Re: [Freesurfer] Ventricle Volumes Decreasing over time?

Hi Bruce, Thank you for your quick reply! The decrease in percent difference vary. I have listed the range here for each region: Left Lateral Ventricle: -26 to -0.06 Left inferior ventricles: -67 to -0.2 Third ventricle: -23 to -0.06 Fourth ventricle: -7 to -0.142 Right lateral ventricle: -21 t

Re: [Freesurfer] rh.white and rh.pial surface manual edit

Hi Farhad, I'd be happy to help you with this problem. This appears to be a topological defect. You can edit the white matter volume (wm.mgz) by using the recon edit button to remove the section of white matter that is connecting the gyri. After making the edits and saving the volume, you can r

Re: [Freesurfer] Error while running recon-all

Hi Ritesh, What operating system and version are you running freesurfer on, ubuntu? Can you also send the fs version build stamp (you can get this by running 'bugr’) best Andrew > On Aug 29, 2017, at 11:41 AM, Ritesh Mahajan > wrote: > > Hello guys, > > I am trying to run recon-all command

Re: [Freesurfer] Philips and Toshiba dicom tag Read - error

yes, it looked like it worked fine. Have you visualized the results? cheers Bruce On Wed, 6 Sep 2017, M Janani wrote: Hi Team,       We would like to process the MRI data obtained using Philips and Toshiba scanners.       Can we do it using Freesurfer?     

Re: [Freesurfer] wm topological defects

Hi Ilona yes, you only need to edit the wm in regions where inaccuracies in the wm.mgz are making the surfaces inaccurate cheers Bruce On Wed, 6 Sep 2017, Ruotsalainen, Ilona wrote: Dear experts, I would have a follow up question for this thread. I have erased voxels from areas which a

[Freesurfer] Cortical Parcellation Yeo2011

Hi list, I have already run by recon-all -all all my subjects in order to run PetSurfer. Output stats is saved in gtm.stats.dat and values correspond to Desikan-Killiany Atlas, However, I am interested in calculating values using Yeo atlas of 7 networks. Do you have any suggestions to get Partial

Re: [Freesurfer] Ventricle Volumes Decreasing over time?

Hi Tamara but have you looked at the two timepoints in freeview to see if the ventricles are actually decreasing or of it is a segmentation error? Is that what you mean when you say you examined it? If the segmentations look accurate I'm not sure what else we can do. I guess you could try inst

Re: [Freesurfer] wm topological defects

Thank you for your reply! Ilona Lähettäjä: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] käyttäjän Bruce Fischl [fis...@nmr.mgh.harvard.edu] puolesta Lähetetty: 6. syyskuuta 2017 16:56 Vastaanottaja: Freesurfer support li

Re: [Freesurfer] patch for ribbon mgz failure. SAME ERROR

what happens if you run recon-all -s subject -cortribbon does it create the ribbon.mgz? On 9/6/17 7:53 AM, Maria Gloria Rossetti wrote: Hi Doug, As you suggested, I copied the mri_segstats patch (mri_segstats.centos6_x86_64 because my system is centos6) to my freesurfer/bin location and re

Re: [Freesurfer] 答复: ROI

Hi Bo have you tried freeview? We don't support tksurfer any more. cheers Bruce On Wed, 6 Sep 2017, Jin Bo wrote: Hi all, I am a new to Freesurfer. I am currently useing freeview to get ROI(small lesion) on 7T MRI, but the ROI  can not display on surface(tksurfer patient lh inflated -ove

Re: [Freesurfer] Error while running recon-all

Thanks Andrew for your response. There were few libraries missing on OS level, i resolved the problem. Thanks, Ritesh Mahajan - Original Message - From: "Hoopes, Andrew" To: "freesurfer" Sent: Wednesday, September 6, 2017 7:24:03 PM Subject: Re: [Freesurfer] Error while running recon-a