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
r-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 2/1/2022 1
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...
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
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
.-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: [Free
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
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
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
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,
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
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
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
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
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
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,
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
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??
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,
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,
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
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
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
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
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
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
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
, 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,
Julie
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
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
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
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:
External Email - Use Caution
Hello FreeSurfer Developers,
I was attempting to execute the mkheadsurf
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:
,
*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 de jan
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
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
Yes, that looks correct
On 12/25/2021 11:07 AM, Miguel Ángel Rivas Fernández wrote:
External Email - Use Caution
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:
External Email - Use Caution
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
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:
External Email - Use Caution
Hi Freesurfer,
I am currently trying to make a patch to make a flat map. I
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,
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:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to run recon-all on structural MRI data of Human
Connectome Project (ex. T1w.nii.gz
Chris/Ruopeng, you can use https://transfer.partners.org
On 12/17/2021 11:41 AM, Christopher Panks wrote:
External Email - Use Caution
Hi Ruopeng,
I can send the niftis to an individual, but I cannot post them to a
listserv.
Version info:
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 at 5
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:
External Email - Use Caution
Oops, forget about the log file.
Here it is
Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
---
*De:* Douglas N. Greve
*Enviado:* terça-feira, 14 de dezembro de 2021
*Para:* Laura
Please sent the log file
On 12/15/2021 7:28 AM, xuan wrote:
External Email - Use Caution
Dear FreeSurfer Experts,
I am attempting to recon-all for my one subject for testing on my lab
server. However, I get following error:
ncopen: filename
You did not create the contrast matrix correctly. There needs to be a
column for each subject, then a column for time point1 and one for time
point 2. Use DOSS (defaults to DODS). Also, I think you could compute
tp2-tp1 if you wanted to (makes things easier).
On 12/14/2021 5:58 PM,
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you
__
Answer by Douglas N. Greve:
Hello FreeSurfer Developers,
I want to perform an analysis of the difference between two groups
incortical thickness, having cortisol
Can you include the previous emails in your current email?
On 12/14/2021 3:46 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Dear Douglas,
Thank you so much for your answer!
Sorry, but I don't think I explained myself correctly in the previous
email.
I want to
on how to fix these defects?
Thanks,
Nilab
*From:* Douglas N. Greve
*Sent:* 11 December 2021 00:24
*To:* Nilab Nasrullah ;
freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Help
The data look pretty noisy
use the asegstats2table command in
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala
You will have to add command line options to specify the subjects you
want. You can then pass the output file with the --table option to
mri_glmfit
On 12/13/2021 3:56 PM, Laura
The model is actually, two independent linear models:
thicknessCU = CUOffset + CUcortisol*CUslope
thicknessCI = CIOffset + CIcortisol*CIslope
There will be four regression parameters:
[CUOffset CUslope CIOffset CIslope]
On 12/9/2021 10:48 PM, Laura Willers de Souza wrote:
External
In that case, you should edits the wm.mgz (first web page) to find the
big defect. There are not any surfaces at this point because it did not
get that far
On 12/9/2021 3:53 AM, Sumit Sharma wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to generate
These two are not mutually exclusive. If you want to perform GLM on the
volume measures of each ROI, then the answer is yes. If you want to go a
VBM style analysis, then no.
On 12/9/2021 9:09 AM, Laura Willers de Souza wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
Can you say more about your approach? Are you subtracting the two time
points explicitly and computing a paired t? Or are you using the
repeated measures anova approach. Send the FSGD file
On 11/30/2021 11:04 AM, PDMD SRALab wrote:
External Email - Use Caution
We are using a paired
You can merge them yourself or you could run mri_annotation2label with
one of the --lobes options to generate a new annotation of lobes, run
use that to generate a new wmparc.mgz file (look in the recon-all.log
file to get the command, specify your new annotation and change the
output file
Hard to say what is going wrong from that. Can you try removing the
trailing "/" from the subject name? Also, do you need --conform? Often
the recon-all output 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
Is the problem that there is an overlap? The exvivo labels and aparc
labels are not going to be mutually exclusive.
On 12/6/2021 5:34 PM, Tsolaki, Evangelia C. wrote:
External Email - Use Caution
Hello Freesurfer Team,
I am interested in using premotor, precentral gyrus and
How did you create the new MNI chimp average surface?
On 12/5/2021 11:08 AM, Trisanna Sprung-Much wrote:
External Email - Use Caution
Hi Bruce
So I have 77 chimp scans reconstructed in FS (NOT registered to MNI
space, but rather a chimp volume template, to avoid scaling). After a
If you run it with --eres-save, it will save the residuals in eres.mgh
On 12/4/2021 11:17 AM, Laura Willers de Souza wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I would like to assess whether my regression model meets the GLM
assumptions, especially if there is
Don, can you send your command line? If you are using surface-based
registration, then the origin should not matter. You are right that
there is not a one-to-one correspondence. The way it works is that it
starts on the target surface, goes through all the vertices and finds
the closest
the defects are.
On 11/29/2021 9:41 AM, Nilab Nasrullah wrote:
External Email - Use Caution
Sure. See attached.
//Nilab
*From:* Douglas N. Greve
*Sent:* 29 November 2021 15:40
*To:* Nilab Nasrullah ;
freesurfer
are you just running gcut or all of recon-all? If all of recon-all,
please send the recon-all.log file
On 12/2/2021 2:43 PM, Vishal Mohanty wrote:
External Email - Use Caution
Hi
This is Vishal Mohanty, a Research Assistant at the CNS Lab
We are not supporting qdec anymore. Try using the "command line stream",
ie, mris_preproc, FSGD, etc
On 12/1/2021 6:47 PM, Arian Klows wrote:
External Email - Use Caution
Dear FS experts,
I have freesurfer-linux-centos7_x86_64-7.1.1 on my computer and when I
run qdec, I get the
There is no way to model a missing cell in the FSGD. You'd have to
figure out a value (eg, using imputation) or exclude those subjects
On 11/30/2021 2:59 PM, Laura Willers de Souza wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I would like to know what I put in
sorry, I don't know what you mean by perimeter
On 11/29/2021 8:09 PM, Fernanda Hansen P. de Moraes wrote:
External Email - Use Caution
Dear FreeSurfer experts,
Is there a way to estimate the perimeter from a surface (e.g. ?h.pial)
for each slice in an automated manner at any
you need to run it as a DOSS, ie, --fsgd Repeted_measure.fsgd doss
On 11/29/2021 6:50 PM, std...@virgilio.it wrote:
External Email - Use Caution
Hi list,
I have two groups undergoing two different treatments: one's placebo
(n=12), one's drug (n=12). Two timepoints, at baseline (T1,
the mask flag would be helpful?
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Monday, November 29, 2021 12:28 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Errors
On 11/29/2021 11:55 AM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
A quick question.
Is it feasible or even possible to edit the aseg.mgz using another
program (i.e. ITK-snap after converting to nifti), and rerunning the
pipeline using the revised aseg as input
In your mkanalysis command, why are you specifying the mask and the
funcstem? These are tricky options to get right ...
On 11/29/2021 9:50 AM, Hiersche, Kelly J. wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
First, I am new to using Freesurfer, so I apologize if
Right. Actually, I don't think it would apply the smoothing to the
annotation anyway
On 11/29/2021 10:43 AM, Daniel Westfall wrote:
External Email - Use Caution
Good afternoon,
It is my understanding that if I am only interested in the already
averaged region ROIs that are output
in a different format.
Thanks,
Nilab
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* 29 November 2021 04:01
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Help
Can you send some
sorry, no picture attached. Can you resend?
On 11/29/2021 2:40 AM, achille.teil...@chu-lyon.fr wrote:
External Email - Use Caution
Dear experts,
We are working with a large MRI dataset (FLAIR, T1) and we are
performing recon-all based on the 3D T1. At the end, no error is
detected
If they are not part of the T1w series, then you can delete them (but
then they should not have caused the error). If they are part of the
series, then they are probably corrupted or perhaps the output of a very
aggressive anonymization.
On 11/25/2021 8:40 AM, Alison McDonnell wrote:
st,
AJ
Scanners used for controls and test subjects:
Achieva_TFE_R1
Achieva_TFE_R2
Ingenia_R1
Ingenia_R2
GE_SPGR_1529_R1
GE_SPGR_1529_R2
GE_SPGR_R1
GE_SPGR_R2
Phillip_Achieva_R1
Achieva_R2
GE_R1
GE_R2
On Sun, Nov 28, 2021, 20:41 Douglas N. Greve
wrote:
Also samseg, see *MailS
This is a bug. I've put a new version of mri_annotation2label here:
https://gate.nmr.mgh.harvard.edu/safelinks/greve/
username 'guest'
password 'collab'
copy it into $FREESUFER/bin (after making a copy of the one that is there).
On 11/22/2021 12:23 PM, Dr. Cornelius Kronlage wrote:
>
That will work; it may be clearer to use mris_fwhm, eg,
mris_fwhm --smooth-only --s sub-0006 --hemi lh --fwhm 5 --cortex --i
input --o output
On 11/26/2021 6:48 AM, Mason Wells wrote:
External Email - Use Caution
Hi Experts,
This question may have been addressed elsewhereon the
For volumes, load labels using the "Load ROI..." under the File menu
For surfaces, use the "Load" button in the "Label" section
On 11/23/2021 2:44 PM, Shapiro, Noah Lorenz wrote:
Hello,
I am very new to FreeSurfer, and I was going through the tutorials and
bumped into difficulties when
Just add -cw256 to the recon-all command line
On 11/23/2021 8:34 AM, Alison McDonnell wrote:
External Email - Use Caution
Hi Tim,
I looked at orig.mgz and it seemed fine and could see the whole head.
i dont know what is meant by the flag -cw256 error. I am taking over a
project
Can you send some pictures?
On 11/23/2021 4:02 AM, Nilab Nasrullah wrote:
External Email - Use Caution
Hi,
I am editing subjects for a research project. After reconstruction,
some parts of the brain are not included in the segmentation. Often,
some parts of the temporal lobe and
Yes, but if there is an anat2orig2diff.bbr.lta file, use that instead
On 11/22/2021 12:48 PM, Zeng, Qi wrote:
External Email - Use Caution
Sorry for the trouble, I seemed to find the registration matrix
located in xfms/anatorig2diff.bbr.dat. Is that one correct?
Best,
Jackie
On
I noticed that you are explicitly setting the mask and funcstem in
mkanalysis-sess. Is there a reason for that? Also, I'd set -poly to 5.
On 11/21/2021 1:11 PM, Hiersche, Kelly J. wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
First, I am new to using Freesurfer,
I see what you mean, though I don't think either one look that great.
The first thing to do is to backup and look at the registration to
fsaverage_sym by mapping the lh and rh curv to lh.fsaverage_sym and see
if the curv patterns match up with those in fsaverage_sym and to each
other (use
That is a label atlas; you cannot run that through FS. You will need a
t1-weighted image to use as input to recon-all to start.
On 11/19/2021 1:59 PM, Flanagan, Shawn D wrote:
External Email - Use Caution
Hello,
I would like to use the Brainnectome atlas for cortical thickness
Also samseg, see https://pubmed.ncbi.nlm.nih.gov/33940143/
On 11/26/2021 11:16 AM, Fischl, Bruce wrote:
Hi AJ
you might try SynthSeg, as that is one of the advantages of it - it
isn't biased towards any particular MRI sequence
cheers
Bruce
Hi Christine, yes, your interpretation is correct. The -3T flag only
applied when using the mni tools, so it has no effect with ANTS. What
was the nature of the failure? We might be able to tweak the ANTS
command line to improve it.
doug
On 11/15/2021 12:52 PM, Notestine, Christine wrote:
it is not clear why it failed. Can you look at nu.mgz to see if
anything looks weird about it?
On 11/18/2021 1:43 AM, Wei Shao wrote:
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Hi, Dear Freesurfer experts
I'm have met a recon-all errors with data collected recently like this
They are mni305 coordinates
On 11/19/2021 9:41 AM, Gonzalo Rojas Costa wrote:
> External Email - Use Caution
>
> Hi:
>
> "Vertex Talairach" in tksurfer: how does it relate to MNI coordinates?
>
> Sincerely,
>
>
> Gonzalo Rojas Costa
> Department of Radiology
> Clínica las Condes
have you looked at this page?
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 11/19/2021 9:15 AM, Gonzalo Rojas Costa wrote:
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>
> Hi:
>
>I have MNI 152 coordinates equivalent to 10-10 and 10-20 EEG
> electrodes (see Supplementary Tables 1
don't know. try figuring out which step is actually changing
On 11/18/2021 2:03 PM, Brusaferri, Ludovica wrote:
Hi!
I am using a pipeline that was implemented and validated using fs 5.3 , which
does the following:
* compute transformation matrix for linear registration of SUV with T1-2mm,
For those interested in PET and BIDS, this should be pretty useful.
Forwarded Message
Subject:OpenNeuroPET hackathon at MGH -- Dec 6th and 7th
Date: Wed, 17 Nov 2021 19:31:48 -0500
From: Wighton, Paul
To: Greve, Douglas N.,Ph.D.
Hi Doug,
I was hoping you
: Option T2.reg
is unknown"
*Gesendet:* Mittwoch, 17. November 2021 um 16:11 Uhr
*Von:* "Douglas N. Greve"
*An:* freesurfer@nmr.mgh.harvard.edu
*Betreff:* Re: [Freesurfer] Using Mri_vol2surf
Can you be more specific about why it is not working? You definitely
need to run bbregister to cre
wow, that is weird. The RH extends far into the LH. What does the
aseg.presurf.mgz look like? Are the cortices and WM properly separated
left-right?
On 11/15/2021 4:33 AM, Alec Süwolto wrote:
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Hello freesurfers,
I’m new to freesurfer and I can’t fix a
You need to tell it what to do, eg, -all to do everything.
On 11/15/2021 8:49 AM, Alison McDonnell wrote:
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recon-all.log is attached. have tried to run again with different data
and had the same problem
On Wed, 10 Nov 2021 at 22:39, Douglas N. Greve
You have 16 groups so you need 16 items in the contrast vector (assuming
no continuous variables), so you need something like
-1 +1 repeated 8 times to give you 16
On 11/17/2021 7:23 AM, Thalhammer, Melissa wrote:
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Dear Freesurfers,
I am struggling with
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