g9G-wR9wyOb75unRTkOLmt6TdQaQOuwNtXEYTplcji1G5_OxnR7lzApwg6p1TnoWwCm1hdhkjdzw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLGI__;!!AIv8Mrc!_zif_gc_qZJfmYGB6AxETsBfWkprrxnEsOgn6g4g5ZPo3QFoRz3wFE7cSQOEj1n7YVvl0KehPmd93THbISFFiVaZ1L-Y$>
On 1/10/2024 9:52 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry)
External Email - Use Caution
Hi,
We were wondering what the preferred command is for extracting mean gray matter
thickness/LGI
I am aware that FS outputs left/right mean thickness but wanted to be conscious
of the fact that left/right hemisphere might have different sizes.
External Email - Use Caution
Hi all,
First time using FS7.4 for subfields specifically hippo/amy. I've used
segment_subregions this time around, and it seems the function for
concatenating the volumes, quantifyHAsubregions doesn't work anymore. I suspect
its because the .v21
External Email - Use Caution
Hi developers,
Using freesurfer-linux-centos7_x86_64-dev-20230216-9bc2be6, I receive an error
following mri_synthsr.
It says :
get_data() is deprecated in favor of get_fdata(), which has a more predictable
return type. To obtain get_data()
External Email - Use Caution
Hi all, I just want to follow up with this email since it has been a while with
no replies. Thanks
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: Zeng, Victor (BIDMC - Keshavan - Psychiatry
-produce it here. Which
.annot are you referring to? Also, can you provide the command sequences that
you used to generate mpm.vpnl+aseg.mgz?
Thanks.
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Sent: Tuesday, November 8, 2022 4
you are saying. Are you saying that the annot/surf looks
right but the seg in the volume looks wrong or that they both look wrong?
On 10/31/2022 2:58 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi Freesurfer devs,
We have used mri_aparc2aseg
External Email - Use Caution
Hi Freesurfer devs,
We have used mri_aparc2aseg to map the Stanford mpm/vpnl labels unto the gray
matter ribbon. We notice that when analyzing the resulting mpm.vpnl+aseg.mgz
that the regions/voxels of the mpm.vpnl+aseg.mgz stretch out the
6FVVL$>
for a patch
On 10/14/2022 1:46 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
I receive an error when I try to run the sclimbic module, do you have any
suggestions on why this might be happening? : Loaded input image from
/mnt/V/Datas
External Email - Use Caution
I receive an error when I try to run the sclimbic module, do you have any
suggestions on why this might be happening? : Loaded input image from
/mnt/V/Datasets/BSNIP2/Processing/Finished_q2/GP1462~1/mri/nu.mgz
Traceback (most recent call last):
External Email - Use Caution
Hi all,
I am receiving this error when trying to run sclimbic module. It's not being
very descriptive about what the error is so I was wondering if you all can help
debug. My SUBJECTS_DIR is correct
mri_sclimbic_seg --s GP0050
MYA-NNT8_dZjejPL7rLo0QkpoeWvneHWmq0w8tdBAyrnFHoDWyg$>
On Jul 27, 2022, at 15:03, Zeng, Victor (BIDMC - Keshavan - Psychiatry)
mailto:vz...@bidmc.harvard.edu>> wrote:
External Email - Use Caution
Hi all,
I've downloaded a new dev version of FS 7/19/2022 - and I receive an error w
External Email - Use Caution
Hi all,
I've downloaded a new dev version of FS 7/19/2022 - and I receive an error with
running subunits:
mri_segment_hypothalamic_subunits --s 10893/
using 1 thread
/mnt/QBERT/freesurfer/python/scripts/mri_segment_hypothalamic_subunits:1023:
External Email - Use Caution
Hi,
Can someone send me the full ICC for all of the thalamus subnuclei that are
parcellated? Just want to have that ready if a reviewer asks.
Thanks
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
External Email - Use Caution
Hi developers,
I have some colleagues who have been assigned to quality check brain scans
remotely on their laptops (macs), and they have space constraints. Is there a
stand alone freeview-only installation that doesn't require the ~10gb needed
for
@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] [External] Re: Reversing mri_convert
The ASL has a different vox2ras transform.
How did you register the ASL to the anatoical?
How did you convert the ASL to the anatomical space?
On 5/6/2022 4:47 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry
External Email - Use Caution
I simply put the desired brains in SUBJECTS_DIR, and then with SUBJECTS_DIR as
the pwd, type quantifyThalamicSubnuclei.sh thal.txt T1
and that works. Perhaps drop mentioning the parent directories?
Victor Zeng
Beth Israel Deaconess Medical Center
aying the same i/j/k ras" mean? In what tool? What is the
result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
For some reason it isn't displaying the same i/j/k ras. The T1 and the
registered
he -rl (“reslice like”) option:
mri_convert -rl template.mgz vol_to_convert.nii vol_like_template.mgz
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Sent: Thursday, May 5, 2022 4:09 AM
To: freesurfer@nmr.mgh.harva
vMGjuU!rHiQafTzmK0wTaLT_IjY-1kM4Fz9OLO4DEJabDexgR3JTcK7u_-hgWR5knK0sqaFxGR3sg$
Von: freesurfer-boun...@nmr.mgh.harvard.edu
im Auftrag von Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: freesurfer@nmr.mgh.harvard.edu
B
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move it back to
Freesurfer space. How would you go about doing that? I am assuming I would do
the inverse of the
External Email - Use Caution
Hi,
My lab has been using tkmedit, although it is deprecated, for pial edits. We
resist transitioning towards freeview due to changed functionality, which I
understand because freeview is used for more than just pial edits but - Are
there any tools
kef>
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Sent: Wednesday, March 16, 2022 5:52:54 PM
To: Freesurfer support list
Subject: Re: [External] Re: [Freesurfer] [External] Re: classes for GLM analysis
Sorry for the different approach - but I just propensity matched
s
Can't tell without the fsgd file
On 3/7/2022 8:30 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Just to double check the numbers - I seem to have been getting into an error in
how many columns in the FSGD it is expecting.
I have 9 different sites
External Email - Use Caution
I receive FWHM values much larger than what
average/mult-comp-cor/fsaverage/rh/cortex has (around ~50) w/ LGI, but normal
when looking at GM thickness. Is this expected?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
cd
z-8vKc-W35SxGCTR7slBrlWoSLntQcxVoI5N_W36lxBKe00LuMnuLFccVkMttfaKkDki2gEKr8rEZfBAP4oLIvzypnlk5I1Xvxx0pH9IvNr3Jhcz2dIr3phyRLDzKH1xF2zITaP2GCEjdSzIMvOq7JGNJG1jnPXQseKuq2b3dOWmyQa-nctRxcywiYYaHXfKoduT5XAwSGGo-wLjxNlMJmdBY1XoH2zdiyw/https%3A%2F%2Faka.ms%2Fo0ukef>
____
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Sent: Monday,
, there are hybrid ways to
analyze the data (but you can't use an FSGD at that point)
On 2/6/2022 10:41 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are
classes
matter measurements
for labels/annotations
You'll have to create an annotation first (maybe with mris_label2annot), then
use mri_surf2volseg to create the segmentation. Look at the command line to
create wmparc.mgz
On 2/4/2022 10:03 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Ex
External Email - Use Caution
Hi, I was hoping to extract mean LGI, similar to how there is a mean thickness.
But the default LGI output includes the eTIV rather. What would the command be
to collect the stats into a csv for this mean LGI?
Get Outlook for
External Email - Use Caution
Hi all,
I am doing an analysis and generating the FSGD. I understand sex and race are
classes in this context, but something I was also hoping to regress out is the
effects of scanner/sequences. We have a large participant size, so we have
around
:10 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
Hi,
is it possible to extract white matter volume estimations for
labels/annotations? I am specifically wondering about the brodmann atlas and
the stanford atlas that is already included in lat
External Email - Use Caution
Hi,
is it possible to extract white matter volume estimations for
labels/annotations? I am specifically wondering about the brodmann atlas and
the stanford atlas that is already included in latest FS.
Thanks,
Victor Zeng
Beth Israel Deaconess
is already conformed, so --conformed is not usually needed. It would be
interesting to know if this is making it fail.
On 12/6/2021 5:40 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
I receive this error when I try to run mri_sclimbic_seg in dev 2021 12 0
External Email - Use Caution
I receive this error when I try to run mri_sclimbic_seg in dev 2021 12 06
How can I fix this?
mri_sclimbic_seg --s 10105_S1200QUM/ --conform
/usr/local/freesurfer/dev7/python/scripts/mri_sclimbic_seg --s 10105_S1200QUM/
--conform
Excluding seg [853]
External Email - Use Caution
?Hi all,
I was wondering if any of you guys have had experience wanting to segment the
claustrum in 3T scans. It is a label that is found in Freesurfer, but isn't
reported in the stats. Is that something that Freesurfer hopes to develop. Or
is
: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Sent: Monday, June 28, 2021 9:28 AM
To: Freesurfer support list
Subject: [Freesurfer] The differences in stats between BA_exvivo and
BA_exvivo.thresh
Hi all,
I am wondering to see what
Hi all,
I am wondering to see what the .thresh files mean. I'm assuming its some sort
of thresholded value, but there isn't a lot of details in the BA page:
?Hi,
Sometimes I see empty space inside the CA1 in the FS7 hippo parcellations.
These are voxels of bright intensities. Is this where the alveus is supposed to
be labelled and are these brain scans that we should still be using for hippo?
Victor Zeng
Beth Israel Deaconess Medical Center
Hi all,
I am trying to extract LGI measures as prescribed in
?Hi,
I am visually quality checking the hippocampal and the thalamic subnuclei
parcellations that Iglesias designed. I see that the hippocampal tail and the
PuM (pulvinar) overlay with each other. What should I make of that? Is that a
brain worth removing from analysis?
Victor Zeng
Beth
Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I try to run -localGI. Is there a package I might
be missing? Or am I using an outdated version of Matlab?
=
mris_smooth -nw -n 30
thinks so because its in SUBJECTS_DIR).
What should I do to fix this?
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Sent: Sunday, December
Hi FS developers,
I am following the instructions based on:
@nmr.mgh.harvard.edu
Cc: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Subject: [External] [Freesurfer] question about
mri_segment_hypothalamic_subunits
Hello Victor,
If you used the 7.1.1 installer package,
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-darwin-macOS-7.1.1.pkg<ht
?Hi all,
I installed the most recent dev version of FS7.1, and copied its files over the
old FS7.1. I entered sudo mri_segment_hypothalamic_subunits into xquartz, and
receive an error:
error: freesurfer has not properly been sourced
I am using mac os Catalina 10.15.6. How can I fix this?
er2 deprecated for FS7.1?
{Disarmed}
Sorry, don't use --mgz ( just changed the wiki)
On 9/2/2020 11:27 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
I inputted
tkregisterfv --mgz --s tal_before --fstal --surf orig
?like it is written in the website, and it says that the --mgz option is not
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] [External] Re: tkregister2 deprecated for FS7.1?
{Disarmed}
Sorry, don't use --mgz ( just changed the wiki)
On 9/2/2020 11:27 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
I inputted
tkregisterfv --mgz --s tal_before --fstal --surf orig
?like
XTQ=ziAm16qmlGqGtX5PhV9Harh0DYcHWCNZ9xWh5fPQIi0=lHKgFsyj0gxwS5cKG88JTcA2JG2p6UeXYSx0nK8z4eQ=p-8LrCgdLX69uq6RWPrfbnWDqjSkWtp_yaR96K7EO3Y=>
On 8/31/20 3:42 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi FS devs,
I am following
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview
Hi FS devs,
I am following
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? as a
tutorial to fix the bad talaiarch file I have. I know that tkmedit is
deprecated, but I was wondering if tkregister2 is too. If so, I was wondering
what software I would use (or commands,
Hi all,
I am using a freesurfer 6 dev version of tkmedit and opening one of my brain
scans that was processed through 7.1 (I copy the ?h.pial.T1 -> ?h.pial to
accept the -surfs command). I get the note mrisurf.c:4077 trial: 0
nextPendingSIze:2 BEVIN IS LOOKING FOR AN EXAMPLE THAT DOES THIS
You may be interested in https://www.oxcns.org/aal3.html? AAL3, which has the
estimations of the thalamus nucleis from fs6
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of ???
Sent:
y94=>
From: on behalf of "Zeng, Victor
(BIDMC - Keshavan - Psychiatry)"
Reply-To: Freesurfer support list
Date: Thursday, June 25, 2020 at 17:56
To: Freesurfer support list
Cc: "joliehoan...@gmail.com"
Subject: [Freesurfer] Subfield parcellation in 1.5 T and 2
?
Hi FS developers,
We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would
be sufficient for a subfield analysis (amygdala, hippocampus, thalamus).
Thanks,
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
This
Hi FS developers,
I have a dataset that I am working on that has a mix of build stamps, including
centos v6.0.0-2beb96c, centos dev-20190118, and dev-20180220 (a mess that was a
little bit out of my control). I understand that these are all variations of
FS6, and was wondering if its
?Hi,
Can someone from the martinos center who has access to
/n/app/martinos/freesurfer in the Harvard O2 cluster upload freesurfer 7.1?
Right now it just has freesufer 6.0.
Thanks in advance,
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
Sorry - made a typo, I meant the aparc.presurfs rather than the aparc.auto.mgz
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Sent: Saturday, May 2, 2020 2:58 AM
To: Freesurfer support
--
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Sent: Sunday, April 26, 2020 7:28 PM
To: Freesurfer support list
Subject: Re: [External] Re: [Freesurfer] Intensity inhomogeneity messing with
the wm.mgz
Hi,
Thanks for the clarification. From my understanding
To: Freesurfer support list
Subject: Re: [Freesurfer] [External] Re: Quick question on tkregister {Disarmed}
Hi Victor, what are the contents of /usr/local/freesurfer/build-stamp.txt? Are
you using a dev version?
Andrew
From: on behalf of "Zeng, Victor
(BIDMC - Keshavan - Psychiatry)&qu
N. Greve
Sent: Tuesday, April 28, 2020 6:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] Quick question on tkregister
What OS are you using? tkregister2 as a GUI is not available on Mac. This is an
oversight on our part...
On 4/28/2020 2:50 PM, Zeng, Victor (BIDMC
?Hi all,
I'm a little confused about what the most latest GUI software to fix the
talairach is at the moment. This page refers to:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? but
the software, tkregister2 seems to be unavailable. Has it been deprecated by
in the brain your wm.mgz edits are
unliekly to fix things
cheers
Bruce
On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan -
Psychiatry)
wrote:
>
>
> Hi Freesurfer developers,
>
>
> I have a subsample of a FS dataset that have scanner-originated
> hyperintensities in the bila
Hi Freesurfer developers,
I have a subsample of a FS dataset that have scanner-originated
hyperintensities in the bilateral supramarginal/temporal lobes. I've manually
removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable
to recognize these edits when looking at the
Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
From: Zeng,Victor (BIDMC - Keshavan - Psychiatry)
Sent: Sunday, March 15, 2020 2:35 PM
To: Freesurfer support list
Subject: Re: [External] Re: [Freesurfer] HP and thalamic subfield quality
Hi all,
I am still trying to adapt to working from home, and I am forced to work with
incredibly slow download speeds. I am trying to download FS6.0 for mac for the
sole purpose of using tkmedit, rather than the entire toolbox, just so I can
edit brains (I anticipate downloading FS6.0 for mac
Ii0=2NtYE10aXwkKwoDvvBLfuQ2bz3TpD2g_eJjUVeelxCM=6zObkYj4gcWTdm7w8-Lh69QIzEe4DuWO2QjyS_cOtwI=>
From: on behalf of "Zeng, Victor
(BIDMC - Keshavan - Psychiatry)"
Reply-To: Freesurfer support list
Date: Sunday, March 15, 2020 at 14:24
To: "freesurfer@nmr.mgh.harvard.edu"
Hi all,
>From my understanding from the log files, the subfield segmentations (and in
>general the aparc.mgz) relies on the norm.mgz (which is based off the
>brainmask.mgz). What if hypothetically, you have a not so good segmentation of
>the cerebral cortex, but willing to individually qc the
the orig.mgz instead
On 2/25/20 8:44 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
>
> Hi Freesurfer team,
>
>
> I've run samseg for one participant, using the /mri/T1.mgz as the
> input, but the output seg.mgz is awful, w/ the ventricles being
> overestimated an
Hi Freesurfer team,
I've run samseg for one participant, using the /mri/T1.mgz as the input, but
the output seg.mgz is awful, w/ the ventricles being overestimated and the
outer perimeter of the gray matter considered as the "Head-ExtraCerebral." I
know in mind you all just want to know if it
68 matches
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