Hi Wade,
You just need to adjust the min/mid/max settings for the wm on the sidebar
under the Color map drop-down menu. Try using 0/100/255. How are you
trying to erase? Either shift+left-click, or enable right-click erasing
under Edit->Preferences.
-Louis
On Wed, 16 Jul 2014, Weber, Wade
Hi Pavitra,
In Freeview, go to File -> Save Movie Frames. For the fly through option
select Frame. There is no command line option for this feature yet, but
hopefully soon.
-Louis
On Fri, 11 Jul 2014, pavit...@nmr.mgh.harvard.edu wrote:
> Hi Freesurfer Team,
> I have a 4D volume mask of MRI m
Hi Doety,
Consider these options for uploading data:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I think recon-all is expecting your wm.mgz to be conformed or 256^3.
Something like: mri_convert wm.mgz wm.conform.mgz --conf
Hi Qijing,
Under the 'Freeview dev build' section on this wiki page you can download
an updated version of freeview.
http://freesurfer.net/fswiki/Download
-Louis
On Mon, 7 Jul 2014, Qijing Yu wrote:
> Hi Doug,
>
> By new version, do you mean v5.3.0?
>
> Qijing
>
>
> On Mon, Jul 7, 2014 at
Hi Paras,
The tcsh warning is ok, but see this link for more info and a fix:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg28980.html
The unrecognized flag error is because you have a space between the dash
and subjid, just delete that space.
-Louis
On Thu, 3 Jul 2014, Paras Pa
Hi James,
If you draw in 255 voxels on the wm.mgz to connect that stray blob of red
voxels to the others, then the wm surf should include it on a rerun. Look
through a couple slices in that area for any disconnected wm voxels since
it may be occuring on multiple slices.
-Louis
On Thu, 3 Jul
Hi Teo,
You might just need to adjust the contrast/brightness settings when
viewing the volume in freeview. If you move your mouse around do any
non-zero values appear in the bottom right voxel info panel?
The T1.mgz for bert should be 4.6mb, so you can see if what you have
matches that.
O
?
Thanks
James
On Tue, Jul 1, 2014 at 10:30 PM, Louis Nicholas Vinke
wrote:
Hi James,
Freeview has a "Write Movie Frames" option which will grab multiple
screenshots throughout a
volume. I recently requested a commandline option for this. I've run into the
&quo
Hi Max,
Could you send a snapshot of an area where your wm edits did not have an
effect? Keep in mind the wm voxels you add to the wm.mgz should be well
connected to the rest of the wm mask, or else it will tend to get pruned
off. You can look at the ?h.orig.nofix surfaces to see if the
intia
Hi James,
Freeview has a "Write Movie Frames" option which will grab multiple
screenshots throughout a volume. I recently requested a commandline
option for this. I've run into the "no X11 on cluster" limitation as
well, and I don't have a work-around at this point.
The snapshot-to-html scr
Hi Bryan,
Re: 1a) Did you run the case all the way through recon-all? Even if the
skullstripping looks poor, it's possible that the surfaces will turn out
ok and might only require some pial edits. Otherwise, this site has some
helpful info on rerunning the skullstripping step:
https://surf
Hi Teo,
Yes it does, but you can use the -no-wsgcaatlas flag. You can also try
using gcut which doesn't use an atlas (almost certain).
Link with skullstripping info:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
-Louis
On Fri, 27 Jun 2014, Teo Gelles wrote:
Hi
Hi Sam,
With the voxel edit tool in freeview, you can select the flood fill tool
(paint bucket icon), and check the box labeled "Flood fill multiple slices
at a time". You might have to play with the tolerance percentage to get a
good rough-start segmentation of the tumor tissue.
-Louis
On W
Hi Andrea,
To regenerate the aseg.stats file after aseg edits you can run:
recon-all -segstats -s
-Louis
On Wed, 25 Jun 2014, Andrea Horváth wrote:
Dear All,
After running recon-all and checked all the required steps, some part of the
right cerebral white matter was
still segmented as righ
Hi Fabio,
I don't believe the 5.1 version of freeview had that flag. The tutorial
instructions are written for 5.3 version of freeview. You can download a
more recent version of freeview here (under Other Downloads & Info):
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
You may want to ma
Hi Emad,
In your recon-all command what does 03551671 correspond to? I don't see
03551671 in the scan.info file corresponding to any of the runs. I think
you want to use 03557285. Also, run 26 apparently has 176 frames which
shouldn't be the case.
-Louis
On Wed, 4 Jun 2014, Emad Ahmadi wro
Hi Elisabetta,
The cortex measure (surface-based) reported in the aseg.stats file would
be best. See this site for details on various morphometry measures:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Thu, 5 Jun 2014, Elisabetta del Re wrote:
> Dear Freesurfer team,wha
Hi Victor,
This recon was originally processed with FS5.3, but when you reran it with
autorecon2-cp -autorecon3 you used FS5.1. Could you try rerunning this
case again with the same (314) control points using FS5.3 instead and see
if the right frontal area of the wm surface is severely underes
al Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Louis Nicholas
Vinke
Sent: Tuesday, May 27, 2014 3:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] FW: WG: WG: [Fwd: WG: missing temporal lobes],
calculati
Hi Kristina,
This page has the details I believe you are looking for:
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Tue, 27 May 2014, Mayer Kristina wrote:
Oh, I see. So in the calculation of total GM in aseg.stats does it include the
hippocampus, although it is not s
Hi Ben,
There should be a procsurffast flag called -volproj_lowmem which avoids
this mri_vol2vol memory issue.
-Louis
On Wed, 21 May 2014, Douglas N Greve wrote:
>
> mri_vol2vol when used in this way does not manage memory very well. It
> resamples the time series into a 256^3 volume of floats.
Hi Rujing,
If you load the surface up in freeview you can change the background
color.
-Louis
On Wed, 14 May 2014, charujing123 wrote:
Hi Bruce and Doug,
Ok, I see. That's all right.
All the best.
Rujing Zha
2014-05-14
___
Ok, could you send the entire terminal output?
Thanks.
-Louis
On Mon, 12 May 2014, Francesca Strappini wrote:
> Thanks Louis!
>
> Yes, I did run tkmedit from the same terminal window I have sourced
> freesurfer...
>
> Francesca
>
> 2014-05-12 16:57 GMT+03:00 Loui
Hi Francesca,
Are you trying to run the tkmedit command in the same terminal window you
have sourced freesurfer? You'll need to source freesurfer in any new
terminal window you open before being able to run any freesurfer commands.
It's possible to set it up so that freesurfer is sourced automa
Hi Charmaine,
Sounds like you just need to change the folder permissions for,
/Applications/freesurfer/
before attempting to copy the .license file to that location.
-Louis
On Thu, 1 May 2014, Demanuele, Charmaine wrote:
> Hi,
>
> I am trying to install freesurfer on my mac, and I got a licens
2014-04-11 17:23 GMT+02:00 Louis Nicholas Vinke :
Hi Markus,
You can try running mri_gcut with a slightly higher T value,
default is 0.4.
command would be something like (running from within subject's
mri dir):
mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.
ssive?
Thank you for help!
Markus
2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke
:
Hi Markus,
It will only skullstrip the T1 and generate a new
brainmask.mgz. So you'll need to run autorecon2 and
3 afterwards.
to correct the segmentation?
Thanks,
Andrea
On Fri, Mar 7, 2014 at 3:25 PM, Louis Nicholas Vinke
wrote:
Hi Andrea,
You can use the contour tool in the voxel edit mode to quickly and
roughly fill
in wm. Use the tool with the wm.mgz selected in the volume layer list
but set
ks!
Markus
2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke :
Hi Markus,
Instructions for using gcut within recon-all can be found on this wiki
page, near the
bottom.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
-Louis
On Mon,
Hi Saurabh,
Are you receiving any type of error messages? The Buckner tutorial data
tar file is 11GB so it might be the case that the network you are on has
some file size limits imposed.
Try downloading this for instance, which is only 17.3MB but located in the
same ftp directory as the Buckn
Hi Markus,
Instructions for using gcut within recon-all can be found on this wiki
page, near the bottom.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview
-Louis
On Mon, 7 Apr 2014, Bruce Fischl wrote:
Hi Markus
that looks pretty blurry and low contrast, although
Hi Saurabh,
Did the wget command fail for you? I just tried it and the download
started without any issues. You can also just paste the ftp address into
your browser and download it that way as well.
-Louis
On Mon, 7 Apr 2014, Saurabh Thakur wrote:
> Hello Freesurfer Expert,
>
> I am working
Hi Gabor,
Thanks, should be fixed now. Any of the links with the _tktools suffix
can be replaced with _freeview to view an alternate version of the wiki
page using freeview commands.
-Louis
On Tue, 1 Apr 2014, Gabor Perlaki wrote:
> Dear all,
>
> Most of the links on
> https://surfer.nmr.mgh.h
Hi Andreia,
If you remove the underscore from aparc_pial for the --parc flag in the
aparcstats2table command, that should do the trick.
-Louis
On Wed, 26 Mar 2014, _andre...@sapo.pt wrote:
> Hello list,
>
> I'm trying to get aparc surface area from the pial surface in a table
> using aparcstats2
Hi Francesco,
This wiki page has pretty good definitions for the morphometry
stats. Let us know if you want to clarify anything though.
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Tue, 25 Mar 2014, Francesco Puccettone wrote:
> Hello,
>
> I've read that cortical thic
Attached are examples of the bvals.dat and bvecs.dat files extracted from
siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s.
On Thu, 13 Mar 2014, Chris Watson wrote:
dcm2nii should give you bvecs and bvals
If you just want to transpose the file, I wrote a script to do it (a
g
On Mon, Mar 10, 2014 at 8:01 PM, Louis Nicholas Vinke
wrote:
Hi Kaiming,
I'm almost certain you are right at the medial line and what you are
seeing is the
transition from one hemi to the other. Most likely the brain is slightly
oblique and
so the sagittal slic
Hi Kaiming,
I'm almost certain you are right at the medial line and what you are
seeing is the transition from one hemi to the other. Most likely the
brain is slightly oblique and so the sagittal slice does not perfectly
bisect the two hemispheres.
-Louis
On Mon, 10 Mar 2014, Kaiming Yin wrote
Hi Rujing,
You might try drawing in the wm thicker than it is already. Also, check
there are no disconnects between the wm voxels in the wm.mgz.
-Louis
On Tue, 4 Mar 2014, charujing123 wrote:
Hi all.
In troubleshooting, I want to sign some area as white matter by control point
and wm edit.
Hi Pfannmoe,
I don't believe it is possible to edit a voxel via tcl scripts. If so the
command would be listed on this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScripting
-Louis
On Wed, 5 Mar 2014, Joerg Pfannmoeller wrote:
> Hello,
>
> if I have sel
Hi Andrea,
You can use the contour tool in the voxel edit mode to quickly and roughly
fill in wm. Use the tool with the wm.mgz selected in the volume layer
list but set the brainmask (or T1) as the reference. Set brush value to
255, and then do crtl+alt+leftbutton while dragging the mouse to a
Just to follow-up, the sd command is an alias for setting the SUBJECTS_DIR
environmental variable to the present working directory.
Mihaela was able to get rid of the "Bad fd number" error by running the
following commands on her ubuntu workstation. It seems like this error is
not freesurfer-
Hi Emad,
Which version of FS are you using? The freeview in the 5.3 release has
the clone tool within the voxel edit mode, but it's not in 5.1 or earlier.
It's represented by an icon with a blue and gray rectangle.
Take a look at the 5th section on this page:
https://surfer.nmr.mgh.harvard.ed
Hi Sabin,
What command did you run? Sending the recon-all.log file in the scripts
dir might be a little more helpful. It's failing because the ribbon.mgz
does not exist which requires surfaces.
This thread might be relevant:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876
Hi Osei,
Check out this wiki page for how to check the talairach transform and fix
it if necessary. If everything looks decent then you can use the
-notal-check flag to bypass this step in recon-all.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
-Louis
On Thu, 13 F
It should be posted momentarily, sorry for the delay.
-Louis
On Thu, 13 Feb 2014, charujing123 wrote:
Hi Bruce,
I did try, but I am so sorry that size of the attachment is too big to send in
the
mail list.
All the best.
Rujing Zha
2014-02-13
_
d get a black box drawn on the screen. It seems that I am not combining
button-clicks or values for the eraser and adding correctly.
Thank you
Sent with Good (www.good.com)
-Original Message-
From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu]
Sent: Monday, February 10, 2014 02:
Hi Alexander,
If you are editing FS recons, then you should keep the eraser value set to
"1" so that the edits can be detected by recon-all.
-Louis
On Mon, 10 Feb 2014, Ruopeng Wang wrote:
> Hi Alexander,
>
> Eraser value is used for erasing. Brush value is used for drawing. To
> erase, just hol
Hi Salil,
You should be able to apply an isosurface to each subfield label in
freeview. You can set the color for each isosurface as well, since the
default is gray. You need to be in the 3D view in order to display
isosurfaces.
-Louis
On Thu, 6 Feb 2014, Salil Soman wrote:
Hi,
I generate
Hi Jon,
If it's the colorbar you are looking for then right-click on the viewing
window, then Show Color Bar -> inflated_thickness. There are some
additional options under Configure Overlay located on the left sidebar.
-Louis
On Wed, 5 Feb 2014, Jonathan Holt wrote:
Hi all,
I’ve pulled up a
Hi Rotem,
Check out the -dti flag in freeview, pass it a vector and FA volume. You
can display the colormap as vectors as well once everything is loaded up.
Example command:
freeview -dti V1.nii.gz FA.nii.gz
-Louis
On Mon, 27 Jan 2014, Rotem Saar wrote:
> Hi,
>
> We followed the instructions
Hi Peter,
I think this is due to some maintenance the IT folks are doing on some of
the ftp servers. Should be back up by late afternoon (EST).
-Louis
On Mon, 27 Jan 2014, Davis, Peter wrote:
> Hi,
>
> I am unable to download freesurfer. Is there a problem at the ftp?
>
> Thank you,
> Peter
>
bash: setenv: command not found
best,
Neda
On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke
wrote:
Hi Neda,
Have you read over the linux install directions in the link below? You
will need to register and get a license file.
After that you should look over the setu
Hi Neda,
Have you read over the linux install directions in the link below? You
will need to register and get a license file. After that you should look
over the setup and config instructions.
https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall
https://surfer.nmr.mgh.harvard.edu/fswiki/Setu
Hi Jeni,
Yes it's possible. You could download the most recent version of FS and
then just source that version for when you want to use freeview, or copy
the freeview.bin over to your current version. If you tell me the OS
version you are running I'll send you the proper freeview.bin file.
Ju
Hi Krista,
I believe the v?.thresh labels are thresholded at p=0.8. This threshold
is based on comparisons of actual and predicted V1 boundary with an
independent dataset.
Relevant pub:
https://surfer.nmr.mgh.harvard.edu/ftp/articles/hinds2008accurate.pdf
-Louis
On Thu, 16 Jan 2014, krista
Hi Michael,
The aseg lookup table should be generated from all the subjects in the
dataset you are working with initially, then passed with the -asegLUT flag
along with any other QA options. I believe the aseg outliers are just any
subject measure which is 2 SD above/below the mean for your da
Hi Alan,
You can use mri_binarize to pull it out of the aseg.mgz. FYI: Once loaded
into freeview you can also generate an isosurface for the hippocampus
label in the 3D view.
-Louis
On Thu, 5 Dec 2013, Alan Francis wrote:
> Hi Bruce et al,
>
> Is it possible to load just the Hippocampal mask/
If you don't have MATLAB you could try using Octave instead.
On Wed, 4 Dec 2013, Douglas N Greve wrote:
>
> If you don't have matlab, then I don't know of one. The design matrix is
> in the glmdir folder (Xg.dat), so if SPSS or some other software can
> read that in, then the analysis will be the
or other
button/key.
Thanks in advance.
All the best.
2013-12-03
Rujing Zha
____
发件人：Louis Nicholas Vinke
发送时间：2013-12-03 03:50
主题：Re: [Freesurfer]
ks in advance.
All the best.
2013-12-03
Rujing Zha
发件人：Louis Nicholas Vinke
发送时间：2013-12-03 03:58
主题：Re: [Freesurfer] recon-all strip skul
Hi Rujing,
Even if there is some skull/dura left after the skullstrip step in
recon-all, it still may not negatively impact the surfaces. It might be
worth running the remaining recon-all steps to see how the surfaces turn
out.
If you want to swap-in a better skullstripped volume into the re
Hi Rujing,
You can use a tcl script to take several snapshots in tkmedit, then you
could use the convert command (part of ImageMagick distro) or
something similar to create an animated gif. With the convert command you
would use the -adjoin and -delay flags. You could use one of the tcl
scri
Hi Koene,
It looks like Nick copied that volume over on 11/27. Thanks for pointing
that out.
-Louis
On Tue, 26 Nov 2013, Koene Van Dijk wrote:
> Hi there,
>
> We've been using this local version of Freesurfer:
> /cluster/freesurfer/centos6_x86_64/stable5
>
> And this file was relevant:
> /clust
Hi Janosch,
The link on the course schedule page should point to the correct version
now.
http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.failure_modes.ppt
-Louis
On Wed, 27 Nov 2013, Janosch Linkersdörfer wrote:
Hi,
thank you very much for providing the lectures of the last
Hi Pietro,
I think you should try redoing the control points from scratch, but with
fewer control points and sparser placement. Currently you have 198
control points tightly packed in only a couple regions. Furthermore,
there is one control point at 128, 128, 128 which is right in the thalamu
Hi Anna,
Yes, search for 'build-stamp' in the recon-all.log. There's also the
build-stamp.txt in the scripts dir, but the recon-all.log will tell you if
different versions were run by looking at the build-stamp for each
invocation in the log.
-Louis
On Fri, 15 Nov 2013, Anna Jonsson wrote:
>
Yes, just tar/zip it up first.
On Mon, 11 Nov 2013, pietro de rossi wrote:
ok. is it possible to upload the whole subject folder?
2013/11/11 Louis Nicholas Vinke
Hi Pietro,
Yes, the filedrop would be fine or you can upload using ftp.
https://surfer.nmr.mgh.harvard.edu
Hi Pietro,
Yes, the filedrop would be fine or you can upload using ftp.
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-Louis
On Mon, 11 Nov 2013, pietro de rossi wrote:
Dear Freesurfers,
I am working on the segmentation of mdeft structural images (Siemens Allegra
3T-acquired) of
Hi Shahin,
You can use mri_convert to convert the mri_glmfit output to GIFTI (.gii).
-Louis
On Fri, 8 Nov 2013, SHAHIN NASR wrote:
Hi Surfers
I have done a surface-based group-averaged mapping and now I need to
save the results of the mri_glmfit (sig.nii) command in GIFTI .func.gii
format.
ell me what is the input file that free surfer used to calculate
> STV.
> I am not sure the webpage below gives that information.
> Thanks,
> Rashmi
>
> On 11/7/13 1:57 PM, "Louis Nicholas Vinke"
> wrote:
>
>> Hi Rashmi,
>> This page has the defi
2013, Rashmi Singh wrote:
> I am using version V5.1.0 is it different for that or the information is
> the same irrespective of the version I use.
> Rashmi
>
> On 11/7/13 1:57 PM, "Louis Nicholas Vinke"
> wrote:
>
>> Hi Rashmi,
>> This page
Hi Rashmi,
This page has the definition you are looking for (FS v5.3).
https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
-Louis
On Thu, 7 Nov 2013, Rashmi Singh wrote:
FreeSurfer experts,
May you please educate me how the supra tentorial volume (STV) measured by
FreeSurfer and which
assed to
recon-all.
-Louis
On Tue, 5 Nov 2013, Jonathan Holt wrote:
Also, quick question . . .
How exactly do you run a recon from scratch without nifti images? I’d always
delete the directory and restart with mri_convert -i …
Jon
On Nov 5, 2013, at 10:40 AM, Louis Nicholas Vinke
wrote:
H
Hi Anita,
I don't believe you have the complete path set to your SUBJECTS_DIR
environmental variable, unless Desktop is in your root dir which I doubt
is the case.
Easy way to set the variable:
cd /path/to/tutorial/data/
setenv SUBJECTS_DIR $PWD
Also, check you have fsaverage symlinked to th
con-all -autorecon2-noaseg -subjid
>>>>>
>>>>> that doesn?t work, the empty space is simply resegmented and the surface
>>>>> doesn?t change.. I should note that this has worked for me in the past on
>>>>> some brains.
>>&g
Hi Jon,
The limit numbers correspond to voxel intensities in the brainmask.mgz. I
believe you will want a lower number for the -wlo/-wm_low flag to make the
wm surf extend further out, assuming that the wm voxels that are not being
captured by the surface is hypo-intense (<< 110).
-Louis
On
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertOptionsFile
On Mon, 28 Oct 2013, Jon Holt wrote:
Where can I find more info on expert opts?
On Oct 28, 2013, at 6:22 PM, Bruce Fischl wrote:
Hi Jon
The segmentation looks really poor, which probably causes a topological defect
resul
Hi Elissa,
The invalid drawable terminal output you can ignore when running Freeview.
Presumably bert is not located in /Applications/freesurfer/elissa_thesis/,
so that's why the bert commands are failing. Not the same subjects
directory that ABU is in.
To fix the tkmedit library error it lo
Hi Philippe,
See link below regarding the error you are getting, although recon-all is
probably failing because you need to pass not only the path but one dicom
file which is part of the T1-weighted scan. If you run the command below
in the directory where you copied the dicom files, you will
Hi Jon,
You can do this with using the -c flag followed by the path to the
control.dat file, presumably in the tmp folder of the subject's recon
folder.
FYI: under the help menu in Freeview is a quick reference guide for
shortcut keys and common actions.
Also, type 'freeview -help' in a termin
Hi Francesco,
Could you maybe send a snapshot of the brainmask and wm volumes where you
are seeing this?
If you deleted any voxels on the wm mask then they should be a value of 1.
You might want to look at the ?h.orig.nofix surfaces to see if that area
in question looks better (or at least diff
Hi Stefano,
Take a look at the lobe mapping section on this wiki page. Example
commands near the end.
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
-Louis
On Wed, 4 Sep 2013, std...@virgilio.it wrote:
> Hi list,
> I need to create a mask of frontal, parietal, temporal and occ
Hi Sinead,
In short, it is most likely a bug. I think the current version of the QA
tools scripts expects a 5.1 recon-all stream, so the output order of files
being slightly different in 5.2/5.3 causes this error/warning to appear.
In the future you should just run QA tools with the -snaps-onl
Hi,
We figured out was the problem was. Just so others on the list are aware,
when deleting voxels from the brainmask.mgz or
brainmask.finalsurfs.manedit.mgz volumes in Freeview, you should verify
that the deleted voxels have a value of 1, not 0. The 5.3 version of
Freeview has a "Recon Edit
Hi Daniel,
With the volume highlighted in the side bar you should have an opacity
slide bar which you can move to adjust the transparency of the volume.
-Louis
On Fri, 2 Aug 2013, Yang, Daniel wrote:
> Hi FreeSurer Expert,
>
> I am wondering if there is a way that the annotation can be made som
Hi Chris,
I believe if you do not include the -clean-bm flag then it should have an
effect when run multiple times. You should make a copy of the
brainmask.mgz and brainmask.gcuts.mgz to compare before/after to verify
if there are any differences.
-Louis
On Tue, 30 Jul 2013, Chris Watson wrote
Forwarding to the list so others can chime in.
-- Forwarded message --
Date: Mon, 29 Jul 2013 18:19:38 -0400
From: Subhabrata Chaudhury
To: Louis Nicholas Vinke ,
Aaron Tanenbaum
Subject: Re: [Freesurfer] break up time course nifti
Greetings Dr. Vinke and Dr. Tanenbaum,
I
Hi Aaron,
You can use the -f or -nth flags with mri_convert.
-Louis
On Mon, 29 Jul 2013, Aaron Tanenbaum wrote:
> hola freesurfers,
> I have a time course surface nii files. I would like to break up the time
> course into many nii
> files for each time frame. Is there an easy way of doing this.
Jul 29, 2013 at 1:37 PM, Louis Nicholas Vinke
wrote:
ok, that's good. Just make a symlink to the fsaverage dir from your
subjects dir
(/home/pom/Software/freesurfer/subjects)
i.e.
cd /home/pom/Software/freesurfer/subjects
ln -s ./fsavg/fsaverage .
[pom@PomLinux /home/pom]% cd fsavg
[pom@PomLinux /home/pom]% ls
fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 lh.EC_average
rh.EC_average V1_average
thanks again.
On Mon, Jul 29, 2013 at 1:23 PM, Louis Nicholas Vinke
wrote:
what is fsavg in that same directory? Maybe fsav
-xr-x 2 pom pom 4096 2012-04-21 15:33 sample
-rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit
/
I think it linked to itself, should I re-install freesurfer.
thanks
Pom
On Mon, Jul 29, 2013 at 1:09 PM, Louis Nicholas Vinke
wr
Hi Pom,
Does the following path exist?
/home/pom/Software/freesurfer/subjects/fsaverage/label/
if so, do it contain lh.BA1.label? It probably has something do with the
fsaverage symbolic link. A few lines up in your error log it prints "Too
many levels of symbolic links".
-Louis
On Mon, 29
Hi Laouchedi,
You'll have to run autorecon3 as well to regenerate the pial surfaces.
FYI: aseg.mgz, brain.finalsurfs.mgz, wm.mgz and filled.mgz are all
volumes, not surfaces. All play a part in generating the surfaces though.
-Louis
On Fri, 19 Jul 2013, LAOUCHEDI MAKHLOUF wrote:
Hi
in fac
Hi Jason,
If the hemi masks look peculiar in the filled.mgz then you can try seed
points for the corpus callosum. See this page for details, go to section
titled "seed points, fill and cut".
https://surfer.nmr.mgh.harvard.edu/fswiki/Edits
-Louis
On Thu, 18 Jul 2013, Jason Tourville wrote:
>
Hi Jon,
Also, delete the IsRunning.lh+rh file in the scripts recon dir, or add the
'-no-isrunning' flag to the recon-all command when re-running.
-Louis
On Thu, 18 Jul 2013, Z K wrote:
> Jon,
>
> The way to solve this problem is to use the "nohup" command, for example:
>
> $nohup recon-all -s te
Hi Jason,
Yes, although I think it's only an option in freeview from the 5.2/5.3
Freesurfer releases.
-Louis
On Thu, 18 Jul 2013, Jason Tourville wrote:
Hi there,The tksurfer/tkmedit combo allowed one to select and save a point on
the
inflated surface and then go to that point in the volume.
Hi Panos,
The motion correction itself is carried out using the mri_robust_template
binary. The motion correction step also includes an mri_convert command to
conform the volume and mri_add_xform_to_header.
example taken from recon-all dev table:
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAl
Hi Ye,
Is the dura in question affecting the surfaces? If so you can delete the
dura, add control points and then run command 4 below. You don't need to
rerun autorecon1.
-Louis
On Thu, 11 Jul 2013, ye tian wrote:
> Dear freesurfers,
> I have a subject for which I need to delete some dura in
Hi Ye,
A couple control points should do the trick.
-Louis
On Thu, 11 Jul 2013, ye tian wrote:
> Dear Freesurfers,
> Is it true that a small piece of the brain is missing in the attached (all
> three
> views)? How do I correct this problem?
>
> Thank you very much!
>
> Sincerely,
> Ye
>
>
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