Re: [Freesurfer] Dicom from CT

Sorry, yes we would like to calculate some volume statistics and surfaces models. Thanks, Will Message: 8 Date: Fri, 05 Dec 2014 15:42:16 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] Dicom from CT To: freesurfer@nmr.mgh.harvard.edu Message-ID: <548218a8.7020...@nmr.mgh.harvard.edu> Cont

[Freesurfer] Best possible atlas to extract hippocampus

Hello, As the complete recon process takes huge time for a single image, is it possible to register the MRI image using a simple atlas. If yes, please explain how to do it. My primary goal is to extract hippocampus in a fastest possible way. Pradeep Kumar Mahato __

Re: [Freesurfer] Extracting hippocampus

Hi Pradeep you could only run recon-all -autorecon2 instead of -all which should save you some time. 30 hours is pretty long though. What hardware are you using? If you have a modern Linux box with say 4-8 cores it should take less than 10. Or with 2 cores and >4G of ram you could run 2 recons

Re: [Freesurfer] Dicom from CT

Hi Will CT scans don't have enough contrast between gray and white matter to build models from. You will need an MRI to go with them sorry Bruce On Mon, 8 Dec 2014, will brown wrote: Sorry, yes we would like to calculate some volume statistics and surfaces models. Thanks, Will Message: 8

Re: [Freesurfer] Best possible atlas to extract hippocampus

Hi Pradeep you can do this kind of thing but it won't be as accurate cheers Bruce On Mon, 8 Dec 2014, pradeep mahato wrote: > Hello, > > As the complete recon process takes huge time for a single image, is it > possible to register the MRI image using a simple atlas. If yes, please > explain h

[Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

Dear freesurfer experts, I used Freesurfer 5 to do the retinotopic analysis followed by https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. However, finally I didn't get a red, green and blue map as I expected. This is the first time for me to analyze retinotopic data. I

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

I saw Doug recommended rtview, But I can't access this website: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview. On Mon, Dec 8, 2014 at 6:48 AM, zhang mingxia wrote: > Dear freesurfer experts, > > I used Freesurfer 5 to do the retinotopic analysis followed by > https://surfe

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

try now On 12/08/2014 09:59 AM, zhang mingxia wrote: > I saw Doug recommended rtview, But I can't access this > website:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview. > > On Mon, Dec 8, 2014 at 6:48 AM, zhang mingxia > mailto:zhangmingxia1...@gmail.com>> wrote: > > Dea

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

I'm not sure what you are asking for. Do you see significant activation in the visual cortex? What command are you running to view? On 12/08/2014 09:48 AM, zhang mingxia wrote: > Dear freesurfer experts, > > I used Freesurfer 5 to do the retinotopic analysis followed by > https://surfer.nmr.mg

[Freesurfer] Pial and White Matter Bumps

Hello, After running recon-all on one particular participant, there seems to be a tiny hills that extend past the brain in the inflated view. Normally, I notice small imperfections but these seem to be more substantial. I was wondering what I can do to fix these imperfections. I have attached a

Re: [Freesurfer] Pial and White Matter Bumps

HI Colleen I think it reflects the overall noisiness of your data cheers Bruce On Mon, 8 Dec 2014, colleen takahashi wrote: Hello,   After running recon-all on one particular participant, there seems to be a tiny hills that extend past the brain in the inflated view. Normally, I notice sma

[Freesurfer] thickness from pial and white

Hi All, Cortical surface reconstructed using caret from a high resolution MRI data (0.25 mm) has been converted to freesurfer format, and viewed correctly using freeview. My questions are whether it is possible to generate 1) a ?h.thickness from the ?h.pial and ?h.white; 2) wm

Re: [Freesurfer] --reg in mri_vol2surf

Hi Bruce, Thanks a lot for the suggestions! Here are some followup questions. 1) The functional volume was PET data and anatomical data have been processed with Freesurfer. I run the bbregister as: bbregister --mov PET.nii --s subject_name --reg register.dat --t1 --init-header It does not regis

Re: [Freesurfer] using mri_convert with multiframe dicom

Hi all, Doug, just wondering if anyone has had time to look into the issue of using mri_convert with multiframe/enhanced DICOM. My colleague, Lauren Wallace drop boxed (via your dropbox) some sample phantom data in this format back in October, I believe. (I also work with John Flavin who rais

Re: [Freesurfer] Command '-qa' in TRACULA

Thank you, Anastasia. I had downloaded the updated software and unzipped it, but I couldn't find the command "-qa." I found "-qa" in the trac-all text file in the updated software. However there are no "-qa" in terminal when I run "trac-all." Do I have to move the file somewhere?

Re: [Freesurfer] retinotopy analysis viewing problem in Freesurfer 5

Hi Doug, I followed this guide: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis. I used "tksurfer-sess" to view. Does "significant activation in the visual cortex" mean the map from"tksurfer-sess -a rtopy.self.?h -s sessid"? If so, yes. My question is (1) What do the

[Freesurfer] (no subject)

Hello,everyone Your reply said I can't use alphasim with qdec.By the way ,Could I use alphasim in other ways in FreeSurfer,for example command line ? Best regards. Xin-Fa Shi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.

Re: [Freesurfer] Extracting hippocampus

Hi Bruce, I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 Using autorecon2 process , I got error saying nu.mgz file is missing. Error : mghRead(/home/nsb/oasis/OAS2_RAW_PART1/OAS1_2/mri/nu.mgz, -1): coul