have you tried asking the ANTS people?
On 4/6/2022 10:05 AM, Nathan Kindred (PGR) wrote:
External Email - Use Caution
Hi,
I have been using DenoiseImage from ANTs during pre-processing
(DenoiseImage -i T1.nii -o denoised.nii.gz -v), however for some scans
I am having an issue where
The rawavg.mgz should be the same dimension as your T1 MPRAGE. Why are
they not? Look at the dims for the volume subject/mri/orig/001.mgz
On 4/4/2022 2:25 AM, Aleksandra Szum-Jakubowska wrote:
External Email - Use Caution
Dear Freesurfer Experts,
I conduct the segmentations'
" "S0738")
recon-all -autorecon1 -subjid "$i"_FS
end
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Monday, April 4, 2022 at 10:56
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] Tkregister2 not opening
om: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Date: *Sunday, March 27, 2022 at 16:59
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] Tkregister2 not opening GUI
*CAUTION:* This email originated from outside of Georgian College. Do
not click links or open at
You can give mkanalysis-sess the slice order with -stc as you would with
an ordinary non-accellerated scan. Then give it the number of slice
groups with -ngroups nSliceGroups
I don't quite remember what nSliceGroups means, but I think it means the
number of simultaneously acquired slices.
On
I would probably just use the 1st option.
On 3/30/2022 5:20 AM, Falko Mecklenbrauck wrote:
External Email - Use Caution
Dear FreeSurfer-Experts,
I’m in need of your experience to help me with a decision in my
current project:
I want to use certain areas, that were identified by
Have you visually verified that the registration is correct (only work
with LTAs) using tkregisterfv ?
How are you viewing the combined anatomical/functional in pics? If you
just load the functional without a registration file, then that is not
right.
On 3/29/2022 11:28 AM, Manenti, Giorgio
?
It is just the thickness values at each point. They xyz is implicitly
associated with the point.
I appreciate your time and help as always.
Ela
_
From: Douglas N. Greve
? How can I
calculate the difference between the two time points?
Thank you very much.
Best regards,
Agurne
El dom, 27 mar 2022 a las 23:07, Douglas N. Greve
() escribió:
Probably the easiest thing to do since you have only two time
points is to compute the difference between
Can you send the fsgd file?
On 4/1/2022 3:28 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm extracting beta values from some analyzes and I would like to
know if I'm extracting and interpreting these values correctly.
To extract
Have you looked in the destrieux atlas? It is the a2009s annot.
On 4/1/2022 10:28 AM, Patricia Schwery wrote:
External Email - Use Caution
Hi there,
I would like to know if someone could tell me how i can measure the
medial prefrontal cortex (mPFC) with freesurfer as i see it is
Note also that you can use tkmeditfv to run freeview with tkmedit-like
options (and more).
On 3/30/2022 8:00 PM, Wang, Ruopeng wrote:
Hi Victor,
On Mar 30, 2022, at 4:30 PM, Zeng, Victor (BIDMC - Keshavan -
Psychiatry) wrote:
External Email - Use Caution
Hi,
My lab has been
in the correction of multiple comparisons.
Many thanks!
--
On 3/09/2022 15:20 PM, Douglas N. Greve wrote:
Can you just ask the question again so I don't have to sort it out myself
This is actually a bug in version 7.[012]. This area is probably not
valid anyway. We'll have a fix in 7.3
On 3/21/2022 7:31 PM, Gabor Perlaki wrote:
External Email - Use Caution
Dear all,
fswiki suggests that " There are regions where the surfaces are not
intended to be accurate
On 3/24/2022 4:49 PM, Muhammed Görünen wrote:
External Email - Use Caution
Hi,
I run recon-all process for a subject's T1 data. At the end, the pial
files are 0Kb and I cannot open them from python.
Did it end with an error? Did you run out of space? What version of FS?
Can you
tstat_fwep.mgz"
This is with Freesurfer dev 20211206. Thanks and sorry for so many
questions lately
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
On 3/24/2022 2:53 AM, Dongyue Zhou wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I want to calculate mean pial surface area in DKatlas in individual
space.And I know the function read_annotation.m in $FREESURFER_HOME/matlab for
loading this atlas.
And if I
I'm not sure I understand what you are saying or what the problem is.
Can you provide the actual command line you are using, all the terminal
output, and a picture that shows what the problem is?
On 3/23/2022 2:46 PM, Manenti, Giorgio wrote:
> External Email - Use Caution
>
> Dear
You're command line is incomplete (it needs more than just --s). Run it
with --help and/or visit the wiki page
On 3/23/2022 2:40 PM, Alice Tao wrote:
External Email - Use Caution
Thank you so much for the response! Unfortunately, that is the full
command line and output:
$
Probably the easiest thing to do since you have only two time points is
to compute the difference between the two, then just do a simple group
analysis where you include the covariates that you want.
On 3/23/2022 10:00 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Sorry, we are not supporting qdec anymore. You will need to use the
command-line stream
On 3/23/2022 8:02 AM, David wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I have a problem. Can you help me
freesurfer version : 6.0.0
Load qdec when I run qdec.table.dat,
Check the talairach registration (talairch.xfm). It must be badly messed up
On 3/23/2022 4:47 AM, lqcheng2017 wrote:
External Email - Use Caution
Dear experts,
I extracted the eTIV using the mri_segstats, but it showed negative
value. How could I solve this problem?
Thank you very
please send the command line, log file, version of FS, etc
On 3/22/2022 11:59 AM, Zoe O'Brien-Moran wrote:
External Email - Use Caution
Dear FS Experts
I am having continued issues with the mri_normalize function on MPRAGE
data
I get an error message:
3d normalization pass 1 of 2
uot;S0524" "S0525" "S0528" "S0537" "S0544"
"S0557" "S0589" "S0601" "S0650" "S0669" "S0676" "S0682" "S0715"
"S0727" "S0738" "S0741" "S0747"
What version of FS are you running?
On 3/20/2022 8:47 PM, Billah, Tashrif wrote:
It does not exist and cannot be created in a shared cluster. Is there
a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?
===
Douglas N. Greve Wed, 09 Mar 2022 10:04
On 3/17/2022 4:41 PM, std...@virgilio.it wrote:
External Email - Use Caution
Hi list,
a) I have two maps, one's of rs-fMRI functional connectivity (by
FS-FAST) and one's of receptor density (from a PET-Atlas). Both the
maps are in surface space. How can I measure the vertexwise
Are you trying to create a volume-based binary mask or a surface-based
mask? From the commands below, it looks like surface (but why would you
need it to be in nii?). In the surface case, you can just
mri_binarize --i ocn.mgh --match clusterno --o clusterno.mask.nii
where "ocn" is the ocn file
Can you try tkregisterfv ? The old tk tools are not supported any more.
tkregisterfv uses freeview
On 3/17/2022 6:03 AM, Nathan Kindred (PGR) wrote:
External Email - Use Caution
Hi Isabelle,
It’s been a couple of years since I ran FreeSurfer on a Mac, but I
also have had this issue
If you have an LTA file, you can run
mris_apply_reg --lta lh.white your.lta lh.white.newcoords
On 3/16/2022 4:15 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Dear Freesurfer experts,
Is there a way to move lh.white of a subject to a new coordinate?
Something quite
spot. The log is attached.
Jim
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *Douglas N. Greve
*Sent:* Wednesday, March 09, 2022 12:24 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] recon-all errors after mri_pretess
** External Email - Caution **
Does this
Yes, just specify --regheader subjectname instead of a --reg
On 3/11/2022 9:34 AM, Jacoby, John wrote:
Hi all,
Usually when I want to map volume data to the fsaverage surface, I use
mri_vol2surf with a registration that transforms the volume into the
space of the subject's orig.mgz and with
Yes, oftentimes. You should not smooth the LGI. Also, I would strongly
suggest that you use permutation instead of mcz sim. For perm, the fwhm
won't matter.
On 3/10/2022 3:26 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
I receive FWHM values
What happens if you run
freeview -f
/home/francesca/freesurfer/subjects/sub01_mprage/surf/lh.inflated
On 3/10/2022 7:32 AM, Francesca Strappini wrote:
External Email - Use Caution
Dear Freesurfer experts,
I'm trying to load the flat surface that I created with this command line:
On 3/9/2022 2:15 PM, Jingyi Wang wrote:
External Email - Use Caution
Hello Freesurfer experts,
I ran the recon-all command and got all the .label files for the
segmentations of the cortical areas. However, I have some questions
about the label for primary motor and auditory
Yea, not so easy. You need to see how far it got and then use the
appropriate flags. The most time consuming step is the volume labeling.
See if aseg.presurf.mgz exists. If it does, then you can skip that with
-autorecon2-noaseg -autorecon3. If subject/mri/transforms.m3z and
norm.mgz exist but
t treated
like integers
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, February 13, 2022 12:24 PM
*To:* f
In FreeView
Click on the brain with scissors icon ("Cut"), select your points, then
"Cut Closed Line",
make sure the cusror is in the patch, then hit "Fill Uncut Area",
then save as a patch
On 3/7/2022 12:03 PM, Francesca Strappini wrote:
External Email - Use Caution
Dear
Does this fail every time like this? It looks like it just abruptly
stopped. Does anything print out to standard error?
On 3/4/2022 11:18 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
Hi, we’re running FS 7.2 ‘recon-all -all’ on a subject and are getting
errors on
never heard of FLAWS. My good search says that it is WM and CSF
suppression, so it probably won't work.
On 3/4/2022 6:10 AM, Mathilde Pichon wrote:
External Email - Use Caution
Hello,
I know T1 MPRAGE is the prefered format to perform a recon-all
segmentation.
But some of my
What version are you trying to run? selxavg-sess has been depricated for
years. Try selxavg3-sess
On 3/3/2022 10:59 AM, CALLACHAND Muntasir wrote:
External Email - Use Caution
Hi,
I have a problem when i try to run the function selxavg-sess
It means that you have two frames in the 001.mgz file. Sometimes this
happens with multiecho mprages. If this is the case, you can convert
your input to a single frame with
mri_concat --rms file.mgz --o file.rms.mgz
Then use file.rms.mgz as the input to recon-all
On 3/3/2022 12:04 AM, HYE
You pretty much have to run it through to the end. You can try using
mri_coreg (this is the first step of bbregister). It does not need
anything but two images and will run in a few min.
On 3/3/2022 5:24 AM, Guillem París wrote:
> External Email - Use Caution
>
> Hello,
>
> I'm
.
--
On 2/21/2022 15:20 PM, Douglas N. Greve wrote:
Yes, it is. It is confusing when you talk about area and volume
sincethese are not point measures like thickness (ie, what is the
volume orarea of a vertex?). The area of a vertex is computed
Do you have permission to /scratch? Does it exist?
On 3/2/2022 9:50 AM, Billah, Tashrif wrote:
Hi all,
We are trying to run recon-all with -localGI but running into an
unknown permission denied error:
$ recon-all -s sub-1001 -localGI
```
ive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing>
Thank you in advance,
Hyunwoo Jeong.
2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve
님이 작성:
Can you upload the data to me somewhere? I'd need the input volume
and the fsgd and any contrasts
On 2/21/2022 10:
have any other suggestions? I appreciate your help so far.
Best,
Hyunwoo Jeong
2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
님이 작성:
It looks like it is failing when computing the partial
correlation coef. Try running it with --no-pcc
On 2/16/2022 10:53 AM, 정현우
This is a bit tricky as you need a volume as a template that has the
dimensions/resolution you want. One fast and dirty way to do it is to
upsample the orig to 0.5mm, eg
mri_convert --upsample 2 orig.mgz orig.us2.mgz
You can then run
mri_vol2vol --mov T2.nii.gz --lta reg.lta --targ orig.us2.mgz
You can't tell from the image whether the wm in cerebellum or dura is
attached. you need to look at the wm.mgz volume to see. You can load the
?h.orig.nofix as well. In the terminal output of recon-all/topofix, it
should give a vertex number of the topodefect. Go to that vertex n the
nofix
From: * on behalf of "Douglas
N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Friday, February 25, 2022 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
Are you doing an ROI analysis or a voxel-
I'm not sure what question you are asking
On 2/25/2022 1:17 PM, Knut J Bjuland wrote:
External Email - Use Caution
DearFreesurferexperts,
IgetthiserrorwhenIamrunning FreeSurfer.
Checkingfor(invalid)multi-frameinputs...
ERROR:input(s)cannothavemultipleframes!
half of "Douglas
N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Tuesday, February 22, 2022 at 3:00 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
I don't understand. What mask?
On 2/22/2022 8:55 A
ed. For my work, I am
> looking at ventricular volume and so it would be good to not have to manually
> correct a large number of my scans.
>
> From: Douglas N. Greve
> Sent: Tuesday, January 4, 2022 1:19 PM
> To: freesurfer@nmr.mgh.harvard.edu
>
r descriptions.
Thanks,
Alex
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Tuesday, February 22, 2022 5:20:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy
VOI to Freesufer-proc
of Douglas N. Greve
*Sent:* Monday, February 21, 2022 6:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while
regressing out cortical thickness
I just updated the code to accept PVRs. I'm not sure what I have to do
to test it; I guess I need to run
I see it in the help:
-b
tabular output
On 2/24/2022 12:23 PM, Jacoby, John wrote:
Hi Doug, thanks for the pointer. That was exactly what I was looking for.
When I copied the command from recon-all.log, it used a -b flag. I
can't find documentation for this flag
You can also look in pctsurfcon. This compute the percent gray/white
contrast. It does so on the T1w, but you could look inside the script to
see how it does it and adapt to your situation.
On 2/23/2022 3:26 PM, Adam Martersteck wrote:
External Email - Use Caution
Hi Dylan,
Give
Drive
Columbia, MO 65211
Contact: 573-884-8779
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, February 21, 2022 9:21 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re
You don't need to go that far. You can run mris_annotoical_stats. Look
in recon-all.log to find the command line used to create the
?h.aparc.annot and just change the annot and output file
On 2/22/2022 10:02 AM, Jacoby, John wrote:
Hi all,
We were sent a FreeSurfer annotation file that
mgz/7T_MEMPRAGE.mgz --init-reg
> 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 --s 126346
> ...
> Loading mov
> error:
> mghRead(/home/mtisdall/Research/7TAnalysis/subjects/subject-unknown/mri/orig.mgz,
> -1): could not open file
>
>
> Any oth
emv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harva
this?
We can try using the samseg stream as Bruce has kindly suggested, but
we hoped to find a way to make our standard fs pipeline work with v7.
Many thanks!!!
Edan @ PrincetonBrainDevLab
On Mon, Feb 21, 2022 at 5:04 PM Douglas N. Greve
wrote:
If this is not something you have to do a lot
Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:*
F to be twice that of M (or half). This usually does not make
sense.
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent
half of "Douglas
N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Monday, February 21, 2022 at 2:02 PM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
You need to first map your pet to the anatomical
\
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save
Best,
Asim
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Dougla
I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF)
for an SVS VOI. How can I register the svs file to the
Freesurfer-processed brain and
On 2/19/2022 6:10 PM, fernanda rohrsetzer wrote:
External Email - Use Caution
Hi guys,
I'm a beginner in Freesurfer and I want to perform an analysis of the
difference between 3 groups in cortical thickness,volume and area
having age, mean thickness and etiv as covariate.
my design
Yes, it is. It is confusing when you talk about area and volume since
these are not point measures like thickness (ie, what is the volume or
area of a vertex?). The area of a vertex is computed as the mean of the
adjacent triangles of the vertex. The volume is the mean of the
neighboring
you are right! Just fixed it.
thanks
On 2/18/2022 2:15 PM, Gomez, Daniel wrote:
> There is a minor bug/typo in mri_surf2vol that was leading to registration
> issues if the "--fillribbon" flag is used, like in my case.
>
>
You can use something like
mris_apply_reg --lta lh.white reg.lta lh.white.reg
The direction of reg.lta does not matter -- it will figure out the right
direction based on the geometry info
On 2/16/2022 12:20 PM, Gomez, Daniel wrote:
> Dear FS users,
>
> I’m trying to get surface indices from
Did the perms to that file change during the run?
On 2/17/2022 10:36 AM, Jacoby, John wrote:
Hi all,
I have a recon that looks like it ran (almost) to completion, but then
threw a permissions error in the stdout and directed me to the log. I
can't determine what the issue might have been.
!
Edan @ Princeton BrainDevLab
On Thu, Feb 17, 2022 at 6:07 PM Douglas N. Greve
wrote:
The edits you are making only change the initial surface;
the surface placement then refines the placement.
Sometimes the surface placement can
#150 Santa Monica, CA 90404
*Phone:* 310-525-0865 | *Fax: *310-315-4069
*From: * on behalf of "Douglas
N. Greve"
*Reply-To: *Freesurfer support list
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
*Subject: *Re: [Freesurfer] PetSurfer:
Is there a blank subject line in the lta file? If so, it is probably
trying to get the subject from there. You can try putting the --s after
the --lta
On 2/21/2022 3:43 PM, Tisdall, Dylan wrote:
> External Email - Use Caution
>
> Hi all,
>
> Quick question on a puzzling error with
:* Douglas N. Greve
*Enviado:* quinta-feira, 17 de fevereiro de 2022 20:25
*Para:* Laura Willers de Souza
*Assunto:* Re: [Freesurfer] Question glm analysis g4v0
No, that was only for interactions between the covariates and the groups
On 2/17/2022 10:05 AM, Laura Willers de Souza wrote
Did you specify a hemi? If you run it with --help it will give you docs.
You can also find them on line. You should also send the command line
On 2/17/2022 9:23 AM, Koustav Chatterjee wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I need your help.
I am trying to run
Sorry, the surfaces are 3D structures, it's not going to work on a 2d slice
On 2/17/2022 8:47 AM, 陆玉恒 wrote:
External Email - Use Caution
Dear,
I tried to reconstruct the white and pial surface from a sinlge brain
slice (not MRI, it's a histology slice that converted to a nifti
fsaverage should not be empty. Maybe it is a link to an empty folder? It
should point to $FREESURFER/subjects/fsaverage. You should not mix the
streams in this way (insert Ghost Busters joke here)
On 2/16/2022 4:33 PM, Willett, Andrew Sunday wrote:
Dr. Greve,
I don't believe that file
On 2/16/2022 3:35 PM, Martin Kavec wrote:
External Email - Use Caution
Hi all,
previous question from Florent triggered my interest in SAMSEG and I
am running now couple of cases to see what it gives. I would like to ask
* SAMSEG can also output a mesh. How is the mesh stored
with this!
*Bryna Goeckner* (she/her)
Graduate Student
Medical College of Wisconsin
Neuroscience Doctoral Program
*From: *Douglas N. Greve
*Date: *Monday, February 14, 2022 at 10:27 AM
*To: *Goeckner, Bryna , Freesurfer support list
*Subject: *Re: FW: [Freesurfer] Problems with recon
The edits you are making only change the initial surface; the surface
placement then refines the placement. Sometimes the surface placement
can be quite stubborn. If this is the case, the ?h.orig.nofix and
?h.orig will reflect your edits (nofix exactly; ?h.orig to some extent).
Also check the
.
In the 'three_group_comparison.area' folder, the following files were
created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.
Do you have any idea what could have been the problem?
Thanks,
Hyunwoo Jeong
2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
님이 작성:
Did it create the output
On 2/16/2022 4:12 AM, k3...@free.fr wrote:
> External Email - Use Caution
>
> Hi FreeSurfer community,
>
> I recently discovered the SAMSEG application in the FreeSurfer 7.2.0 release
> and started to give a try on few subjects were FreeSurfer was having a hard
> time to segment brain
Does that file exist?
ps. Please remember to post to the list. Thanks!
On 2/15/2022 5:06 PM, Willett, Andrew Sunday wrote:
Dr. Greve,
I hope this email finds you well. Thank you for your response to my
listed question on Freesurfer’s mailing list on Sunday! I wanted to
reach out to followup
he
Xg.dat file below.
Hyunwoo Jeong
2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:
can you send your fsgd file and the Xg.dat file?
On 2/14/2022 1:21 AM, 정현우 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compare cortical su
I just sent info on how to do this, but see step 5 in the wiki
On 2/14/2022 6:27 PM, Jennifer Bramen wrote:
External Email - Use Caution
Dear Freesurfer Developers
I am doing an ROI--based amyloid PET scan analysis. I am following the
steps from the PetSurfer wiki. I see
If you want to do an ROI analysis using FS-based ROIs, you should do
that at the individual level. Resample the PET to the anatoimical space,
then run mri_segstats passing the PET with --i and using --seg to spec
the segmentation. If you really want to do it in MNI305 space, then it
is the
.ms%2Fo0ukef>
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Sunday, February 13, 2022 10:42:41 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [External] Re: [Freesurfer] [Ex
), can I run the same?
On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve,
wrote:
You can run a group analysis
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Gro
I would not expect the different subjects to be the same (they are
different subjects). I don't know how you'd get them back to native
space. The opposite of how you normalized them I guess.
On 2/12/2022 8:15 AM, Aleksandra Lecei wrote:
External Email - Use Caution
Hi,
I'm new to
s there another preferred way to do this)?
>
> Thanks again for your help with this!
>
> Bryna Goeckner (she/her)
> Graduate Student
> Medical College of Wisconsin
> Neuroscience Doctoral Program
>
> -Original Message-
> From: Douglas N. Greve
> Sent: Sunday, Febr
can you send your fsgd file and the Xg.dat file?
On 2/14/2022 1:21 AM, 정현우 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compare cortical surface area among three groups
while controlling for estimated total intracranial volume (eTIV), as
You can run a group analysis
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
One of the outputs will be the correlation (along with the sig of the
correlation)
On 2/13/2022 6:35 PM, Koustav Chatterjee wrote:
External Email - Use Caution
Dear FreeSurfer experts,
You will definitely get systematic differences between using T2 and not,
so you could have a false positive (or negative) if you are comparing
those two groups. On the other hand, you probably changed the T1
protocol a lot between now and 10 years ago, so you are likely to have
bias either
I'm pretty sure you will have some systematic differences between them,
though they might be small. So off the top of my head, I'd recommend
against it.
On 2/10/2022 12:56 PM, Anik Dar wrote:
External Email - Use Caution
Hi All,
I have some datasets processed with freesurfer 6 and
you did not point out the lines that worry you. At the end, it says
"finished without error", which means that you should not visually check
your results.
On 2/9/2022 6:28 PM, HYE JUNG YOUN wrote:
External Email - Use Caution
Good day,
I hope this email finds you well.
I’d love
Sorry, I don't understand the R terminology. in the FSGD, you will have
(4+1)*3 = 15 columns to the design matrix (4=2x2=number of classes, 3 =
no of continuous variables). Each column will mean something. How many
columns will you have in your R analysis and what will they mean? If you
can
On 2/9/2022 5:18 AM, Lin Qiu wrote:
External Email - Use Caution
Dear Freesurfer experts,
My analysis is in FSL. But I wish to use the more detailed
segmentaHA_T1.shavailable in Freesurfer.
I wish to avoid the time & resource to ‘recon-all’ all my
participants’ T1 images, and
can you send a log file?
On 2/9/2022 5:11 AM, REEM ABU BAKR BAHATHIQ wrote:
External Email - Use Caution
Hi all,
I use a supercomputer to process my data
When I run "recon-all –qcache", and after two days of processing there are a lot of
Error messages saying "rm:
No match."
, Bryna wrote:
>> External Email - Use Caution
>>
>> We are using FS 7.2
>>
>> Bryna Goeckner (she/her)
>> Graduate Student
>> Medical College of Wisconsin
>> Neuroscience Doctoral Program
>>
>> Date: Wed, 26 Jan 2022 16:4
801 - 900 of 8964 matches
Mail list logo
