm, it is almost certainly not. Click on the center of it and look in a different view and you will see that it is connected through-plane

Re: [Freesurfer] recon-all

nope, that shouldn't matter for the cortical models (if that is what you care about). Frequently brainstem is very far from isocenter and coil elements, and hence low SNR causing this to happen. cheers Bruce On Fri, 25 Aug 2017, John Anderson wrote: > Dear FS experts, > Attached is a snapshot

Re: [Freesurfer] Skull striping problems

Hi Mateus you need to send us your command lines and screen output. If you do it properly (recreating brainmask.mgz), then yes, the new masking should be used in everything cheers Bruce On Fri, 25 Aug 2017, MATEUS ROZALEM ARANHA wrote: Hi! When I run recon-all on my data, some skull and

[Freesurfer] Skull striping problems

Hi! When I run recon-all on my data, some skull and dura is left behind and affects the surfaces and the parcellation. I re-run the data using a lower watershed (I tried 20, 15, 10 and 05). The brainmask changed, but the remaining skull still affects the parcellation and surfaces. My doubt is:

[Freesurfer] -refeventdur in mkanalysis-sess?

Hi FreeSurfer Team, I was wondering if you could provide a bit more clarification on what the "-refeventdur" flag is referring to in the mkanalysis-sess command? The description in the help screen states it should be the "duration (sec) of reference event for scaling." I am unsure what the

Re: [Freesurfer] Recon-all error

Hi Bronwyn, Doug is out of the office today. What is the command you ran after deleting everything in the surf folder? Can you send us the recon-all.log? Best, Emma - Emma Boyd Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical

Re: [Freesurfer] [SpamVerdacht!] Re: cudadetect fails: wrong amount of memory and number of cores detected

Hi Richard, thank you for that hint. I will try to download all required packages and to compile FreeSurfer myself. Kind regards, Markus Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] im Auftrag von R Edgar

Re: [Freesurfer] Error with recon-all long

Hi Bronwyn, I would guess that there has been a problem with the way you run the base. Take one case, copy the cross sectionals into a new directory and re-run the base from scratch. If your two time points are named like: TPID_001 and TPID_002 then the base command should be: recon-all