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 t
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 either
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 thi
ancke 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
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 denote
ster --mov 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
Sorry, your previous emails were cut off so I'm not sure what command
you are referring to.
On 2/22/2022 9:15 AM, Laura Willers de Souza wrote:
External Email - Use Caution
Thanks so much for the explanation!
There is something different in the analysis of volume and surface
area in
biM_eemv-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.
o overcome 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
NS Core 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
cting 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
behalf 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 spa
sgm.lh/eres.mgh \
--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 b
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 e
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 trunca
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.
>
> https://github.com/freesurfer/freesurfer/blob/dev/mri_surf2vol/mri_surf2v
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 surf
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. I'v
there any way we can overcome this stubbornness?
Many thanks!
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 ref
St. #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] PetSur
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 bbreg
-
*De:* 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
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 m
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 file)
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 exists-
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 in
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 reco
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
surface, and
Xg.dat.
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:
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 cortic
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 instructions
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 same
.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 th
ach (or is 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: Sund
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
describ
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,
I
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 way.
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 o
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 you
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 mak
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 onl
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." (althou
, Goeckner, 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
Re: long run time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of
the raw thickness map (lh.thickness.fwhm10.mgh)
On 2/8/2022 4:12 PM, Dhungana, Asim wrote:
Dear Freesurfer experts,
I am trying to run a GLM analysis comparing
How about this?
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
On 2/8/2022 2:02 PM, REEM ABU BAKR BAHATHIQ wrote:
External Email - Use Caution
Hi everyone,
Now that I have done the recon all preprocessing on my structural MRI
data, I want to extract the volume and
I'm not sure what the error is as I cannot find an actual error below.
If the error is in the base creation, then send the log file for that.
On 2/8/2022 10:47 AM, Willett, Andrew Sunday wrote:
This is my first time seeking support here so I apologize if I am not
familiar with the community's
On 2/7/2022 5:29 PM, Salar Dini, Elaheh wrote:
External Email - Use Caution
Thank you so much. This actually worked well. Just two simple
follow-up questions:
1. Do I assume right that this solution doesn't work on aparc+aseg?
Correct, that will not work
1.
2. If I want to
It is probably not going to work very well if you have some classes that
only have one member. You can eliminate members of classes that only
have a few members. If you really need to have those cases, there are
hybrid ways to analyze the data (but you can't use an FSGD at that point)
On 2/6/2
surfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Friday, February 4, 2022 7:10:17 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [External] Re: [Freesurfer] white matter measurements for
labels/annotations
Do you mean something like wmparc.mgz and wmparc.stats?
On 2/1/2
Hard to say. This is one reason we are not supporting qdec anymore. Was
there anything printed to the terminal?
On 2/3/2022 8:27 AM, Mateus Aranha wrote:
External Email - Use Caution
Dear all,
I'm constantly getting the following error and I have no idea where
the problem is...
im
You can try registering them together like
mri_coreg ---mov betmaskvolume.nii.gz --targ orig.mgz --reg reg.lta
Then
mri_vol2vol --mov betmaskvol.nii.gz --targ orig.mgz --reg.lta --o
betmask-in-fs.mgz --interp nearest
The betmaskvol should be the intensity image (like orig.mgz) and not a
binary m
What do you mean by the interaction contrast? Or do you mean the
intercept? It is not surprising that the intercept is completely yellow
as that is just testing whether the mean thickness is different than 0,
which it always will be.
On 2/2/2022 2:47 PM, Laura Willers de Souza wrote:
Yes, once you take the difference between two time points, then the
steps are the same as cross-sectional analysis. But if you took the
difference, you should have only one entry in the FSGD file for each
subject (looks like you have 2). Also, it is probably a good idea to
normalize the ages (o
.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
> ____
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> im Auftrag von Douglas N. Greve
>
> Gesendet: Mittwoch, 26. Januar 2022 23:02:04
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesur
Do you mean something like wmparc.mgz and wmparc.stats?
On 2/1/2022 1:10 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 br
Can you send all the terminal output? Also, you only have 4 time points
in time.dat. Is this accurate? It's going to be hard to do KM with 4
time points.
On 1/31/2022 5:00 PM, Jennifer Bramen wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to analyze
It will impact it some as it changes the talairach reg. See
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
On 1/31/2022 2:59 PM, Ritobrato Datta wrote:
External Email - Use Caution
Hi All,
I have inherited some T1 data that are defaced.
If I run the defaced images through fr
You can mask it out. First, create a mask of your cluster with something
like
mri_binarize --i ocn.mgh --match clusterno --o mask.clusterno.mgh
Then
mri_mask pcc.mgh mask.clusterno.mgh pcc.masked.mgh
On 1/31/2022 9:26 AM, Andrei Bieger wrote:
External Email - Use Caution
Hi, Douglas,
bbregister will compute the matrix, you don't have to give it a matrix.
You can use mri_vol2vol to apply the matrix. There is also an option to
apply the matrix in bbregister
On 1/31/2022 7:24 AM, m-maiw...@web.de wrote:
External Email - Use Caution
Hi,
I ran recon-all on a MPRAGE-fi
Can you send the recon-all.log file?
On 1/31/2022 5:02 AM, Dr. Cornelius Kronlage wrote:
> External Email - Use Caution
>
> Dear Falk,
>
> thanks for the hint! My understanding was that the "robust" MP2 actually
> reintroduces some of the field inhomogeneity artefacts that MP2RAGE is
>
Not sure what you are trying to do. extracting the vent vol to a surface
does not make sense to me
On 1/28/2022 1:23 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi,
I saw the same question has been asked and no answer was provided:
I run
"mri_cor2label --c fsaverage/mri/
See the --lta option to mris_apply_reg
On 1/28/2022 10:07 PM, Yixin Ma wrote:
External Email - Use Caution
Hi FreeSurfer developer,
I want to transform surfaces files (lh.white, lh.pial, rh.white, and
rh.pial) with a registration matrix that has 12 degrees of freedom. Is
there a fu
ed, 26 Jan 2022 16:43:44 -0500
> From: "Douglas N. Greve"
> Subject: Re: [Freesurfer] Problems with recon for manually fixed
> Talairach
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <8e0752c5-13fa-755e-c416-4253ce504...@mgh.harvard.edu>
> Content-Type:
If it works for others, then I don't know what could be going wrong.
Also, it is unclear what you mean by not being able to edit it
(permission? voxels don't change). Also note that you only need to
change the wm.mgz if the surfaces are not following the gray white
boundary. It is not used for
You need to use both to totally turn it off. There are two types of
PVEs. One is due to blurring/smoothing (fixed with --psf). The other is
due to multiple tissue types being in the same voxel (the tissue
fraction effect (TFE))
On 1/27/2022 12:40 PM, Zhener Zhang wrote:
External Ema
Sorry, the developer of this program has moved on in her career so we
have no one to support it anymore. We maybe looking at it again in the
next year or so.
On 1/25/2022 4:49 AM, Bernardoni, Fabio wrote:
> External Email - Use Caution
>
> Dear all
>
> as some other posted before me, so
what happens if you convert it to an mgz file and then use mri_info to
look at the orientation string?
On 1/11/2022 11:52 AM, Xiaojiang Yang wrote:
External Email - Use Caution
Dear Freesurfer Developers,
I have scrutinized the Freesurfer source code from github, found that this
migh
you should ask the supercomputer administrators
On 1/26/2022 12:24 PM, REEM ABU BAKR BAHATHIQ wrote:
External Email - Use Caution
Hi dear freesurfer list.
I want to run recon-all command on 400 NIFTI images using laptop
connected to my universty supercomputer
How can I do that?? Any
I'm not sure what is happening or why the tal reg is apparently failing.
My guess is that it is something non-standard about the image. The first
thing to try is to run it at 1mm (without the -hires). At some point,
you may have to send us the volume (or at least some pictures in axial,
sag, an
I think that should work.
One other issue is that the wm.seg.mgz might need to be uchar (a relic
of when computers did not have so much memory). If it does not work with
falk's command, you can try
mri_convert -odt uchar --no_scale 1 wm.seg.mgz wm.seg.mgz
On 1/24/2022 2:47 AM, falk.luesebr...@m
Not sure about #1 and #2, and #4 depends on those. For #3, the age
Variable will regress out age. The time diff variable will regress out
the effect of duration.
On 1/21/2022 8:19 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi,
I got a couple of questions regarding group analys
what version of FS are you using?
On 1/21/2022 2:21 PM, Goeckner, Bryna wrote:
External Email - Use Caution
Hi,
I am trying to decide how to proceed after manually updating a
talairach since various ways I’ve tried the recon process give me
different results.
Our group used Freesu
On 1/21/2022 7:49 AM, 刘卫 wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
Hello, I would like to ask if there are other correction methods besides
multiple comparison correction when surface based group analysis.
You can use FDR (mri_fdr)
Can I use the 6.0 versio
When you say movement "correction" here I'm assuming you mean including
regressors. I don't have anything that will compute the 24 regressors
you mention. But if you have something that will, you can create a table
that has a row for each time point and 24 columns, then pass it to
mkanalysis-se
You can run mris_preproc to get a stack of the thicknesses (one frame
for each subject), then run
mri_concat stack.mgz --mean --o mean.mgz
Then load the mean with
tksurferfv fsaverage lh inflated -aparc -ov mean.mgz -fminmax .01 3
On 1/15/2022 7:37 PM, Fischl, Bruce wrote:
Hi Rahul
If you hav
You can use eg, -auto-runseq mgz, this will unpack all scans as
runno.seqname.mgz (eg, 0004.mprage.mgz). You might want to add
-no-exit-on-error so that it does not exit when it finds a run that it
cannot convert.
On 1/14/2022 8:44 PM, Shi, Yuelin wrote:
External Email - Use Caution
It is probably reasonable to correct for either TIV or total HTh volume.
Each of these tests a different hypothesis, so just know what hypothesis
you are testing.
On 1/12/2022 10:32 PM, Xiaotong Zhang wrote:
External Email - Use Caution
In the statistical analysis of the volume of th
I think the issue may be the use of commas (,) instead of decimal points
(.). You an convert it easily with
cat yourfsgd | sed 's/,/\./g' > yournewfsgd
On 1/12/2022 12:10 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I want to perform an
16:11, Douglas N. Greve
wrote:
Try mri_segcentroids. Run it with --help to get docs
On 12/20/2021 3:34 AM, Julie Ottoy wrote:
External Email - Use Caution
Hi Doug,
Just checking in with the question below. Does Freesurfer have
such an option?
Thanks,
The direction cosines (DCs) for the row, col, and slice.
The DCs for the row and column are obtained from DICOM (20,37),
which is a string of the form "cx\cy\cz\rx\ry\rz". The slice DC is
obtained from the ASCII header. The x, y, and z components are from
three lines of the form "sSli
Hi, I don't know what is causing the discrepancy. Try taking the table
input that you are passing to SPSS and pass it to mri_glmfit with the
--table option. Oftentimes the SPSS model ends up being different than
the model using by mri_glmfit. There could also be some issues with
poorly conditio
On 1/8/2022 3:25 AM, zhoudong...@mail.dlut.edu.cn wrote:
Dear FreeSurfer experts:
I am confused how vertex position is determined. Is the vertex's
position on surface is determined?
Each vertex in fsaverage is mapped back to the surfaces of 40 subjects.
The xyz for the vertex is the mean
I have made some edits to this recently. Can you try the new one?
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkheadsurf
guest
collab
On 1/7/2022 11:11 AM, Yong-Jun Lin wrote:
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Hello FreeSurfer Developers,
I was attempting to execute the mkheadsurf s
but I can see the blue mark on the region
On Sun 2 Jan 2022, 21:13 Douglas N. Greve, wrote:
You have to make sure that you click in the region that you want
to keep (ie, you should be able to see the cursor in your region)
On 12/20/2021 8:11 AM, Alison McDonnell wrote:
Best,
*Laura Willers de Souza *
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
-----------
*De:* Douglas N. Greve
*Enviado:* domingo, 02 d
Hi Jee Won and Priyanka, there are several things going on here. First,
the original aseg (aseg.presurf.mgz) has these areas labeled as nothing
(0); they show up as WM in aseg.mgz and aparc+aseg.mgz. Obviously, it
would be good to have them properly labeled, but is this critical to
your applica
It should use whatever matlab is in your path. It looks like it is
expecting to find it in /usr/local/freesurfer/stable5_1_0/matlab/
which is kind of strange since you are using FS6. Look in your cshrc or
bashrc file to see if that is being added to your path and if so remove
it. What happens if
Yes, that looks correct
On 12/25/2021 11:07 AM, Miguel Ángel Rivas Fernández wrote:
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Sorry, I wrote this previous email from a different adress because I
did not receive emails from the freesurfer's support list 😅
Thank you!
El sáb., 25 dic. 2021 17:01,
On 12/20/2021 9:20 PM, Laura Willers de Souza wrote:
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Dear Douglas,
Thanks so much for your answer.
Could you check if the following commands to perform ROI analysis with
GLM are correct?
*1.* Create the table with the volumes of the hippocampal segmen
You have to make sure that you click in the region that you want to keep
(ie, you should be able to see the cursor in your region)
On 12/20/2021 8:11 AM, Alison McDonnell wrote:
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Hi Freesurfer,
I am currently trying to make a patch to make a flat map. I ma
Try mri_segcentroids. Run it with --help to get docs
On 12/20/2021 3:34 AM, Julie Ottoy wrote:
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Hi Doug,
Just checking in with the question below. Does Freesurfer have such an
option?
Thanks,
Julie
On Tue, 14 Dec 2021 at 18:38, Julie Ottoy
wrote:
Not sure what is going on here. Can you run it without the -parallel flag?
On 12/19/2021 3:37 AM, Atsushi Yamaguchi wrote:
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Hello FreeSurfer Developers,
I'm attempting to run recon-all on structural MRI data of Human
Connectome Project (ex. T1w.nii.gz fro
Chris/Ruopeng, you can use https://transfer.partners.org
On 12/17/2021 11:41 AM, Christopher Panks wrote:
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Hi Ruopeng,
I can send the niftis to an individual, but I cannot post them to a
listserv.
Version info:
freesurfer-linux-ubuntu18_x86_64-dev-2021
airedAnalysis>)
so yes we are subtracting the two time points explicitly and computing
a paired t-test as you suggested. I've attached both the first fsgd
file (pairs.fsgd) and the second fsgd file (paired-diff.fsgd) for
your reference.
Thanks for the help! - Doug M
On Fri, Dec 10, 2021
Can you check to make sure the disk is not filling up?
Also, see if subject/mri/tmp.mri_nu_correct.mni.13492/nu1.mnc exists and
is of a size similar to orig.mgz
On 12/15/2021 7:27 PM, xuan wrote:
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Oops, forget about the log file.
Here it is
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