Re: [Freesurfer] error in manual edit by freeview

Would it be possible to send use the brain volume file? Thanks, Ruopeng > On Aug 17, 2016, at 9:30 PM, 陈聪 <3110103...@zju.edu.cn> wrote: > > Hi Doug > Thank you for reply, My problem is shown in picture. > Regards > Cong > > > ___ > Freesurfer ma

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

Try using mri_convert to convert one set and see if that fixes it. If so, then never use unpack_fsl.sh again. Note that unpack_fsl.sh is not part of the FSL suit of tools, so don't blame them ... On 08/17/2016 01:57 PM, Afzal, Afsana wrote: > I opened up the functional and anatomical (original a

Re: [Freesurfer] malloc_error_break/ can't allocate region

Hello Paul, Doug is essential correct. You can download 5.3 (or the development version) and just extract it to a different location. Something like: $> mkdir /usr/local/freesurfer_5.3 $> tar -C /usr/local/freesurfer_5.3 -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz Then you

[Freesurfer] Hiring: Cloud and HPC Engineer at NIMH in Bethesda, MD

NIMH is hiring a Cloud and HPC Engineer. Please spread the word! https://github.com/nih-fmrif/hpc_job_ad HIRING: CLOUD AND HPC ENGINEER The National Institute of Mental Health (NIMH) is the lead federal agency for research on mental disorders. NIMH is one of the 27 Institutes and Centers that ma

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

I opened up the functional and anatomical (original and reversed) in freeview and the functional volume is better aligned with the reversed anatomical than with the original anatomical. I realize this is a gross visual check that is probably unreliable but I don't have any other guesses as so wh

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

what do you mean "visual inspection shows that they are actually reversed"? Please give details On 08/17/2016 01:31 PM, Afzal, Afsana wrote: > I'm trying to understand why the coregistration for a bunch of subjects are > bad/failing (mincost value > 8). > > The orientation for the anatomical mat

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

I'm trying to understand why the coregistration for a bunch of subjects are bad/failing (mincost value > 8). The orientation for the anatomical matches the functional (after FSL unpacking) but visual inspection shows that they are actually reversed. Then I used mri_convert to change the orient

[Freesurfer] opening at the University of Sydney

-- Forwarded message -- Date: Tue, 16 Aug 2016 22:55:47 + From: Sasha Klistorner Research Fellow - Neuroimaging Save Sight Institute and Brain and Mind Centre Sydney Medical School Reference no. 1332/0816 · Join a collaborative and supportive research team · Bri

Re: [Freesurfer] malloc_error_break/ can't allocate region

Zeke will know better than me, but I think the new version folder name will be different, so there should not be any conflict. You will just need to reference the new source file On 08/17/2016 12:23 PM, miracoo...@gmail.com wrote: > Sure. Also, do you know how I can upgrade to either without uni

Re: [Freesurfer] FSFAST ROI atlas

Hi Michael- Is there anyway I can get those Gordon parcellation annot files? Cheers, Sabin Khadka On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael wrote: > > FYI: I supplied a version of the “Gordon” parcellation in .annot format to > Bruce a while back. He had expressed an interest in possibl

Re: [Freesurfer] malloc_error_break/ can't allocate region

Sure. Also, do you know how I can upgrade to either without uninstalling FS 5.1? Sent from my BlackBerry 10 smartphone.   Original Message   From: Douglas N Greve Sent: Tuesday, August 16, 2016 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] m

Re: [Freesurfer] FA/MD.nii to fsaverage space

First register the DTI to the anatomical with bbregister to create a register.dat file for each DTI (you can use the same one for FA and MD; for the "mov" volume, use whatever reference you used for motion correction). You can then run mri_vol2surf --mov FA.nii --reg register.dat --projfrac 0.

Re: [Freesurfer] Mixed anisotropic data

It will have some effect, but it is not clear exactly what. Probably the difference in 1.5 and 3T will be bigger. See the paper by Jorge Jovicich for more info about the diffs between 1.5 and 3T. You should make sure to have a balanced design if you want to publish it. On 8/16/16 4:52 PM, Mah

Re: [Freesurfer] FSFAST ROI atlas

FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0. cheers, -MH --  Michael Harms, Ph.D. ---

Re: [Freesurfer] FSFAST ROI atlas

I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line, look in the recon-all to find out ho

Re: [Freesurfer] Recon-all Correcting Defect 0

Can you send the log file? On 8/17/16 8:46 AM, Heidi Foo wrote: Dear FreeSurfer team, I am currently running recon-all for my subjects but for 2 of them, it stops at correcting defect. Do you have any ideas how I can deal with this problem? Thanks. Regards, Heidi Foo ___

Re: [Freesurfer] error in manual edit by freeview

I'm not sure what you are describing. Can you send a picture? On 8/17/16 8:42 AM, 陈聪 wrote: > Hi dear all > I am using freeview to edit segmentation, I found one slice in coronal > view in brainmask.mgz mismatch with other slice, this slice obviously move > down. WM and T1.mgz are normal,

Re: [Freesurfer] recon-all version update not showing in log file

It will not overwrite the log file so as to retain everything that has been done to the data set; new information is appended to the end of it. On 8/17/16 3:58 AM, Donna Cosgrove wrote: Hi, I am updating previously recon'd datasets done with FS versions 4.4 and 5.2 to v5.3. I'm running the r

[Freesurfer] ISMRM diffusion workshop: -1 month!

Dear FreeSurfers, This is just a reminder that the countdown for the ISMRM workshop on breaking the barriers of diffusion MRI has started. The meeting will take place in Lisbon, 11-16 September. Please check http://www.ismrm.org/workshops/Diffusion16/

Re: [Freesurfer] FSFAST ROI atlas

Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done. Thanks for your help! Cheers, Sabin Khadka On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve wrote: > I have not used them myself. > > On 8/15/16 10:23 AM, Sabin Khadka wrote: > > H

[Freesurfer] Recon-all Correcting Defect 0

Dear FreeSurfer team, I am currently running recon-all for my subjects but for 2 of them, it stops at correcting defect. Do you have any ideas how I can deal with this problem? Thanks. Regards, Heidi Foo ___ Freesurfer mailing list Freesurfer@nmr.mgh.h

[Freesurfer] error in manual edit by freeview

Hi dear all I am using freeview to edit segmentation, I found one slice in coronal view in brainmask.mgz mismatch with other slice, this slice obviously move down. WM and T1.mgz are normal, I don’t know how to move this wrong slice back. Any advice will be appreciated. thanks very much. C

Re: [Freesurfer] REPOST: problem with Qdecrc file

Hi Martin, I tried both. Neither of the options worked, though. I have created a subdirectory SUBJECTS_DIR/qdec2stage/ where I have my dat file, the .Qdecrc, the level files etc. But when I start qdec in that folder, load the data table and prepare everything I still can't choose spc (for examp

[Freesurfer] FA/MD.nii to fsaverage space

Dear Freesurfer developers, I would like to perform an analysis that requires me to have all of my subjects surface based and diffusion data in the same space. I have performed recon-all -qcache so that all my surface based measures are in fsaverage space. I now would like to register the FA.n

[Freesurfer] recon-all version update not showing in log file

Hi, I am updating previously recon'd datasets done with FS versions 4.4 and 5.2 to v5.3. I'm running the recon-all command on the previously done subjects to retain any edits. However, when I had a look at the recon-all.log, it still has a date from the previous recon in 2013. The pctsurfcon.log