You can invert the gca with somehting like
mri_ca_register -invert-and-save cvs.gca inv.cvs.gca
The apply inv.cvs.gca to map from CVS space back to the native space
On 12/6/2024 3:51 AM, Tanxin Dong wrote:
External Email - Use Caution
To whom this may concern:
Hi, I’ve been working
External Email - Use Caution
To whom this may concern:
Hi, I’ve been working on creating a template for a certain metric using the
applyMorph command to project the calculated metrics onto the CVS template.
However, I'm curious if there’s a way to reverse this process.
Specificall
Apologies! I don’t believe you can run the recon-all-clinical approach for
longitudinal work, as many of our intermediate files (e.g., norm.mgz) are not
directly comparable to the ones in the standard recon-all stream as of now.
Karthik
On Nov 26, 2024, at 9:03 AM, 王又劼 wrote:
Externa
External Email - Use Caution
Hello,
I have longitudinal imaging data for some participants. Due to the data
collection protocol, the T1w image from the first timepoint (TP1) is a clinical
sequence (e.g., slice thickness of 5mm or 6.5mm), while subsequent timepoints
collected 3D
] | [
http://www.neura.edu.au/help-research/subscribe | Subscribe ]
From: "Douglas N. Greve"
To: "Freesurfer support list"
Sent: Friday, 20 September, 2024 11:43:57 PM
Subject: Re: [Freesurfer] Questions re Freesurfer editing
I'm not sure what to do about the media
I'm not sure what to do about the medial surfaces. I don't think I've
run into that problem before. For the other issue, those areas are the
transverse sinus veins. In the next version, I have something that will
segment those areas. You can get it now in the dev version. Then run
mri_vsinus_se
External Email - Use Caution
Dear Martin Reuter and Bruce Fischl,
Hi all,
When we use the longitudinal pipeline of FreeSurfer, I know there are three
steps: 1. cross-sectional, 2: base, 3: long. When we create the subject
template, it uses median and intensity scaling in the seco
External Email - Use Caution
It looks like you are transforming it to fsaverage space before
computing the statistics. If this is correct, then that will explain the
differences as that transform will involve some interpolation which will
change the values. But they should be ver
External Email - Use Caution
Dear FreeSurfer developers,
When I extract the surface area of the brain regions
corresponding to the DK atlas in fsaverage space with the following command,
the corresponding DK atlas brain regions calculated after summation or
averaging, whet
External Email - Use Caution
when you convert to fsaverage space, there is some interpolation that
will cause the two to be not exactly the same. They should be very close
though
On 8/17/2023 11:27 AM, 1500787798 wrote:
External Email - Use Caution
Dear FreeSurfer dev
External Email - Use Caution
Dear FreeSurfer developers,
The surface area in fsaverage space that I extracted
with the first command below is not the same as the value under the same DK
brain region extracted from the lh.parc.stats file generated as a result of
prepro
,
Karthik
Subject: Re: [Freesurfer] Questions for the estimated brain volume based on new
version of FreeSurfer
External Email - Use Caution
First of all, you are not going to get the same answer from these different
programs. For ento, recon-all will zero the thickness in some areas around
External Email - Use Caution
First of all, you are not going to get the same answer from these
different programs. For ento, recon-all will zero the thickness in some
areas around ento, and clinical is probably not doing that. Still a
factor of 4 seems pretty large. Maybe Karthik
External Email - Use Caution
Dear FS developers,
Hi,
I am very happy that we can use new features of FreeSurfer (e.g.,
recon-all-clinical.sh, SynthSeg, SynthSR, etc.)
While using a variety of functions from FreeSurfer (v7.3.2 and v7.4.1), we
would like to hear the answers to the
External Email - Use Caution
Dear experts,
I have been using the mri_normalize in FSv7.3.2 to standardize the
intensity of FLAIR images , and I've observed that increasing the sigma
parameter up to 25 is effective in improving the quality of the normalized
images for noisy datasets
External Email - Use Caution
Dear Dr Greve, thank you so much for answers to my questions.
Regarding question 2, yes I meant leaving only columns I need, for instance
I am interested in lobes. I ran these commands on my data
# mri_annotation2label --subject subject --hemi lh --lob
On 12/20/2022 12:22 PM, James Brown wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your
help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surfac
External Email - Use Caution
Dear Freesurfer experts,
I have 2 questions about the command mri_glmfit and I appreciate your help.
1- Are there any settings or flags that can be used in mri_glmfit to
restrict statistical comparison of surface based analysis to specific ROIs
rather t
External Email - Use Caution
Dear Bruce Fischl,
Hi, I'm Yoonho.
I know that new features, such as SynthSeg, SynthStrip, segment_subfields
(beta version), etc, based on deep learning have been added after the
FreeSurfer 7.3.2.
Here I have questions (I read papers related to SynthSe
Dear Wenjun,
It’s perfectly fine. Just make sure to report the versions you used if you use
the outputs to publish anything ;-)
Cheers,
Juan Eugenio Iglesias
http://www.jeiglesias.com
On 18 May 2022, at 23:42, Wenjun Huang mailto:wh2...@nyu.edu>>
wrote:
External Email - Use Caut
External Email - Use Caution
Hi,
I'm attempting to use segmentThalamicNuclei.sh(
https://secure-web.cisco.com/1RV2omTbdlZNcuz2LjtNOfF_gXU-a1Zh7ZafxTa7vX-y1Z1LZxS0Oc2hhSnAz_ddkvbDogx-Es0B0cIzDL7ZBQVIpT6ABl0fiNwLa2arhoBRKoZI3G7JqVRilClK3470W9etqhZAuTI73h8WIryqVSmuffGYEmzC_qBEEG32btzr
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 str
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 structural graph
theoretical analyses based on the FreeSurfer parcellation and DTI data,
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
External Email - Use Caution
Hi,
I got a couple of questions regarding group analysis of tracula with a
longitudinal pipeline, freeview output heatmap key, and pair analysis's
fsgd & correction analysis.
1). I followed FsTutorial/TraculaStatistics - Free Surfer Wiki (harvard.edu)
External Email - Use Caution
Got it!
Thank you so much,
Laura.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
e janeiro de 2022
*Para:* Laura Willers de Souza
*Cc:*freesurfer@nmr.mgh.harvard.edu
*Assunto:* Re: [Freesurfer] Questions about contrasts
Dear Douglas,
Again, thanks for the reply.
Please check if I understand correctly:
* First I do the contrast [0 0 -1 1] to test if there is
Porto Alegre/RS - Brazil
---
De: Douglas N. Greve
Enviado: domingo, 02 de janeiro de 2022
Para: Laura Willers de Souza
Cc: freesurfer@nmr.mgh.harvard.edu
Assunto: Re: [Freesurfer] Questions about contrasts
Dear Douglas,
Again, thanks for the reply.
Please check if I understand correctly:
* F
External Email - Use Caution
Dear Douglas,
Thank you so much for all the help!
Now I think I finally get it.
Best regards,
Laura Willers de Souza
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
Willers de Souza
*Cc:*freesurfer@nmr.mgh.harvard.edu
*Assunto:* Re: [Freesurfer] Questions about contrasts
This contrast will do it: [1 -1 0 0]
But I would first test [0 0 -1 1] to see if the slopes are different.
If not, then use [1 -1 0] with DOSS instead of DODS
-feira, 14 de dezembro de 2021
Para: Laura Willers de Souza
Cc: freesurfer@nmr.mgh.harvard.edu
Assunto: Re: [Freesurfer] Questions about contrasts
This contrast will do it: [1 -1 0 0]
But I would first test [0 0 -1 1] to see if the slopes are different. If not,
then use [1 -1 0] with DOSS instead
viado:* terça-feira, 14 de dezembro de 2021 18:54
*Para:* Laura Willers de Souza
*Cc:* freesurfer@nmr.mgh.harvard.edu
*Assunto:* Re: [Freesurfer] Questions about contrasts
Can you include the previous emails in your current email?
On 12/14/2021 3:46 PM, Laura Willers de Souza wrote:
External
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 anal
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 analyze the difference in cortical thickness between two groups (CU
and CI), adjusting for a covariate (cortisol
External Email - Use Caution
Dear Douglas,
Thank you for the answer!
Best regards,
Laura Willers de Souza
Master Student in Biochemistry
Zimmer Lab - Federal University of Rio Grande do Sul
- Porto Alegre/RS - Brazil
___
Freesurf
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 Em
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 n
External Email - Use Caution
Hello FreeSurfer Developers,
I would like to assess whether my regression model meets the GLM assumptions,
especially if there is no multicollinearity.
Is it possible to perform this diagnosis in freesurfer?
If not, is there a way to extract the mod
edu>
*主题: *Re: [Freesurfer] FreeSurfer questions exchange
On 8/9/2021 5:51 AM, 刘 亚飞wrote:
*External Email - Use Caution *
Hello!
In the process of learning freeSurefer, I have two questions:
The first question is that I want to convert a file in .stl format
to
. Greve
发送时间: 2021年8月18日 5:27
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] FreeSurfer questions exchange
On 8/9/2021 5:51 AM, 刘 亚飞 wrote:
External Email - Use Caution
Hello!
In the process of learning freeSurefer, I have two questions:
The first question is that I want
On 8/9/2021 5:51 AM, 刘 亚飞 wrote:
External Email - Use Caution
Hello!
In the process of learning freeSurefer, I have two questions:
The first question is that I want to convert a file in .stl format to
a .pial file, but the error "does not apear to be an STL file" appears
when usin
External Email - Use Caution
Hello!
In the process of learning freeSurefer, I have two questions:
The first question is that I want to convert a file in .stl format to a .pial
file, but the error "does not apear to be an STL file" appears when using the
mris_convert command, an
External Email - Use Caution
Hello Nana,
Your browser should display a “CAPTCHA” box at the bottom of the freesurfer
license page just above the button where you click “I AGREE”.
If you do not see the CAPTCHA box in your browser then it is probably blocking
some javascript that w
External Email - Use Caution
Dear Sir:
I met registration error when I provided all the personal information to
register the copy of FreeSurfer and obtain the license.txt key file, is there
any way for me to get the license file? The error figure is attached and thank
you
On 3/24/2021 5:11 PM, Blanpain, Lou wrote:
External Email - Use Caution
External Email - Use Caution
Hello,
I had the following 2 general questions regarding Freesurfer:
1. Is there an extensive list of anatomical labels for each atlas
used? For instance, what are all
External Email - Use Caution
Hello,
I had the following 2 general questions regarding Freesurfer:
1. Is there an extensive list of anatomical labels for each atlas used? For
instance, what are all the potential labels used in wmparc.mgz? I am aware of
the extensive list of l
for confirming what I had suspected!
Thanks,
Lisanne
From: on behalf of "Douglas N. Greve"
Reply-To: Freesurfer support list
Date: Monday, February 22, 2021 at 9:18 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: Re: [Freesurfer] Questions related to combining
On 2/18/2021 9:52 AM, Lisanne Michelle Jenkins wrote:
External Email - Use Caution
Hi experts,
We want to combine two large datasets (of patients with different
diseases) that have been processed and manually edited using
Freesurfer 5.3 and Freesurfer 6.0.
From the Freesurfer web
External Email - Use Caution
Hi experts,
We want to combine two large datasets (of patients with different diseases)
that have been processed and manually edited using Freesurfer 5.3 and
Freesurfer 6.0.
From the Freesurfer website and previous posts, we have read that we should
Rather than -parrallel, use -threads to indicate the number of
processors to use
On 8/5/20 10:47 AM, Yang Molly wrote:
External Email - Use Caution
Hi list,
I tried to run some longitudinal data with two time points with the
latest version Freesurfer (7.1.0) on the Ubantu 16 system.
External Email - Use Caution
Hi list,
I tried to run some longitudinal data with two time points with the latest
version Freesurfer (7.1.0) on the Ubantu 16 system. "recon-all -base" with
two time points need 5 hours to complete on my PC, and recon-all -long need
2 hours. I try to
Doug is saying that you should replace:
--out lh.pial_lgi
with
--out lh.pial_lgi.mgh
on your command line
cheers
Bruce
On Thu, 30 Apr 2020, 肖伏龙 wrote:
External Email - Use Caution
so how to get the pial_lgi.mgh from the pial_lgi file?
MailScanner has detected a possib
External Email - Use Caution
so how to get the pial_lgi.mgh from the pial_lgi file?
| |
肖伏龙
|
|
邮箱：xiaofulong1...@163.com
|
签名由 网易邮箱大师 定制
On 04/30/2020 06:18, Douglas N. Greve wrote:
It needs to have an extension, eg, lh.pial_lgi.mgz
On 4/29/2020 9:02 AM, 肖伏龙 wrote:
It needs to have an extension, eg, lh.pial_lgi.mgz
On 4/29/2020 9:02 AM, 肖伏龙 wrote:
External Email - Use Caution
hello everyone
I have a question about statistics on LGI. for the LGI data, named as
lh.pial_lgi, I used mris_preproc as following:
mris_preproc --fsgd fsgd.fsgd --cache-i
External Email - Use Caution
hello everyone
I have a question about statistics on LGI. for the LGI data, named as
lh.pial_lgi, I used mris_preproc as following:
mris_preproc --fsgd fsgd.fsgd --cache-in pial_lgi --target fsaverage --hemi lh
--out lh.pial_lgi
but freesurfer said
E
Try
mris_convert -n lh.white lh.white.norm.asc
On 3/6/2020 11:07 AM, Jedy wrote:
External Email - Use Caution
Dear FreeSurfer friends,
Does anybody know how to extract vertex information of lh.white and
lh.pial? I would like to extract normal vector and other information
of eac
External Email - Use Caution
Dear FreeSurfer friends,
Does anybody know how to extract vertex information of lh.white and
lh.pial? I would like to extract normal vector and other information of
each vetex.
I would be very appreciated if someone can give me some suggestions.
Hi,
looks like someone changed the default python to version 3, and you are
still using a script written for python 2. I think Andrew updated this
recently, so obtaining a newer version of the long_submit_jobs script
from dev may fix this.
Best, Martin
On Tue, 2020-02-11 at 18:03 +, Huang,
Hi there,
I am trying to run some longitudinal data using freesurfer long_submit_jobs
command on cluster. I have double checked my directory and files setup
according to freesurfer longitudinal preprocessing
wiki:https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts. And it seems
there
On 11/15/19 4:19 AM, Soo-Jong Kim wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I am a student in neuroimaging using FreeSurfer.
> I have some questions and I don't know where to send questions.
> That's why I found this mail and writing.
>
> I've studied PetSur
External Email - Use Caution
Dear FreeSurfer experts,
I am a student in neuroimaging using FreeSurfer.
I have some questions and I don't know where to send questions.
That's why I found this mail and writing.
I've studied PetSurfer for partial volume correction of PET.
I saw the
Hi David,
I am not very optimistic:
5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You
will certainly get something, but it can be very unreliable and
completely wrong. Especially longitudinally these thick slices will
induce large variance due to different head positioning (an
External Email - Use Caution
Freesurfers,
First of all, I'd like to express my gratitude to the community for the support
that keeps researchers like myself afloat!
I have a unique set of oncology patients that I want to evaluate for brain
atrophy in a retrospective longitud
Not that I know of, it is pretty limited.
On 9/13/19 11:13 AM, Zeng,Victor (BIDMC - Psychiatry) wrote:
Hi all,
I know tkmedit has been deprecated, but we're thinking about using it just for
quality check purposes since we found that it is less resource intensive. We're
trying to load multip
Hi all,
?
I know tkmedit has been deprecated, but we're thinking about using it just for
quality check purposes since we found that it is less resource intensive. We're
trying to load multiple labels, is there a way to do that so that each label is
assigned a different color (we know that's po
Hi,
I am new to Free Surfer and am working on the resting state fMRI data analysis
using FS-FAST. When I used the tkregister-sess command to see the registration
quality (from structural image to fMRI image), I found that there is one
registration not good (QA value = 0.9). So I did manual reg
External Email - Use Caution
Thank you very much for your detailed explanation. About the second
question, I am still confusing on the permutation and CWP map calculation:
1. Whether the CFT is applied to the uncorrected p-value map first (e.g.,
the sig.nii.gz generated by 'mri_gl
On 4/25/19 10:54 AM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Dear FreeSurfer experts,
>
> I am reading your work 'False positive rates in surface-based
> anatomical analysis' and having several questions about multiple test
> correction in mri_glmfit-sim:
>
> 1. The permutati
External Email - Use Caution
Dear FreeSurfer experts,
I am reading your work 'False positive rates in surface-based anatomical
analysis' and having several questions about multiple test correction in
mri_glmfit-sim:
1. The permutation is permuting the design matrix, but how to pe
External Email - Use Caution
Hi,
I am interested in the Hippocampal Subfields And Nuclei Of Amygdala module and
have a few questions regarding its functionalities.
Regarding the segmentation of amygdala nuclei, you say that currently, "volumes
of the nuclei must be interprete
External Email - Use Caution
Dr. Greve,
Thank you for this information. The input to mri_glmfit was an mgh file of
structural MRI data from several subjects warped into a common space and
concatenated. What would that make the units of the input (--y) file and
the output gamma fil
On 1/9/19 10:35 AM, Max Owens wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I just wanted to follow up and see if there was anyone who could
> answer my questions:
>
> 1.What is the unit of effect size for the gamma.mgh file created by
> vertexwise GLM Analysis using mri_glmfit?
S
External Email - Use Caution
Hi,
I just wanted to follow up and see if there was anyone who could answer my
questions:
1. What is the unit of effect size for the gamma.mgh file created by
vertexwise GLM Analysis using mri_glmfit?
2. Based on two previous posts (
https://www.mail
External Email - Use Caution
Hi Freesurfer Experts,
I have two related questions about the measures of effect size that can be
derived from a vertexwise GLM analyses conducted in Freesurfer:
1. What is the unit of effect size for the gamma.mgh file created by
vertexwise GLM Analy
Most of FS/recon-all will run using the T1 only. The T2 can be used to refine
the pial surface (-T2 T2file.mgz -T2pial)
On 9/18/18 4:56 AM, limiyu wrote:
External Email - Use Caution
Dear developers
I have a question on how could I segment two registered MRI images and
get o
External Email - Use Caution
Dear developers
I have a question on how could I segment two registered MRI images and
get only one segmentation result, by command recon-all ?
In details, I have two MRI images which are T1-weighted and
T2-weighted. They a
identify step size of the equally sized step you mentioned above?
Thanks!
Qianwen
-- --
??: "Yendiki, Anastasia";
: 2018??9??13??(??) 11:44
??: "Freesurfer support list";
????: Re: [Freesurfer]?? questions
answer my doubts. Thanks!
Qianwen
-- --
??: "Yendiki, Anastasia";
: 2018??9??12??(??) 10:40
??: "Freesurfer support list";
: Re: [Freesurfer] questions about trac-all -stat
Hi Qianwen ?C You don??t
rfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] questions about trac-all -stat
External Email - Use Caution
Dear experts,
I have some questions about along-path analysis:
(1)how to determine the first position and last position of all subjects'
pathway when converting all pathsta
External Email - Use Caution
Dear experts,I have some questions about along-path analysis:
(1)how to determine the first position and last position of all subjects'
pathway when converting all pathstats.byvoxel.txt files to a table for group
analyses?
(2)how to complete corresp
, 2018 at 1:58 PM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>"
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] questions about Tracula and doeddy=1 or 0
Dear FreeSurfer experts,
I had sent several times this email since th
drew"
Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
The subfield part never started. Recon-all died earlier.
Andrew: any ideas?
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
Univers
/
From: on behalf of 姜时泽
Reply-To: Freesurfer support list
Date: Friday, 24 August 2018 at 15:14
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Hi Eugenio
I did not find the log file you mentioned. Attached
t 23:02
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Hi Juan
Thank you for your kindly help. Attached is the log file with error. I am not
sure if this is the file for hippocampus subfield segmentati
Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - Use Caution
Hi Juan
Thank you for your kindly help. Attached is the log file with error. I am not
sure if this is the file for hippocampus subfield segmentation.
Thank you very much
Shize
在 2018-08-24 05
ndon
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From:freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 姜时泽
Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error
External Email - U
://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of 姜时泽
Sent: Thursday, August 23, 2018 5:08:51 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] questions about hippocampus subfield error
ting (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of 姜时泽
Reply-To: Freesurfer support list
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] questions about hippoc
Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: on behalf of 姜时泽
Reply-To: Freesurfer support list
Date: Thursday, 23 August 2018 at 15:10
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] questions about hippocampus subf
Dear FreeSurfer experts,
I had sent several times this email since the last few months, and never
obtained any reply. Would anyone be able to provide me little bit of insight
please?
I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0.
b1=0, b2=3000 s/mm2 and diff dire
Dear FreeSurfer experts,
I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0.
b1=0, b2=3000 s/mm2 and diff directions = 90.
Surprisingly the trac-all reconstruction with doeddy =1 was not as good as
with doeddy = 0 on average on all the subjects, as in our dataset ther
Hi Stacey
we recommend processing all of your subjects the same way. Do you
understand why some would have a big bias field and some would not? It was
always the same coil, wasn't it?
cheers
Bruce
On Mon, 9 Jul 2018, STACEY M SCHAEFER
wrote:
External Email - Use Caution
External Email - Use Caution
Hello Freesurfer experts,
Our current 3T T1s exhibit structural hyperintensities due to the inhomogeneity
of the receiver coil, but not all scans have hyperintensity issues. The local
MRI physicist suggests running N4BiasFieldCorrection through mul
External Email - Use Caution
Hi Rob,
It works. Many thanks for your kindly help.
All the best
Shize
At 2018-06-27 05:01:37, "Dicamillo, Robert" wrote:
Hello Shize,
Try downloading the following zip archive, and double click on it to uncompress
it
https://drive.google.com/
Hello Shize,
Try downloading the following zip archive, and double click on it to uncompress
it
https://drive.google.com/file/d/1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR/view?usp=sharing
There is a README file in the archive describing how to update a couple of
files. Please try to
apply the updates,
External Email - Use Caution
Hi Ruopeng,
Thanks for your reply. I have tried many types of volume file, including the
example files. Freeview all quit unexpectedly. I am not sure if there are
still something wrong with the volume file itself.
Many thanks for your help
Shize
External Email - Use Caution
Hi Rob,
Thank you for your kindly help. This is the log file from terminal. could you
helps me to figure out what was wrong with it. Many thanks.
Shize
Jun 26 16:31:33 Jiang-Shizes-MacBook-Pro loginwindow[95]:
-[SFLListManager(ServiceReplyPr
Would it be possible for you send us the volume file that caused the crash?
Best,
Ruopeng
On 06/26/2018 01:30 PM, 姜时泽 wrote:
External Email - Use Caution
Hi Rob
Many thanks for your feedback. There is no notification pop up. The
GUI of freeview just quit. I am not sure what was wro
Hi Shize,
You could try looking at the system log. Before you launch Freeview open a
terminal window and do,
$ tail -f /var/log/system.log
There will be some output there already from the last recorded system events.
Then launch Freeview, load your file, and when it crashes, see if anything
External Email - Use Caution
Hi Rob
Many thanks for your feedback. There is no notification pop up. The GUI of
freeview just quit. I am not sure what was wrong with this. DO you have any
ideas about this? Thank you .
Best wishes
Shize
At 2018-06-27 00:54:45, "Dicamillo, Rob
1 - 100 of 295 matches
Mail list logo
