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I am currently running FreeSurfer 7.4. I wrote a script using the program
mri_volsynth. I noticed for the first time the program was trying to write
files where it did not have write permissions. It outputted a few error
messages but gave a 0 exit
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I noticed the "-" used for the i and all is longer than the one used for
the s. It's a subtle difference and a problem if you are copying text from
Windows to Linux. Just replace the long hyphen with the short one.
On Sat, Apr 15, 2023 at 7:02 PM
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Recently FSL has changed the location of the bin directory they want you to
use.
The FreeSurfer setup script adds the old binary folder to the PATH not the
new one. This is causing quite a bit of trouble for me. I made changes to
the
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We acquired some data this morning where the participant's head was in an
unusual orientation. The participant has cervical dystonia. I have
processed data like this before and freesurfer always fails. I am assuming
Freesurfer is unable to register the
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Good luck. It requires a 7T to separate the compacta and reticulata.
Localizing the the substantia nigra is impossible with standard MPRAGES
but can be done if you modify the sequence or use a adequate T2 . There
are papers that discuss how to
d. Dunno if FreeSurfer offers this.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Aaron
> Tanenbaum
> *Reply-To: *Freesurfer support list
> *Date: *Friday, March 3, 2023 at 7:26 PM
> *To: *Freesurfer
> *Subject: *[Freesurfer] Apply a nonlinear transform to a surfac
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I am working on a project that will involve applying nonlinear work to a
freesurfer surface. This project is in its infancy. I have not figured
out all the details. The nonlinear transform will be in either FNIRT or
ANTS format. Does anyone know how
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Hi,
I saw this thread and was wondering about the details of this patch. Does
this patch affect the standard recon-all call or is this meant for a
special flag. Also I was also wondering what issue did it solve?
Thank you.
On Wed, Feb 22, 2023 at
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Is there a flag on the command line to turn on neurological view or do I
have to turn it on in the GUI.
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, email will be ignored.
Aaron Tanenbaum
Senior Neuroimaging Engineer,ReqJR72355.docx
Description: MS-Word 2007 document
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On Mon, Jan 30, 2023 at 12:40 PM Lee, Sang Hoon
wrote:
> External Email - Use Caution
>
> Dear, Matt,
>
>
>
> What kind of issues did you have with version 7.x and the hires stream?
>
> It would help us to know what we are facing…
>
> Thanks.
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Hello FreeSurfers,
I just need to know if the FSL is used in the recon-all scripts. Basically
if FSL_DIR is different will the recon-all produce different values.
Thank you
Aaron.
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I should have said I am using FS 7.3 on Ubuntu 20.04
On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum <
aaron.b.tanenb...@gmail.com> wrote:
> Hello,
> FYI, I recently noticed that mri_mask returns a zero exit status when it
> is
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Hello,
FYI, I recently noticed that mri_mask returns a zero exit status when it is
unable to write the output.
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Hello,
Is there a way to set a loaded volume as read only in freeview on the
command line?
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Hello,
I am trying to generate a mgz with identical header and dimensions as
another mgz file. However I would like all voxels to be set to one value.
What is the best way to do this?
Thank you
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I have noticed a change made in the release of FSL 6.0.6 that may affect
FreeSurfer. FSL executables now lie in ${FSLDIR}/share/fsl/bin not
${FSLDIR}/bin. The Freesurfer set up script adds ${FSLDIR}/bin to the PATH.
Not sure if this causes any
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I am looking set up freesurfer to do two things. If they are not currently
possible then I would like to submit two feature requests for freeview.
Here they are
When making voxel edits, it would be useful to see all voxels the mouse is
pointing to.
supercomputers run Redhat which worked great when you compiled
with CentOS. I was wondering if you are going to consider either rocky or
almalinux. Both are distributions that came out of the ashes of centos
which is why I ask.
Aaron Tanenbaum
.
On Wed, Jun 22, 2022, 9:23 AM Aaron Tanenbaum
wrote:
> So I believe I posted something like this a while ago. My observation is
> that edits removing voxel from the brain mask does not always remove
> inclusions for the cerebellum. It seem to work for the rest of the brain.
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So I believe I posted something like this a while ago. My observation is
that edits removing voxel from the brain mask does not always remove
inclusions for the cerebellum. It seem to work for the rest of the brain.
I find this to be a common
You should be able to run 7.2 on top of the 5.3 and at will take all your
> edits (make a copy of your 5.3 data first:)
>
>
> On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands
I just changed the freesurfer version , thnx for
> your help
>
> Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum
> a écrit :
>
>> External Email - Use Caution
>>
>> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
>> to do. I see th
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Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to
do. I see that you can give freesurfer a brainmask. I was thinking of
giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
wise idea? Do you have any
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What about for 7.1?
On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve
wrote:
> What version are you running? In 7.2, it will automatically set the t2pial
> flag when you specify -t2
>
> On 9/27/2021 11:53 AM, Aaron Tan
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What does Freesurfer do with a T2 if you do not use the t2pial flag?
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Read the release notes. Can I with the new version run a recon-all over
processed 7.1.1. I am interested in the ability to edit filled.mgz and
applying this to 7.1.1 recons.
On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve
wrote:
> We are please
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Ideally, what should Virchow–Robin space be labeled as.
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freeze to value 247 (FreezeSurface in
> $FREESURFER_HOME/FreeSurferColorLUT.txt)
> Then run recon-all with -autorecon2-surfonly -autorecon3
>
>
> On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
> So I never got a response for my question. At le
t; have any examples of when this should be used?
>
> Aaron Tanenbaum
>
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es of when this should be used?
Aaron Tanenbaum
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to see what works and what does not on different
versions of centos.
Aaron Tanenbaum
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I noticed that you guys released a fix to improve the -hires option. I
have been processing some of our data using the hires flag. if i use this
fix do i need to run recon-all from the beginning or can I run over the old
folders?
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Thank you dude
On Sun, Sep 8, 2019 at 9:22 AM Bruce Fischl
wrote:
> Hi Aaron
>
> you may need to motion correct and average them yourself. We'll put it on
> our feature request list though
>
> cheers
> Bruce
> On Sat, 7 S
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Does freesurfer 6.0 have the ability to use multiple T2s in recon-all. If
so how does one get it to work. It only seems to use the last T2 in the
call to recon-all.
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, 2019 at 2:20 PM Aaron Tanenbaum
wrote:
> Eugenio,
> You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but
> the Flair is. Is a FLAIR in general not benifisiol
>
> On Fri, May 18, 2018 at 2:02 PM Anik Dar wrote:
>
>> External Email - Use Caution
&g
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Eugenio,
You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but
the Flair is. Is a FLAIR in general not benifisiol
On Fri, May 18, 2018 at 2:02 PM Anik Dar wrote:
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>
> Hi All,
>
> I have
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I am wondering if there is any documentation about getting FreeSurfer to
use a custom Talairach target.
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I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu.
The super computer is about 3 years old. Of those 38 subjects, 7 exceeded
20 hour time limit on the batch script. The others took about 12 hours to
finish. All subjects had a
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I am working on a project where we are attempting to automate localization
of white matter hyper intensities. So far it looks good. I was wondering is
there a way to feeding this mask to FreeSurfer 6.0 to help improve of the
parcellation and
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I am not too sure if I have asked you this question before. I know the use
of a flair or T2 helps with dealing with the dura. I was wondering if there
are other benefits?
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Hello freesurfers,
Our lab has been using freesurfer 5.3 for a while. We use the following
flag when we run the initial recon-all
-mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon
-custom-tal-atlas
that list, as Mike has
> done a lot of work on the HCP-Style acquisition protocols.
>
> Matt.
>
> From: on behalf of Aaron
> Tanenbaum
> Reply-To: Freesurfer support list
> Date: Friday, October 19, 2018 at 3:23 PM
> To: Freesurfer
> Subject: Re: [Free
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I suggest you talk to the folks at Washington university in St Louis. There
has been considerable amount of work looking at this. You should contact
the following individuals
Steve Petersen s...@wustl.edu
Avi Snyder azsny...@wustl.edu
Michael harms
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I tried updating freesurfer 6.0 using the command fs_update. I get the
following output.
> Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
>Running this will update some of your freesurfer binaries.
>
> Shall I proceed?
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Hello Freesurfers.
I was wondering of for the purposes of editing wm.mgz if changing
voxel values to anything but 255 and 1 will be useful in anyway. If so
I was wondering if you can explain to me what the following values
mean and how do I use them.
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I just noticed that this problem is a now and resolved. I just have to
replace the mri_segstats.
Thank you for your time.
On Fri, Jul 13, 2018 at 6:08 PM Aaron Tanenbaum
wrote:
> Yes, I first ran autorecon1 and 2 for the initial processing
xist?
>
> Peace,
>
> Matt.
>
> From: on behalf of Aaron
> Tanenbaum
> Reply-To: Freesurfer support list
> Date: Friday, July 13, 2018 at 5:24 PM
> To: Freesurfer
> Subject: [Freesurfer] missing ribbon.mgz
>
> External Email - Use Caution
>
> I am a
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I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04. I am
getting an error, see below
I am using the command
recon-all -s BOLD-52_v1 -mprage -autorecon2
This has happened before. What did I do wrong.
#@# ASeg Stats Fri Jul 13
h
> can be
> an issue with FreeSurfer).
>
> $ cat /proc/sys/crypto/fips_enabled
>
> If it returns zero, it could be an issue with a system library like glibc
> on CentOS 7.5
> (that does not happen on older versions of CentOS).
>
> Either way, this is not your doing ;-)
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I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
When i get to the part where MRI_convert is creating the the orig001.mgz
its gives me a segmentation fault. if i run this on a centos 6 system it
works fine. below is the output of
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Hello FreeSurfers,
I am trying to find what the -l flag does for the program mri_ca_register
program. Does not seem to be documented anywhere but i could be mistaken.
Aaron Tanenbaum
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Hello FreeSurfers
When should I use the MPRAGE flag for recon-all?
Aaron Tanenbaum
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, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
> Hi Aaron
>
> we compute the warp and save it in the mri/transforms/talairach.m3z, but
> don't apply it (so
> don't require an extra resampling). I know we have some tools around to
> convert to ANTS
> format,
tra resampling). I know we have some
> tools around to convert to ANTS format, but I'm not sure about fnirt. I'll
> cc MJ who may know (hi MJ!)
>
> cheers
> Bruce
>
>
>
> On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:
>
> Is the warp saved anywhere and where can I find i
edu>
wrote:
> in the last stage there is a nonlinear atlas alignment that is specific to
> each timepoint. We are working on building a nonlinear base, but it is not
> distributed yet.
>
> cheers
> Bruce
> On Sun, 14 Jan 2018, Aaron
> Tanenbaum wrote:
>
> >
&
I am interested in knowing what type of alignment goes into the last stage
of the longitudinal pipeline. Are each longitudinal time point non-linearly
aligned to the base image? If so can I find the warp?
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I would like to get a clarification on what some the the files generated by
FreeSurfer recon-all
based on the URL
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles
The web pages says the nu.mgz "This is a intensity normalized volume
generated after correcting for non-uniformity in
Hello All
Several years ago Freesurfer 5.1 was patched to resolve some issues. I
just remember the patch resolved issues plaguing 5.1 and earlier. how does
one get the patch version. no where on the FTP server i can see patched
versions and instruction on performing a patch.
Aaron Tanenbaum
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.
Thank you
Aaron Tanenbaum
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Freesurfer
on to a specific
atlas volume. Does anyone know of a way to do this. Any help will be
highly appreciated.
Gracias
Aaron Tanenbaum
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