Re: [Freesurfer] Watershed surfaces error

.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Sunday, September 10, 2023 1:38:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Watershed surfaces error External Email - Use Caution What command are you using to generate the surfaces? I don't think this i

Re: [Freesurfer] Watershed surfaces error

External Email - Use Caution What command are you using to generate the surfaces? I don't think this is done by default in recon-all On 9/3/2023 1:22 PM, Srishyla, Diksha wrote: External Email - Use Caution Hello FreeSurfer Developers, I am attempting to produce waters

Re: [Freesurfer] watershed, saving issue

errors. Then I need to create BEM surfaces using the FreeSurfer watershed algorithm for MEG data analysis using MNE-Python. So the next command in the terminal is: mne watershed_bem --subject subjectname And it runs e.g. till: mri_watershed ru_nivcsw   12490 mri_watershed done and quits with errors

[Freesurfer] watershed, saving issue

External Email - Use Caution Hallo everybody, I am not entirely sure whether this is FreeSurfer error actually. I am doing first recon all which completes without errors. Then I need to create BEM surfaces using the FreeSurfer watershed algorithm for MEG data analysis using MNE

[Freesurfer] watershed error again

Hi all, I posted this problem earlier, but did not get an answer, so I am posting it again, sorry! --- recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.

[Freesurfer] watershed problem

Hello, I have some unexpected results from the mne_watershed_bem script that uses Freesurfer mri_watershed program. For one of my subject's the inner scull surface ( _inner_scull_surface in bem/watershed/) partially excludes cerebellum (the left screen shot). All my other subjects have c

Re: [Freesurfer] watershed surface to volume rendering repost

> > PH: 937.705.1025 > FAX: 937.705.1095 > EMAIL: matt.sherw...@wright.edu > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Tuesday, September 02, 2014 6:49 PM

Re: [Freesurfer] watershed surface to volume rendering repost

Behalf Of Bruce Fischl Sent: Tuesday, September 02, 2014 6:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] watershed surface to volume rendering repost Hi Matthew, yes, you can use mris_fill to fill the interior of a topologically correct, closed surface. You'll need to run some bo

Re: [Freesurfer] watershed surface to volume rendering repost

Hi Matthew, yes, you can use mris_fill to fill the interior of a topologically correct, closed surface. You'll need to run some boolean operations on them to get the volumes you want, but it should be pretty easy I think. cheers Bruce On Tue, 2 Sep 2014, Sherwood, Matt wrote: Freesurfer,

[Freesurfer] watershed surface to volume rendering repost

Freesurfer, Sorry for the repost, but I did not get any further details: We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, i

Re: [Freesurfer] watershed surface to volume rendering

Hi Matt you might want to email Matti about this. I think that you can, but he might know the details cheers Bruce On Tue, 26 Aug 2014, Sherwood, Matt wrote: Freesurfer,     We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE

[Freesurfer] watershed surface to volume rendering

Freesurfer, We have scans that have recon-all completed. Following recon-all, we completed watershed (under the MNE toolbox) to extract skull and scalp from the T1 scans. The outputs of this algorithm are outer brain, inner skull, outer skull and outer scalp surfaces. We are part

Re: [Freesurfer] Watershed

@nmr.mgh.harvard.edu] > Sent: Tuesday, July 22, 2014 5:59 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Watershed > > Hi Sourav > > can you explain what failed? Was too much removed? Too little? What did > you try to fix it? > Bruce >> On Tue,

Re: [Freesurfer] Watershed

, 2014 5:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Watershed Hi Sourav can you explain what failed? Was too much removed? Too little? What did you try to fix it? Bruce On Tue, 22 Jul 2014, SOURAV RANJAN KOLE wrote: > Hi Bruce, > > Thank you for your message. > > Y

Re: [Freesurfer] Watershed

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Sunday, July 20, 2014 8:15 PM > To: Freesurfer support list > Cc: gr...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Watershed > > Hi Sourav > Are you sure the sk

Re: [Freesurfer] Watershed

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Sunday, July 20, 2014 8:15 PM To: Freesurfer support list Cc: gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Watershed Hi

Re: [Freesurfer] Watershed

Hi Sourav Are you sure the skull stripping isn't working? It can be hard to tell right on the midline Cheers Bruce > On Jul 18, 2014, at 5:38 PM, SOURAV RANJAN KOLE wrote: > > Sourav ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://

[Freesurfer] watershed error

Hi all, recon-all runs smoothly for all my subjects but one. It throws the error "mri_watershed Error: indices out of bounds" and finishes (see https://www.dropbox.com/s/4del0uy8g1qw5az/recon-all.log). The image quality does not seem to be different... The error has been discussed on the list

Re: [Freesurfer] Watershed and Normalization Problem.

Hello NMR users, Here is a link to my files containing the below Watershed Error. Thank you for taking the time to look at the files. Erica Tatham Hi Erica if you upload this subject dir we will take a look cheers Bruce On Thu, 12 Sep

Re: [Freesurfer] Watershed and Normalization Problem

Hi Bruce and Team, I have uploaded the subject dir to the File Drop under "Watershed and Normalization Problem". Thank you very much for taking a look at these files. Cheers! Erica Hi Erica if you upload this subject dir we will take a look cheers Bruce On Thu, 12 Sep 2013, Erica Tatham

Re: [Freesurfer] Watershed and Normalization Problem

Hi Erica if you upload this subject dir we will take a look cheers Bruce On Thu, 12 Sep 2013, Erica Tatham wrote: Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz an

[Freesurfer] Watershed and Normalization Problem

Hello Freesurfer People, Below is the error that I have been receiving after running a recon-all. There seems to be a problem in the normalization stage. I checked the orig.mgz and the transform.xfm, and both seem to be reasonable. I was hoping for some guidance/expert advice for how to precede fr

Re: [Freesurfer] Watershed gca atlas

Hi Vincent look all algorithms, sometimes that piece fails, particularly if the anatomy in question is an outlier. cheers Bruce On Sat, 24 Mar 2012, Vincent wrote: I noticed in this skull strip tutorial that sometimes when adjusting the watershed threshold the -no-wsgcaatlas option is use

[Freesurfer] Watershed gca atlas

I noticed in this skull strip tutorial that sometimes when adjusting the watershed threshold the -no-wsgcaatlas option is used. I understand that it means that the atlas, which is used to assist in detecting physical features whil

Re: [Freesurfer] watershed error in skull strip routine

Hi Tim that's a new error - congratulations! If you upload the dataset I'll take a look, but I suspect if you add some control points it will work fine. cheers Bruce On Wed, 11 Jan 2012, Holden, Timothy wrote: Hi FS experts,   I?m encountering an error in the Skull Strip routine with

Re: [Freesurfer] Watershed treshold and amygdala volume

Hi Anne I suspect that if you removed enough manually it would change. The atlas-based registration will change if the skull-stripping changes significantly, which will change the resulting segmentation. cheers Bruce On Sun, 20 Mar 2011, Hendrikx, A.A.E.M. (Anne) wrote: > Dear all, > > We,

[Freesurfer] Watershed treshold and amygdala volume

Dear all, We, members from the Donders Institute Nijmegen (The Netherlands), are using FreeSurfer to calculate amygdala volumes on MRI's. After a couple of tests we are suprised about the following: We are wondering why the amygdala volume changes, after changing the watershed threshold. Besid

Re: [Freesurfer] Watershed Errors - Multiple attempts tried

Hi Christian, do you mean a T1 map? Have you tried T1 weighted (is that T1w?)? What sequence is it? If you are really seeing high error rates with T1 weighted images you are welcome to drop some on our site and we'll take a look. cheers, Bruce On Tue, 6 Jul 2010, Christian Lambert wrote: > Hi

[Freesurfer] Watershed Errors - Multiple attempts tried

Hi all, I'm assissting with an aging study and a good handful of their scans are coming up with watershed errors. My assumption was errors with the skull strip leading to empty brain volumes. I have read through all the lists and tried the following: - Manually corgistering to MNI to improve T

Re: [Freesurfer] watershed error...

sorry, it doesn't sound like this is the problem. You could try putting some seed points in the white matter for the watershed. Not sure what the interface is for that. You should also check to make sure that the atlas transform it is using is reasonable. On Wed, 7 Oct 2009, Gonzalo Rojas wro

Re: [Freesurfer] watershed error...

check to see if the intensity normalization worked (does the T1.mgz white matter have intensities of 110 most places) On Wed, 7 Oct 2009, Gonzalo Rojas wrote: > Hi: > > I got the following error... How can I solve it ?... > > recon-all.log >

Re: [Freesurfer] watershed error...

Hi: Ok... I test it with the command that you told me, and I added the option "wsthresh 35"... Then I got a good skull stripped image... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97

Re: [Freesurfer] watershed error...

another thing to try is include the flag -no-wsgcaatlas flag, like this: recon-all -s subjid -skull-strip -no-wsgcaatlas this bypasses usage of the atlas. if that fails, you can send me the 001.mgz input file to the filedrop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html n. On

Re: [Freesurfer] watershed error...

Hi: How can I put the control points in the nu.mgz image ?... Sincerely Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl Nick Schmansky escribió: > check if the whitematter in th

Re: [Freesurfer] watershed error...

Hi: Yes... the occipital white matter has value 110 in general... The frontal white matter has voxels with values 94 to 117 aprox... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-977717

Re: [Freesurfer] watershed error...

check if the whitematter in the file T1.mgz is around value 110. if not, then put some control points in the white matter in nu.mgz and re-run recon-all. n. On Wed, 2009-10-07 at 15:34 -0400, Gonzalo Rojas wrote: > Hi: > >I got the following error... How can I solve it ?... > > recon-all.l

[Freesurfer] watershed error...

Hi: I got the following error... How can I solve it ?... recon-all.log - mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mg

Re: [Freesurfer] Watershed Error

Vina, Can you check the FOV value for the orig.mgz file? That is: cd subj/mri mri_info orig.mgz Is it greater than 256? Are the dimensions >256? I have just recently been looking into this error for someone else, and the source of the problem was improper handling by mri_convert of data tha

Re: [Freesurfer] Watershed Error

Did you explicitly check the quality of talairach_with_skull.lta? Also, what version of FS are you using? We previously had encountered that error in 5 brains processed under FS 4.0.2, and all five of those had errant talairach_with_skull.lta transforms. Generation of talairach_with_skull.lta wa

Re: [Freesurfer] Watershed Error

hmmm, that's interesting. If you send us the data we'll take a look. In any case, you can run, if you create an orig_stripped.mgz you can run: mri_mask T1.mgz orig_stripped.mgz brain.mgz then you should be able to run from after the skull stripping forward (check the recon-all help. You'll ne

[Freesurfer] Watershed Error

Hi all, I get this error for one subject: mri_watershed Error: GLOBAL region of the brain empty ! I check the talairach transformation and it looked good. I also tried just scripting the orig.mgz and I get a wonderful strip. How can I move forward with the recon-all process? Thanks, Vina __

[Freesurfer] watershed values

Hi, I'm trying to adjust the watershed thresholds on a few images, and have a question about the default watershed value.   When I run the skullstrip without specifying a watershed value, the recon-all.log file typically says:   preflooding height equal to 25 percent Sorting... T1-wei