We are pleased to release freesurfer 8.1.0. This contains an important
bug fix so we recommend that you this instead of 8.0.0. It will give the
same output as 8.0.0 while avoiding the "symlink" bug described below.
The biggest new feature is the new infant freesurfer pipeline. Congrats
to Lilla
Sorry, I don't have much to share. Siemens a file on the scanner
computer that holds the spherical harmonics used to do the 3D
correction. Maybe they have one that some how just does the 2D correction.
On 7/18/2025 10:13 AM, Annchen Knodt wrote:
External Email - Use Caution
I have a
on, 3 Feb 2025 09:20:40 -0500
From: "Douglas N. Greve"
Subject: Re: [Freesurfer] longitudinal analysis on one subject
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
Content-Type: text/plain; charset="utf-8"
The glm can be run on this data in theory. With only 5 time points, y
you definitely dont want to add control points into the lesions!
In addition to changing the wm.mgz (set the lesions to 255) you should
also set the same voxels to 255 in the brainmask.finalsurfs.manedit.mgz
that should fix the surface and prevent it from wandering into the the
lesion
On 6/17/
Try using -lta instead of --reg
On 7/5/2025 12:22 PM, Zahnert, Felix wrote:
Dear experts,
I ran into an issue running mri_vol2vol after running bbregister using
freesurfer 8.
Running the same commands in freesurfer 7.4.1 worked well. bbregister
worked in both versions, while mri_vol2vol (8.0.0
I think the problem may be the @ in the path. It is uncommon to have @s
in the linux path. Can you remove it?
On 7/2/2025 11:45 AM, andrew cardona wrote:
External Email - Use Caution
Good afternoon,
I am reaching out as I am trying to trouble shoot one participant, yet
it keeps faili
It is not clear from the log what is happening. Is it possible that you
ran out of memory?
On 7/5/2025 10:30 AM, Nader Razmara wrote:
External Email - Use Caution
Dear
Freesurfer is very sensitive to:
1-memory of system
2- coordinate system of FLAIR image
3- contrast equalization
Che
Aloha,
Mahalo for your response! What do you use for normalization between subjects?
Mālama Pono,
Krystalyn Edwards-Calma
On Jun 27, 2025, at 5:23 AM, Douglas N. Greve wrote:
This is not necessarily a problem. The "e" in eTIV means "estimate". It is a
slight hack where the
can you send the recon-all.log file?
On 6/26/2025 4:42 AM, 岳昊 wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I am a neuroscience student currently working on analyzing ASL MRI
data using ASLPrep. I am encountering difficulties running recon-all
during the preproces
ould like to look at patients one by one.
I ran the mri_glmfit analysis but I received an error message:
ERROR: DOF=0
Is this because I tried to run it on one participant?
Sincerely,
Isa Rosselini
Date: Mon, 3 Feb 2025 09:20:40 -0500
From: "Douglas N. Greve"
Subject: Re: [Freesurfer
This is not necessarily a problem. The "e" in eTIV means "estimate". It
is a slight hack where the registration to MNI space is used to compute
an estimate of the TIV, so it is not based on a segmentation or any real
image processing, so it is sometimes quite off. This ratio was really
just mea
of the ROI averages at the surface for
each subject.
*From: *Douglas N. Greve
*Date: *Thursday, June 19, 2025 at 12:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *[Freesurfer] Re: PetSurfer surface-based SUVR
What do you mean by extract here? What do you want? A map of SUVR? A
group map
On 6/25/2025 4:58 PM, Mahta Abbaspour wrote:
External Email - Use Caution
Hi,
I had a question regarding how FreeSurfer handles high-resolution MRI
scans. I understand that it typically accepts isotropic 1 mm scans
(and up to 1.5 mm). I wanted to confirm whether using the -hires fl
Yes, mri_segstats is the way to go, something like
mri_segstats --slabel fsaverage lh /path/to/label --i z.nii.gz --segid 1
--sum sum.dat
On 6/25/2025 6:32 AM, Federica Tomaiuolo wrote:
External Email - Use Caution
Hi,
I'm experiencing a problem while trying to extract Z score from single
su
x27;s exactly what I mean — the word I should have used was
"nonisotropic".
Is there an easy way to tell what axes row/col/slice corresponds to?
Is it correct that row/col are coronal and sagittal and slice is axial ?
Thanks again!
Message: 1
Date: Thu, 19 Jun 2025 12:35:13 -0400
F
The log file looks like it has everything you have run, but I don't see
an error at the bottom. Maybe it is in there somewhere, but you will
need to extract it for me. When DOF=0 means that you have more
regressors than time points. This can sometimes happen when you
accidentally include a term
the last command I need to
run? Can I extract SUVR values from
all.lh.mgx.ctxgm.fsaverage.sm05.nii.gz?
Thank you
*From: *Douglas N. Greve
*Date: *Wednesday, June 11, 2025 at 4:01 PM
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *[Freesurfer] Re: PetSurfer surface-based SUVR
That is all you
I'm not sure what you mean. Are you saying the fwhm varies across axes?
If so, you can pass different fwhms for each axis to mrI_gtmpvc with the
--psf-col, --psf-row, --psf-slice options. If you are saying that PSF is
space variant, then we don't have good options.
On 6/17/2025 11:03 AM, Finn,
My guess is that the surface file is not formatted properly and/or does
not have the proper geometry in it. Can you successfully run mris_info
on it and load it into freeview (freeview -f surface)? When you convert
to freesurfer format, try specifying the mgz file as the argument to the
--geom
On 6/16/2025 3:29 AM, Jackson Lee wrote:
External Email - Use Caution
Dear FreeSurfer community,
I'm currently working on a study involving three groups, each with two
timepoints, and I'm interested in analysing vertex-wise cortical
thickness using FreeSurfer's longitudinal pipelin
Your design is not necessarily wrong, but your reasoning is not correct.
Since these are categorical variables, there are actually two ways that
you can set up the model: interaction and non-interaction. The
interaction model allows you to test the interaction between your
variables (eg, is the
Almost! When mapping to the right, you still use the left hemi
fsaverage_sym/surf/lh.sphere.reg
I took your solution (with this fix) and added it to the xhemi page
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 6/3/2025 12:27 AM, Zahnert, Felix wrote:
Hi,
I think I have solved it myself,
Am I right to assume that you put the ADC image into samseg? I'm not
sure I've seen that before. If you have an anatomical, I would run
samseg on that, then use mri_coreg (or bbregister if you ran it through
recon-all) to register the anat to the ADC, then use mri_vol2vol to map
the seg to the
In the aseg, 24=CSF is comprised of some indeterminant ventricle space
in the middle of the brain. It is small and not well defined. In
synthseg, it represents that region but is mostly comprised of
extracerebral CSF as you have noted.
On 5/29/2025 5:24 PM, Emma Rodrigues wrote:
Exte
I think you can also just add --samseg to gtmseg
On 5/16/2025 1:45 PM, Simon Jones wrote:
External Email - Use Caution
OK, thank you Yujing
I’ll see if we can update the installation
Simon
___
Freesurfer mailing list
Freesurfer@nmr.mgh.ha
Use something like --maskthresh 0.5
where it will threshold the mask to exclude every voxel whose abs is
less than 0.5.
so you choose your threshhold
On 5/14/2025 6:37 PM, Gonzalo Rojas Costa wrote:
External Email - Use Caution
Hi:
Using "--masksign abs" option: which must be the
No, I don't think so.
On 5/14/2025 11:51 AM, Arianna Menardi wrote:
External Email - Use Caution
Thank you Stefano!
Just an additional curiosity, is there any function within Freesurfer
that you think could be used to map and quantify microbleeds in SWI data?
Thanks for the help,
A
Sadeghi Shabestari wrote:
External Email - Use Caution
Thanks Douglas, looks like it only returns the whole cerebellum volume
(see attached).
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Wednesday, 14 May 2025 at 16:38
*To: *freesurfer
Have you tried using mri_segstats, eg,
mri_segstats --seg cerebellum_17_network_${mask_option}_mask.nii.gz
--sum cerebellum_17_network_${mask_option}_mask.stats
On 5/8/2025 4:15 AM, Payam Sadeghi Shabestari wrote:
External Email - Use Caution
Hi FS team,
I'm trying to obtain anatom
Not necessarily. This error can arise if any of the columns are
linearly dependent. But try rescaling first
On 5/9/2025 8:29 AM, Ane Gurtubay wrote:
External Email - Use Caution
Dear Douglas,
whenever we get this error *ERROR: matrix is ill-conditioned or badly
scaled* as in
http
Hi, sorry for the delay
On 4/23/2025 10:43 PM, Dorian Pustina wrote:
External Email - Use Caution
Hi all, I have some questions regarding failed segmentations on
longitudinal data.
We have large datasets of Huntington's disease with data collected
longitudinally for 3-10 years. Fre
Yes, that is correct
On 4/23/2025 1:59 PM, Y Zeng wrote:
External Email - Use Caution
Hi,
I am currently using mri_gtmpvc from PETSURFER for partial volume
correction. I have registered the PET image to nu.mgz to get the
coregistered PET image (in 1mm T1 space). As I also want to ge
mail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz
--hemi lh --s sub-NSxLxYKx1964 --regmethod surface
Thanks,
Best,
-Loïc
Le ven. 18 avr. 2025 à 11:47, Douglas N. Greve
a écrit :
I should also add the since version 7 recon-all has been using ANTS N4
On 4/18/2025 9:33 AM, Douglas N. Greve wrote:
I don't think it should be a problem to run on skull stripped data.
It is ok to run the default recon-all on the submillimeter data as it
will just downsample it to 1mm
surf2vol does not take labels as an input. Instead, use mri_label2label
to convert it to a mask, then use mri_surf2vol on the mask
On 4/18/2025 11:39 AM, Loïc Daumail wrote:
External Email - Use Caution
Dear all,
I am trying to convert label files into volume ROI masks.
This is my c
I don't think it should be a problem to run on skull stripped data.
It is ok to run the default recon-all on the submillimeter data as it
will just downsample it to 1mm. But using the -hires option is good to
get any hires info. It does take a lot longer and sometimes it does
funny things, but
ed to run it on one participant?
>
> Sincerely,
> Isa Rosselini
>
> Date: Mon, 3 Feb 2025 09:20:40 -0500
> From: "Douglas N. Greve"
> Subject: Re: [Freesurfer] longitudinal analysis on one subject
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> Content
to:freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <mailto:dgr...@mgh.harvard.edu>
*Sent:* Tuesday, April 15, 2025 1:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mail
Yes, follow the instructions here
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
when you use mri_gtmvpc, specify the structure(s) you want to rescale by
with --rescale Id1 where Id1, etc are the segmentation ids as
found in $FREESURFER_HOME/FreeSurferColorLUT.txt (note that they have
to
fanie
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, April 15, 2025 1:14 PM
*To:* freesurfer@nmr.mgh.harvard.edu ;
Zollei, Lilla,Ph.D.
*Subject:* Re: [Freesurfer] clarific
First of all, can you confirm that that file exists and is readable by you?
On 3/28/2025 2:31 PM, Rosalia Dacosta Aguayo wrote:
External Email - Use Caution
Ok,
I found the problem, but now when I run in the terminal is telling me
that a file is missing and the file is not missing.
vard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, April 14, 2025 10:12 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] clarification - recon-all output data
All outputs from recon-all are in native space
On 4/12/2025 5:57 PM, Stefanie Bradley wrote:
External
Is it in the surface annot mapped to native space?
On 4/14/2025 11:22 AM, Simone Cauzzo wrote:
External Email - Use Caution
Dear support
I want to put the Yeo 400 annotations on my recon-all output and
produce a volume.
I'm using the following commands:
mri_surf2surf --srcsubject fs
I don't think you have this set up properly for the RM ANOVA. You'd have
to have a different class for each input. It looks like you've partially
configured for the paired analysis
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis, which is
probably the easier thing to do, but somthing l
All outputs from recon-all are in native space
On 4/12/2025 5:57 PM, Stefanie Bradley wrote:
External Email - Use Caution
Hi there,
I wanted to clarify about the recon-all output: is it in the subject's
native space or is everything already mapped to fsaverage space?
For example, i
What is the command you are running? Also include the terminal output
On 4/2/2025 3:56 PM, Fischl, Bruce R.,PHD wrote:
Sorry, I defer to Doug…
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Stefanie Bradley
*Sent:* Wednesday, April 2, 2025 3:52 PM
*To:* Freesurfer support list
I'm not sure what you mean. by itself mni152 is not a segmentation
template. Or do you want to do the analysis in mni152 space? If so, why?
On 3/27/2025 10:17 AM, Davide Sabbadin wrote:
External Email - Use Caution
Hi all,
Is there the possibility to perform the segmentation through r
Hi Lauri, yes, that's fine. It should give the same answer since you are
not using PVC or accounting for TFE.
doug
On 3/26/2025 11:14 AM, Lauri Tuominen wrote:
External Email - Use Caution
Dear PETsurfers,
I am trying to use PETsurfer and MRTM2 to analyze a SynVesT1 PET scan
with
, the reason
behind this issue.
Thanks in advance,
Tommaso Mariani
Il Mar 25 Mar 2025, 14:39 Douglas N. Greve ha
scritto:
Sorry, I'm a little lost as to what problem we are trying to
solve. In your first post, you included some warnings, but I'm not
sure if those warnings
Have you looked at the registration directly? Eg, there will be a
tkregisterfv command at the end of the register.log file. Run that. If
that does not look good, then there is a registration error. Send the
log file.
On 2/26/2025 5:59 PM, Gonzalo Rojas Costa wrote:
External Email - U
out what's going
on, as this issue is what keeps me apart from being able to use the
brain model for an important project.
Thank you in advance,
Tommaso Mariani
Il Lun 17 Mar 2025, 14:56 Douglas N. Greve ha
scritto:
Did that error happen before you did anything to the volume? Can
That is the right command
On 3/20/2025 4:27 AM, Dr. Cornelius Kronlage wrote:
> External Email - Use Caution
>
> Dear freesurfer team,
>
> in the wiki
> (https://secure-web.cisco.com/1WbYcGgb3srAnGYyZARo_Jad7UgANe_5pADqErCcDyQA2UArBn86DgiUZeOJqNlI42TKZRuTDtqJQ38yg5Lo1zSCGS9QQfUxZ4nuiApJj
Try adding --labelwm to mri_aparc2aseg
On 3/12/2025 12:17 PM, Jin Liu wrote:
External Email - Use Caution
Hello FreeSurfer team,
I’m trying to create a lobe segmentation for white matter. I first
created the annotation files using mri_annotation2label with
--lobesStrict for each hem
Did that error happen before you did anything to the volume? Can you
give a list of commands you used to get to that point? What do you mean
by offset?
On 3/10/2025 4:23 AM, Tommaso Mariani wrote:
External Email - Use Caution
Hi everyone,
I am experiencing a tricky situation in frees
You can try running mri_coreg, eg,
mri_coreg --mov your-non-image.nii.gz --s subject --reg reg.lta
The apply it
mri_vol2vol --mov your-non-image.nii.gz --lta reg.lta --o
you-non-image-in-fs-space.nii.gz
On 3/4/2025 5:59 PM, Chavez, Caitlyn wrote:
External Email - Use Caution
Hello F
Try adding --samseg to the command line
On 3/8/2025 7:06 PM, Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
Dear Freesurfer developers,
I have run the recon-all command with version 8.0.0 and now I would
like to run the gtmseg command. However, I received the messa
Hi Y'all, version 8.0.0 is officially released. You can download from
here https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
Release notes here https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
best
doug
___
Freesurfer mailing list
Freesurfe
Sorry, we don't have that ability. There might be someone out there who
has done this (it was done for monkey)
On 2/16/2025 11:17 PM, Ramesh Babu wrote:
External Email - Use Caution
Dear Experts,
Could you please suggest to me how to optimize FreeSurfer for 3D MRI
Mouse Brain analys
For what it is worth, this is the same thing that v8 generates (we just
call it sTIV)
On 2/12/2025 9:47 AM, Iglesias Gonzalez, Juan E. wrote:
Dear Antonio,
NextBrain provides the ICV via SynthSeg 😉
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
*From: *freesurfer-bo
where did aseg.nii.gz come from? Is it an individual subject or on the
mni305? If from an individual try
mri_vol2vol --interp nearest --mov aseg.mgz --reg
transforms/talairach.xfm.lta --o aseg.mni305.mgz
On 2/8/2025 11:34 AM, neda afzalian wrote:
> External Email - Use Caution
>
> To w
You might be able to use surfa package. It is python so it should work
on windows
On 2/8/2025 2:30 AM, Gonzalo Rojas Costa wrote:
External Email - Use Caution
Hi:
Is there any software for microsoft windows (and/or ubuntu) that
allows you to read mgz file format images, and transfor
The 5th vent, non-wm-hypos, left and right vessel are not worrisome. The
left and right cerebral cortex are probably just a few voxels that did
not get recoded to the surface parcellation. The ento and parahippo are
probably a segmentation error (good that there are only a few of them:)
On 2/
You can merge them together with a combination of mris_annotation2label
to split the annotation into different labels, then merge the labels you
want with mri_mergelabels, then use mris_anatomical_stats to compute a
stats file. Alternatively, and probably easier, is just to compute an
average o
I think what you are doing is fine. Those meshes were made over 25 years
ago, so the details you seek are probably lost
On 2/5/2025 7:26 PM, Samuel D Anderson wrote:
External Email - Use Caution
Hello,
I am working on generating a vertex mapping file that identifies
corresponding ver
I am not sure what caused the difference.
Also, sometimes even when I delete/edit the white matter, the white
matter surface/blue line still does not change.
Am I doing something wrong with recon-all maybe? (I use recon-all
-autorecon2-wm -autorecon3)
Screen Shot 2025-02-03 at 2.28.55 PM.png
Thank you
On 1/28/2025 12:51 PM, Andrade Rey René wrote:
External Email - Use Caution
Dear community,
I have tried the tutorial for PETsurfer. I would like to ask some
questions.
1) I have seen in the tutorial when you do PVC correction it is done
on PET dynamic raw data. Is this correct?
In that post, I'm not saying that we have a meninges segmentation, just
that the meninges might be removed when doing skull stripping. This will
not remove the signal from meninges that has partial-volumed into the
brain. We don't have a way to do that unless there is a meningeal ROI.
On 1/30/
Hippcampus actually looks like it might be ok; are those holes actually
ventricle? I don't see a caudate label on there. Thalamus can often be
underlabeled as there is so much WM in it. You can try running the
thalamic nuclei segmentation, eg,
segment_subregions thalamus --cross subject
This wi
The glm can be run on this data in theory. With only 5 time points, you
probably won't have much power though. What are you trying to test?
On 2/1/2025 11:56 PM, Isabella Rossellini wrote:
External Email - Use Caution
Hello Freesurfer users/experts,
I am working with Freesurfer 7.4.1
Does that file exist?
On 2/2/2025 11:34 AM, Ramesh Babu wrote:
External Email - Use Caution
Dear Experts,
May I know why wmparc2diff is unreadable? Please suggest.
Thank you
Ramesh
On Fri, Jan 31, 2025, 9:01 PM Ramesh Babu
wrote:
Dear Yujing,
For the command,
freevi
samseg does not have a CC seg. You can get the CC with something like
mri_cc -aseg samseg/seg.mgz -o samseg/seg+cc.mgz -lta samseg/cc_up.lta
you can ignore the lta output
On 1/28/2025 7:00 PM, Taghizadeh Mortezaei, Nima wrote:
Dear FreeSurfer Support Team,
I am using FreeSurfer version 7.4.1
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, January 28, 2025 12:41 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Issue with Right Hemisphere
Segmentation/Parcellation
Try using recon-all-clinical.sh
This is a known issue when recon-all v8-beta is run a 2nd time. It will
be fixed in the final v8 release. In the mean time, you can get around
it with
cd $SUBJECTS_DIR/subject/surf
mris_compute_lgi --i lh.pial
mris_compute_lgi --i rh.pial
On 1/27/2025 5:59 AM, Katharina Wittfeld wrote:
Try using recon-all-clinical.sh; it works a lot better on these thick
slice data
On 1/28/2025 12:24 PM, Taghizadeh Mortezaei, Nima wrote:
Hello FreeSurfer Developers and Community,
I am working with an axial T1-weighted post-contrast MRI, with an
original voxel size of 1×1×5.5 mm. I resample
It is hard to say without the data. I checked one of our cases and they
are different, although it was not from v6 (but I would not expect this
to change). Can you try running it in a newer version? Or re-run in v6?
On 1/27/2025 1:42 AM, Taghizadeh Mortezaei, Nima wrote:
Dear FreeSurfer devel
You can edit the brain.finalsurfs.manedit.mgz to remove those voxels.
You may need to removed them from the wm.mgz and filled.mgz
On 1/21/2025 1:41 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team,
We are editing some longitudinal data using FreeSurfer 7.4.1
you can use the two stage model
On 1/15/2025 1:52 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1
year, 1.5 years) using FreeSurfer 7.4.1.
We already analyzed two timepoints (basline[0] and
It says that it cannot find /run/media/user/2TB/freesurfer/ASegStatsLUT.txt
does that file exist on your system?
On 1/16/2025 6:20 PM, 박경일 wrote:
External Email - Use Caution
Dear FS Development Team,
I recently encountered an error while running the recon-all process.
This is the
it says finished without error
On 1/15/2025 5:13 PM, 박경일 wrote:
External Email - Use Caution
Dear FS Development Team,
I recently encountered an error while running the recon-all process.
This is the first time I’ve experienced an issue with this routine
process. Please refer to the
That flag is to perform only the subcortical segmentation, but there are
are steps leading up to it that need to be done. If all you want is a
subcortical seg, then you can just run
mri_synthseg --i orig.mgz --o synthseg.mgz
On 1/15/2025 8:42 AM, Sara Rapuc wrote:
External Email - U
That recon-all.log file says it returned without error:
"recon-all -s E0001 finished without error at Mon Dec 23 12:20:40 KST 2024"
what's the problem?
On 1/13/2025 10:26 PM, 박경일 wrote:
External Email - Use Caution
Dear FS Development Team,
I recently encountered an error while runn
Sorry, I deleted the original thread. Can you remind me of the original
problem?
On 1/13/2025 4:51 PM, Michael Eyre wrote:
External Email - Use Caution
Hi, thanks for your response, apologies for late reply.
nu.mgz looks fine
When I run tkregisterfv --s subject --fstal : orig.mgz(
welcome to freesurfer!
To convert from dicom to mgz, you can do a couple of things:
use mri_convert, eg,
mri_convert /path/to/dicomfile mprage.mgz
Then run recon-all like
recon-all -i mprage.mgz -s subjectname -all
You can also use dcmunpack to unpack all volumes from a dicom directory
See https:/
That is probably the best way. Another way would be to run the seg on a
set of subjects, run fs-synthmorph-reg on those subjects (non-lin reg to
mni152), then map the individuals thal segs to mni, then combine them
together. Not sure which one is base. Certainly just running the thal
seg on the
difference in the
files?
On Wed, Jan 8, 2025 at 8:01 AM Douglas N. Greve
wrote:
I can't see anything wrong either. Does it happen repeatedly? Can
you try running it without the -parallel flag?
On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:
External Email - Use C
You can try something like
mri_convert --in_like template.mgz yourfile.mgz yourfile2.mgz
On 1/7/2025 3:28 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Hello All,
Is there a FreeSurfer tool that will copy header information from one
image to the other with the same dimensi
I can't see anything wrong either. Does it happen repeatedly? Can you
try running it without the -parallel flag?
On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
You are correct. Attached is the correct one
On Tue, Jan 7, 2025 at 8:08 AM Douglas N.
Are you sure this is the right recon-all.log file? At the end it says it
finished without error
On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote:
External Email - Use Caution
Hell All,
I am testing recon-all and found that it returned with an error. I am
not sure where the error is. The r
You have to pass it the name of the subject with the --s flag. The
subject name is that produced by recon-all -s subject ...
On 1/4/2025 7:30 AM, Ramesh Babu wrote:
External Email - Use Caution
Hello,
I want to register JHU-ICBM-tracts-maxprob-thr0-1mm.nii.gz with local
subject spa
I'm not sure what you are trying to do. The HO atlas is volume-based,
isn't it?
On 1/3/2025 4:41 PM, Zeng, Xinglin wrote:
External Email - Use Caution
Dear Community,
I am currently working on visualizing ROI boundaries on the brain
surface using the Harvard-Oxford brain atlas. My g
;.
Another uncommon thing is that, after loading the surfaces, it gives
me an error about the reconstruction of the inverse matrix...
Il Mer 1 Gen 2025, 23:28 Douglas N. Greve ha
scritto:
Hard to say from those images. In the 2nd, the surface is no where
near where it should be -- it
Have you seen this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 12/22/2024 11:05 PM, 권용현 wrote:
External Email - Use Caution
Hello,
I am conducting research using ECoG.
I want to accurately track the location of electrodes.
I am inputting data from a NIfTI fil
For sub-04, can you look at the nu.mgz volume to see if that looks ok?
Can you also see if the talairach registration looks ok? You should be
able to run something like
tkregisterfv --s subject --fstal
It does not have to be perfect, but it is a problem if it is wildly off.
On 12/29/2024 10:
I don't know that anyone has ever really looked at it. It is hard to
define the volume for it as it is just the crossing point of the optic
nerves.
On 12/29/2024 6:26 AM, Knut J Bjuland wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I am examining the optic chiasm seg
Hard to say from those images. In the 2nd, the surface is no where near
where it should be -- it looks like it is misregistered with respect to
the brain (that not an intensity problem). What is your freeview command
to view the images?
On 12/23/2024 8:17 AM, Tommaso Mariani wrote:
When you say that it doesn't work, what do you mean? I was able to run
your command line successfully in 7.1.1
On 12/18/2024 7:34 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi guys,
I need to extract the eTIV from a stats file
Its like this
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, December 10, 2024 11:43 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [External] Re: [Freesurfer] Subject: query about mri_vol2surf
You don't often get email
Use mris_info, eg
mris_info --vx 1000 lh.white
vertexno 1000
xyz -21.1794 -74.9562 37.7794
nxyz 0.9807 0.1533 -0.1214
vertex_area 0.661364
neighbors 6 6
nbr 0 748 0.7216 0.5103 1944 0.2824
nbr 1 102418 0.9059 0.5654 1945 0.2912
nbr 2 991 0.7688 0.4739 2578 0.3172
nbr 3 992 0.9298
You can use mri_surf2vol with the --mkmask option (method 2; see
mri_surf2vol --help), eg,
cd subject/surf
mri_surf2vol --mkmask --hemi lh --o mask.lh.mgz --identity subject
--template ../mri/nu.mgz
If you want to go to another volume, supply the registration to that
volume with --reg instead o
This sometimes happens with noisy data. The difference in SNR between
those two scans is a factor of 2. What is your recon-all command line?
Can you send pics of the brain image with the surface overlaid on a
slice with one of the spikes? What does the white surface look like in
those regions?
1 - 100 of 8409 matches
Mail list logo
