Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

External Email - Use Caution Hi Bruce Thanks so much for your quick reply. I had overlaid the ?h.defect_labels on the inflated.nofix and orig.nofix. I adjusted the threshold to focus on the largest defect. Although I could look at the defect, I couldn't figure how to fix it manual

Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

Hi Jiun-Wei have you looked at the ?h.defect_labels overlaid on the inflated.nofix and orig.nofix surfaces? That will tell you where the defect is that is causing you trouble. If you have lesions they may be the source of the issue. If you can't sort it out you can tar and gzip the entire subj

[Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

External Email - Use Caution Dear freesurfer experts, When executing recon-all in two subjects with brain lesions, the recon-all process stopped at CORRECTING DEFECT 13 (vertices=49319, convex hull=12973, v0=65403) and CORRECTING DEFECT 6 (vertices=23529, convex hull=6740, v0=1602

Re: [Freesurfer] CORRECTING DEFECT

urfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External Hi Brendan usually defects that are that big don't get corrected properly. I would look at the wm.mgz and the lh.orig.nofix to understand what is causing the large defects and correct them manually cheers Bruc

Re: [Freesurfer] CORRECTING DEFECT

f Of Bruce Fischl Sent: Friday, August 9, 2019 11:21 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External yes, because that is the total # of defects. The 29th or 30th isn't the last one, just what it got stuck on. The #30 should look much bigger though (

Re: [Freesurfer] CORRECTING DEFECT

-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, August 9, 2019 11:21 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External yes, because that is the total # of defects. The 29th or 30th isn't the last one, just what it got stuck o

Re: [Freesurfer] CORRECTING DEFECT

half Of Bruce Fischl Sent: Friday, August 9, 2019 11:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External they are an overlay not a surface. Load the surface first then load them as an overlay on top of it (e.g. the lh.inflated.nofix) On Fri, 9 Aug 201

Re: [Freesurfer] CORRECTING DEFECT

mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, August 9, 2019 11:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External they are an overlay not a surface. Load the surface first then load them as an overlay on

Re: [Freesurfer] CORRECTING DEFECT

u] On Behalf Of Bruce Fischl Sent: Friday, August 9, 2019 10:27 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External Hi Brendan the time to correct goes with the square of the size of the defect (actually the convex hull of the defect) so it can take a ver

Re: [Freesurfer] CORRECTING DEFECT

Thanks, Brendan -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, August 9, 2019 10:27 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External Hi Brend

Re: [Freesurfer] CORRECTING DEFECT

Hi Brendan the time to correct goes with the square of the size of the defect (actually the convex hull of the defect) so it can take a very long time for big ones. More importantly, if the defect is that large it may not be corrected in the anatomically desired manner. You should take a look

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Hello, Have you got some time to check my data? I appreciate if you can give me some advices. Thank you very much. Ruwan On Tue, Apr 23, 2019 at 7:41 PM Pradeepa Ruwan < pradee.wanniarach...@gmail.com> wrote: > Dear Prof.Bruce, > > I am sending my ra

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Dear Prof.Bruce, I am sending my raw data and the images that you requested to send. I have two datasets that I got trouble with. I appreciate if you can take a look at this data. Thank you very much in advance. Best regards, Ruwan Freesurfer-ruwan.z

Re: [Freesurfer] CORRECTING DEFECT 1 problem

Hi Ruwan have you looked at the data? Can you tell us what the acquisition parameters are or send us a 3-plane image of the norm.mgz with the lh.orig.nofix and rh.orig.nofix surfaces? The big defects are usually a symptom of something else cheers Bruce On Mon, 22 Apr 2019, Pradeepa Ruwan w

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Dear Freesurfer experts, I frequently get correcting defect error. It seems freezing the recon-all after the defect and it won't run thereafter. Due to this error, I can not use most of the data for connectome analysis. Can you please tell me how to ge

Re: [Freesurfer] CORRECTING DEFECT 1 problem

sorry, I've been traveling On Mon, 22 Apr 2019, Abby tang wrote: External Email - Use Caution Hi BruceI did't get your reply message  yet. I have send the subject file to you. Could you give me your advises? Thank you for your help. Abby Abby tang 于2019年4月19日周五 上午8:32写道：

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Hi Bruce I did't get your reply message yet. I have send the subject file to you. Could you give me your advises? Thank you for your help. Abby Abby tang 于2019年4月19日周五 上午8:32写道： > Hello，Bruce > I attached my subjects. Please help me. > Thank you. >

Re: [Freesurfer] CORRECTING DEFECT 1 problem

External Email - Use Caution Hello，Bruce I attached my subjects. Please help me. Thank you. Abby 2851A_T1_w4.nii Bruce Fischl 于2019年4月18日周四 下午10:53写道： > Hi Abby > > it's hard to tell from the

Re: [Freesurfer] CORRECTING DEFECT 1 problem

Hi Abby it's hard to tell from the image, but it looks like there is a big I/S bias field as well as large amounts of pathology. If you upload the subject to our ftp site we will take a look cheers Bruce On Thu, 18 Apr 2019, Abby tang wrote: External Email - Use Caution

Re: [Freesurfer] Correcting Defect error

That looks pretty awful. You should check the orig.nofix surfaces. I bet your data is extremely noisy On 2/28/19 11:37 AM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > > > Dear Freesurfer devs, > > > I ran the recon-all in one subject and and this process was sto

Re: [Freesurfer] Correcting defect

This is not necessarily a problem. Do the surfaces look ok? You can always check the defect fixing using the defect-seg script. Run it with --help to get more info On 12/27/17 12:28 AM, shi yao wang wrote: Dear FS experts, I am running FS 6.0. There is a error message like this. Inline image

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Loeffler, Martin Sent: Saturday, December 23, 2017 4:26:15 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Dear Bruce, Dear Bram, Thanks a lot for having a look. Unfortunately the left hemisp

[Freesurfer] Correcting defect

Dear FS experts, I am running FS 6.0. There is a error message like this. [image: Inline image 1] are there any way to modify it? thanks Lawrence Radiology Department Emory University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Ryder Gesendet: Mittwoch, 13. Dezember 2017 23:23 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin, We've taken a look at the scans you uploaded, and unfortunately it won't be possible to run the standard recon-all on your subje

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

del of the right hemisphere. Best, Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Loeffler, Martin Sent: Tuesday, December 12, 2017 11:57:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Dea

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

2017 16:35 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin we are happy to take a look, but can't really tell much from a screenshot. Feel free to upload the subject to our ftp site if you want us to help cheers Bruce On Tue, 12 Dec

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

esurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to f

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

ce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Montag, 11. Dezember 2017 22:47 An: Freesurfer support list Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst Hi Martin a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.n

Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin a defect that large means that something big went wrong (skull or dura attached, etc...). Try looking at the ?h.orig.nofix and/or the ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find defect 9 cheers Bruce On Mon, 11 Dec 2017, Loeffler, Martin wrote: Dear

[Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear FreeSurfer team, For a case report I'm running recon-all on a patient with a giant arachnoid cyst in the left hemisphere. It gets stuck at this point (last message): CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849) XL defect detected... It is stuck here since a whole day now,

Re: [Freesurfer] correcting defect

: [Freesurfer] correcting defect To: Freesurfer support list Message-ID: Content-Type: text/plain; charset="utf-8"   Hi Meng   we can't diagnose either of these issues without more information and possibly some screen shots. The topology fixer will take a very long time if the initial surf

Re: [Freesurfer] correcting defect

Hi Meng we can't diagnose either of these issues without more information and possibly some screen shots. The topology fixer will take a very long time if the initial surfaces have large defects. You can view these by visualizing the ?h.inflated.nofix and ?h.orig.nofix. The -openmp flag work

[Freesurfer] correcting defect

Hi all, I tried to use FreeSurfer version 6.0.0 to process fifteen subjects, but half of the subjects was stuck at the ‘Correcting Defect’ step. However, when I changed to FreeSurfer version 5.3.0, the ‘Correcting defect’ step finished successfully. Is it possibility that the unsuccessful ‘Corr

[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,Maryam

Re: [Freesurfer] CORRECTING DEFECT

Hi Bruce,I already uploaded it.File name:  test_emc_039.tar.gz Thanks,Maryam   Regards,Maryam Kouchakidivkolaei On Friday, June 3, 2016 9:35 PM, Bruce Fischl wrote: Hmmm, that sounds like a bug. If you upload the subject we will take a lookCheersBruce On Jun 3, 2016, at 6:54 PM, m

Re: [Freesurfer] CORRECTING DEFECT

Hmmm, that sounds like a bug. If you upload the subject we will take a look Cheers Bruce > On Jun 3, 2016, at 6:54 PM, 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 topologi

[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] Correcting defect

, May 7, 2016 4:03:28 AM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect Hi Katarina how did you create the orig.mgz for these subjects? Either some registration failed badly or you tried to average data from different subjects (see attached tiffs of the orig.mgz you uploaded

Re: [Freesurfer] Correcting defect

...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Thursday, May 5, 2016 4:20:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect Hi Katarina if you want us to look you need to upload the entire subject dirs (tarred and gzipped). TO visualize it, look at the inflated.nofix in

Re: [Freesurfer] Correcting defect

gt; From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Bruce Fischl > > Sent: Wednesday, May 4, 2016 2:35 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Correcting defect > > sure. Or you can load the ?h.inflated.nofix and look at it - it shou

Re: [Freesurfer] Correcting defect

Macedonia From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Wednesday, May 4, 2016 2:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Correcting defect sure. Or you can load the ?h.inflated.nofix and look at it

Re: [Freesurfer] Correcting defect

sure. Or you can load the ?h.inflated.nofix and look at it - it should be obvious if there is a huge defect (you can also load the file ?h.defect_labels as an overlay on that surface and it will show you the segmentation of the defects) cheers Bruce On Wed, 4 May 2016, Katarina Trojacanec wrot

[Freesurfer] Correcting defect

Dear FreeSurfer Team, I have been trying to run creation of template with FreeSurfer. However, for two cases for one patient (case 1: template based on TP1 and TP4, case 2: template based on TP2 and TP4), the correcting defect step is running too long. According to the information in the mail

Re: [Freesurfer] CORRECTING DEFECT

or if the skull is attached or the two hemis. The time it takes to correct a defect is quadratic in the size of the (convex hull of) the defect, so small ones are fast, and big ones take forever. Anything over 15K vertices or so usually means there is something dramatically wrong with your data

Re: [Freesurfer] CORRECTING DEFECT

Hi Chikku, look at the wm.mgz to see if the cerebellum is still attached doug On 02/14/2013 11:22 AM, Varghese Chikku wrote: > Dear All, > I have been trying to recon all a patient and unfortunately nothing > is happening after 24 hrs of processing so far .No error messages > are coming up

[Freesurfer] CORRECTING DEFECT

Dear All, I have been trying to recon all a patient and unfortunately nothing is happening after 24 hrs of processing so far .No error messages are coming up either .This is the line it got stuck,CORRECTING DEFECT 10 vertices 67735 convex hull 9509 This is a rerun after my initial processi