: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
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Hi Annchen,
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 has a release date of May
2013. All your individual programs reported BuildTimeStamp: Dec 19 2017
00:02:05.
H
path to recon-all if Freesurfer
environment is set up correctly)
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Annchen Knodt
Sent: Sunday, June 4, 2023 9:22 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors
ng, Yujing
Sent: Friday, June 2, 2023 4:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
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I followed 5.3 recon-all a little bit. rh will be processed after lh. Your
recon-all stoppe
reesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
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Hi Yujing,
Thanks so much for your response! I tried copying
$FREESURFER_HOME/subjects/fsaverage
original?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Annchen Knodt
Sent: Friday, June 2, 2023 2:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
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Hi Yujing,
@nmr.mgh.harvard.edu
Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
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Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not
sure how to troubleshoot. I'm using essentially the same command
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Hello Freesurfer developers,
I am attempting to create a new atlas for the freesurfer software that would
allow me to analyze rat brain MRI images. I saw on the SurfaceRegAndTemplates
page that I need to register and create an inflated template, but
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OK, I will try later. Thanks!
-原始邮件-
发件人:"Douglas N. Greve"
发送时间:2021-03-18 06:03:24 (星期四)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Troubleshooting: Soft Failures
The contrast is pretty low (probably due t
-
*发件人:*"Douglas N. Greve"
*发送时间:*2021-03-17 00:04:43 (星期三)
*收件人:* freesurfer@nmr.mgh.harvard.edu
*抄送:*
*主题:* Re: [Freesurfer] Troubleshooting: Soft Failures
Can you send the recon-all log file?
On 3/9/2021 2:06 AM, 崔鹏程 wrote:
External E
Can you send the recon-all log file?
On 3/9/2021 2:06 AM, 崔鹏程 wrote:
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Hi FreeSurfer experts,
Recently, I used Fresurfer's */recon-all/*toprocess our own T1
MRIbrain volumes which is 0.7 m3 isotropic.For most young brain cases,
FS performs very well, the s
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Hi FreeSurfer experts,
Recently, I used Fresurfer's recon-all toprocess our own T1 MRI brain
volumes which is 0.7 m3 isotropic. For most young brain cases, FS performs
very well, the segmention is great. But for almost every elderly brain case,
Hi Andy, this is a bug introduced in 7.1.1, some kind of race condition.
You can fix it by commenting out this line in recon-all
if($OMP_NUM_THREADS > 1 && ! $LHonly && ! $RHonly) set cmd = ($cmd
--parallel) # just hemis
doug
On 11/3/2020 12:06 PM, Andy Worth wrote:
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Hello,
We've experienced random crashes when using the -parallel flag with
the official FS docker container at
https://secure-web.cisco.com/1Db9ik7eIvMj7kgkeTafe0s_PlT0VyO4BIvoM6Chj4jvyesjHAuR-kZyjg4ueyTkvPI2tO3aWk76nJniaideisxRFreGgC6FYkFflnw3OJSb2viz
symlinks into referent
file/dir.
best,
Andrew
From: on behalf of "Park, James"
Reply-To: FS Help
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer
Output to Secondary Location
External E
The issue with the ribbon is something we recently became aware of. does
it happen consistently for you? I can send you a recon-all that will fix
this for you, just tell me which version you are running.
On 9/8/2020 11:49 AM, Park, James wrote:
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Sincerely
External Email - Use Caution
Sincerely,
James Park
From: "Park, James"
Date: Tuesday, September 8, 2020 at 11:48 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical
ribbon mask stage during recon-all
Dear Free
also, if you run defect-seg, it will create a segmentation of the
defects which you can visualize in the volume. Run defect-seg with
--help for more info
On 3/13/2020 8:45 PM, Bruce Fischl wrote:
Hi Ricky
how did you try to load the defect_labels? The end of the
recon-all.log file lists a de
Hi Ricky
how did you try to load the defect_labels? The end of the recon-all.log
file lists a defect with 26K vertices, which is probably too big to fix
(it's about 1/5 of a normal surface). You should be able to visualize it
by loading the lh.defect_labels file as an overlay on the
lh.inflat
e mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1
qform or sform are valid
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: <56f15d28.7040...@nmr.mgh.harvard.edu
ate: Tue, 22 Mar 2016 10:56:40 -0400
> From: Douglas Greve
> Subject: Re: [Freesurfer] Troubleshooting for error - neither NIfTI-1
> qform or sform are valid
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <56f15d28.7040...@nmr.mgh.harvard.edu>
> Content-Type: t
To check whether the orientation is correct, you can view it in freeview
or tkmedit. When you click on the axial view it should show up axially,
etc. Though you cannot tell whether it is left-right reversed this way.
You cannot feed it a matrix, but you can specify the direction cosines
on the
Hello FS list subscribers,
Is there a way to manually feed FS with NIfTI-1 qform or sform information?
Or correctly add this information to the original .nii files? My sense of
the problem is that there is a problem with the header information in my
.nii files and FS cannot tell what is anterior,
Hello fellow Freesurfer user,
I am currently working on an ageing data set (~60 subjects between 19 to
81 years old). I mainly want to use Freesurfer for two different things:
1. get a cortical and sub-cortical segmentation to use those regions
for a connectivity analysis
2. use the WM/GM b
Hi Janosch
there should be some corrected subjects in the tutorial. The white matter
surface shouldn follow the perceived boundary, although it may look wrong
when it is when it is curving sharply out of plane. I don't have much
experience with MDEFT, so I can't comment on the parameters
che
Hi Bruce,
thanks for your answer!
Am 30.01.2014 um 14:40 schrieb Bruce Fischl :
> Hi Janosch
>
> it's impossible to tell from a single slice whether those points should be
> added or not. The white matter in your image is *very* dark in these regions,
> do you know why?
No, I don't know why,
Hi Janosch
it's impossible to tell from a single slice whether those points should
be added or not. The white matter in your image is *very* dark in these
regions, do you know why? To decide whether to add them or not you should
check a couple of slices in each direction (or look in multiple
Hi Susie - avscale is part of the FSL package. You have to make sure FSL
is installed and in your path.
a.y
On Wed, 6 Feb 2013, Susan Kuo wrote:
Hi FreeSurfer community, I am currently trying to troubleshoot my
preprocessing part of TRACULA with the
tutorial dataset (for Diff001 as the s
Hi FreeSurfer community,
I am currently trying to troubleshoot my preprocessing part of TRACULA
with the tutorial dataset (for *Diff001* as the subject, specifically),
running *trac-all -corr -c *. I am running the commands in *
subjectID/scripts/trac-all.cmd* one by one because I've had problem
So when viewing with tksurfer I am assuming that -map angle shows the
polar data. It looks ok. There's a lot of yellow and red, which I am
assuming is the overall significance and not significance by position
yes?
tksurfer-sess -a rtopy.self.lh -s sj09 -map angle
To view eccen data, is it
How do the eccen and polar look by themselves? You can look at them with
tksurfer-sess
doug
Michelle Umali wrote:
> Hi Freesurfers,
> I'm troubleshooting my retinotopy data and am still having issues with
> wonky fieldsign data. The registration looked ok, so now I am trying
> to look at the
Hi Freesurfers,
I'm troubleshooting my retinotopy data and am still having issues with
wonky fieldsign data. The registration looked ok, so now I am trying
to look at the retinotopy results using rtview. I got an error
message saying it can't find the register.dof6.dat file. So, now I am
The areas near subcortical structures are not included in thickness
estimates. If you load your subject in tksurfer and load the aparc.annot
you will see a section on the medial side called "unknown". If the regions
you are concerned about fall within here, then you do not have to worry
about i
Hi Sam,
It's kind of suspicious that both hemispheres are so far off. We don't
usually see this. Have you checked the talairach xform to see if it is way
off? If not, feel free to gzip the subject and drop it for us to take a
look at. Do you see this in other subjects?
cheers
Bruce
On Mon, 22
urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Kavec
Sent: Thursday, May 28, 2009 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Troubleshooting
Hi Falk,
On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote:
Hello,
Im having trouble to generate a correct aseg.mgz for one volu
Kavec
Sent: Thursday, May 28, 2009 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Troubleshooting
Hi Falk,
On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote:
> Hello,
>
>
>
> Im having trouble to generate a correct aseg.mgz for one volume of mine.
> The nu_
Hi Falk,
On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote:
> Hello,
>
>
>
> Im having trouble to generate a correct aseg.mgz for one volume of mine.
> The nu_noneck.mgz is also incorrect and therefore I think the -careg stage
> of autorecon2 might fail. Is there a way to do some kind quality
Hello,
Im having trouble to generate a correct aseg.mgz for one volume of mine.
The nu_noneck.mgz is also incorrect and therefore I think the -careg stage
of autorecon2 might fail. Is there a way to do some kind quality check, like
the tal-check during autorecon1, to see whether the talairach.
Hi Amanda,
What are the intensity values of the regions that are being left out? If
they aren't near 110 then you should definitely use some control points.
Where are the rh surfaces including some of the left hemisphere? Is it
along the medial wall?
Jenni
On Wed, 24 May 2006, Amanda Dow
I
ran one of my brains through recon-all and the skull strip
and talairach were normal. When I checked the white matter edits with tkmedit, the
right hemisphere wm and pial surface lines are including some of the left hemisphere, and the
right temporal lobes are not included as white matter or in t
On this page there is a link to a snapshot of different quality scans:
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide
On Tue, 2006-04-25 at 16:38 +0100, Lee HL wrote:
> Hi Bruce,
> Thanks for the reply.
> Specifically, I was not satisfied with the pial outline near the hippoc
Hi HweeLing,
no, the surfaces aren't meant for analyzing the hippocampus, as it's not
neocortical and the assumptions of laminar structure will fail there. The
aseg.mgz file will have an explicit representation of the hippocampus.
cheers,
Bruce
On Tue, 25 Apr 2006, Lee HL wrote:
Hi Bruce,
Hi Bruce,
Thanks for the reply.
Specifically, I was not satisfied with the pial outline near the hippocampus
region at the coronal section. Part of the hippocampus was "excluded" -
outside of the pial outline. How should I edit to include the total
hippocampal region?
I hope this sounds clear to
Hi HweeLing,
sorry, there's not much that we can tell you. Basically the only thing you
can do is to visually assess whether the pial surface representation
follows what you believe is the true pial surface. I think the wiki has
examples of good pial surfaces. If not, we can put some up.
che
Hi,
I'm a freesurfer newbie.
I was wondering what constitutes a good grey-white matter segmentation and a
good pial surface outline?
I've been trying to follow the exercise from the website with respect to the
manual intervention, using my own data as an experience, but I don't know
how best to dec
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