[Freesurfer] CORRECTING DEFECT

Hi Bruce,I am wondering if you saw my last email, about uploading my subject in your ftp server.I uploaded the subject  "test_emc_039.tar.gz".I appreciate any help. Thank you, Maryam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu http

Re: [Freesurfer] CORRECTING DEFECT

Hi Bruce,Did you get my email regarding to the subject I upload in fft server? Best,Maryam   Regards,Maryam Kouchakidivkolaei On Friday, June 3, 2016 10:16 PM, maryam koochaki wrote: Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz Thanks,Maryam   Regards

Re: [Freesurfer] CORRECTING DEFECT

, maryam koochaki wrote: Dear freesurfer experts,I have a subject ending up with this error after recon-all.I tried to edit the aseg and run it, but it stuck at topological step. CORRECTING DEFECT 79 (vertices=54196, convex hull=8490) error in the retessellation normal vector of length zero at

[Freesurfer] CORRECTING DEFECT

Dear freesurfer experts,I have a subject ending up with this error after recon-all.I tried to edit the aseg and run it, but it stuck at topological step. CORRECTING DEFECT 79 (vertices=54196, convex hull=8490) error in the retessellation normal vector of length zero at vertex 97187 with 0 faces v

Re: [Freesurfer] Editing brain.finalsurfs.mgz

    -T1 ${hemi}.brain.finalsurfs $henmi if you want, you can also use -output .test and it will add .test to all the output names so you can see the effect of your edits cheers Bruce On Fri, 29 Apr 2016, maryam koochaki wrote: >  Dear experts,I am trying to fix the surfaces which are cross

[Freesurfer] Editing brain.finalsurfs.mgz

 Dear experts,I am trying to fix the surfaces which are crossing to each other in the middle where the hemispheres reach each other.As Bruce mentioned before I am trying to create two volumes (lh.brain.finalsurfs.mgz  , rh.brain.finalsurfs.mgz ) nad edit them individually.Then I want to rerun th

Re: [Freesurfer] Medial crossing surfaces

er on the midline. If you upload your data I can take a look. For the command line you can check out the recon-all help and just rerun the pial surface generation cheers Bruce On Mon, 7 Mar 2016, maryam koochaki wrote: >  Hi Bruce, > I am editing aseg to correct the boundaries that e

[Freesurfer] Medial crossing surfaces

 Hi Bruce,I am editing aseg to correct the boundaries that excluded the lateral ventricle. The problem with lateral ventricle has been solved after running the process with -noaseg flag. But the boundaries in the middle, is crossing to the other hemesphere in some cases. I even tried -autorecon2

Re: [Freesurfer] Wm correction

Hi Bruce,I uploaded yesterday. best, Maryam   Regards,Maryam Kouchakidivkolaei On Friday, January 29, 2016 5:47 AM, Bruce Fischl wrote: sure, let us know after you have uploaded it. Bruce On Fri, 29 Jan 2016, maryam koochaki wrote: > Thanks, I also have another major prob

Re: [Freesurfer] Wm correction

ke an announcement when we have a beta versionBruce On Jan 28, 2016, at 8:25 PM, maryam koochaki wrote: Hi Bruce, How can I download version 6? Best,Maryam   Regards,Maryam Kouchakidivkolaei On Thursday, January 28, 2016 5:55 AM, Bruce Fischl wrote: Hi Maryam have you look at the as

Re: [Freesurfer] Wm correction

. Try manually editing it. V6 handles this kind of thing significantly better cheers Bruce On Thu, 28 Jan 2016, maryam koochaki wrote: > Hi Bruce, > I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral > Ventricle. As you can see in the image attached, the big part

Re: [Freesurfer] Wm correction

ually editing it. V6 handles this kind of thing significantly better cheers Bruce On Thu, 28 Jan 2016, maryam koochaki wrote: > Hi Bruce, > I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral > Ventricle. As you can see in the image attached, the big part is excl

[Freesurfer] wm correction

Hi Bruce, I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral Ventricle. As you can see in the image attached, the big part is excluded in both hemisphere. I tried to fill it by editing wm volume but the problem still exists.Do you have any suggestion?Thanks,Maryam  

[Freesurfer] Incomplete output

Dear experts,I am kind of new at working with freesurfer.recon-all process has completed without error, but when I look at brainmask volume on freeview, one of the issues is that lateral ventricle is completely excluded. I have tried to edit it with editing the white matter volume, but no succes

[Freesurfer] stuck in 'Fix Topology lh

Hi,I have a subject that every time I run it, it stuck in 'Fix Topology lh or rh' step.The error which I find it in  brainmask volume is, some part of the brain is excluded.So I edited it manually (clone from T1 volume ), then I run it with the following command line;recon-all  -subjid test_emc_