External Email - Use Caution
Dear FreeSurfer team,
We are using the Freesurfer longitudinal pipeline, and we had questions
about accounting for different scanners and acquisition parameters.
We are looking at 3 different timepoints with 2 different scanners (scanner
1 was
Hi all,
Could it be a problem in FreeSurfer longitudinal analysis if I use two
different sequences (T1 MP2RAGE and T1 MPRAGE) for different time
points/follow-ups?
Thanks for the support,
Sara
___
Freesurfer mailing list
Freesurfer
that could certainly be a problem. Is it really just a single value
throughout the brain? If so, that is the problem. On the other hand, it
could be that the freeview intensity limits are not set well, so try
playing with those. You can also click on voxels in the brain and look
at the values i
table (dat format
“qdec.table.dat”).
Thank you!
Best,
Josefine and Co.
Fra: Josefine Tingdal Taube Danielsen
Sendt: 22. juli 2024 21:24
Til: Freesurfer support list
Emne: SV: [Freesurfer] Longitudinal analyses using Repeated measures anova
I am sorry.
We have actually been trying to do this
sefine Tingdal Taube Danielsen
Sendt: 22. juli 2024 21:24
Til: Freesurfer support list
Emne: SV: [Freesurfer] Longitudinal analyses using Repeated measures anova
I am sorry.
We have actually been trying to do this instead:
We decided to run mris_glmfit using the guide for longitudinal two stage model
n fwhm
if __name__ == "__main__":
fwhm = check_fwhm_value()
print(fwhm)
Can you guide us to move on with the analysis?
Best,
Josefine
Fra: freesurfer-boun...@nmr.mgh.harvard.edu
På vegne af Douglas N. Greve
Sendt: 22. juli 2024 15:46
Til: freesurfer@nmr.mgh.harvard.edu
Emn
Sorry, there is nothing here (ie, no fsgd file, no images). Did you mean
to attached?
On 7/10/2024 5:31 AM, Josefine Tingdal Taube Danielsen wrote:
External Email - Use Caution
Hi Freesurfer support,
I'm using Freesurfer version 7.4.1 and Ubuntu 22_x86_64.
freesurfer-linux-ubuntu22_
External Email - Use Caution
Hi again,
We decided to run mris_glmfit using the guide for longitudinal two stage model.
We are not able to run the first script:
long_mris_slopes --qdec qdec.table.dat \
--meas thickness \
--hemi lh \
--sd /mnt/c/CogimmunStudy/FS
, 2024 12:45 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal Analysis Error
External Email - Use Caution
Thank you for your response. I already followed the path in the link provided
in your email. All time points are already processed with recon-all. What I
could see
External Email - Use Caution
Hi Freesurfer support,
I'm using Freesurfer version 7.4.1 and Ubuntu 22_x86_64.
freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460.
I'm trying to run longitudinal analysis using Repeated Measures Anova
(https://surfer.nmr.mgh.harvard.edu/fsw
gh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ahmet Kaya
> *Sent:* Sunday, July 7, 2024 9:23 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Longitudinal Analysis Error
>
>
>
> *External Email - Use Caution*
/LongitudinalProcessing
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Ahmet Kaya
Sent: Sunday, July 7, 2024 9:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal Analysis Error
External Email - Use Caution
Hello FreeSurfer Developers,
I am
bruary 28, 2024 20:41
> To: Hoffmann, Malte,PhD
> Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Longitudinal Freesurfer in the presence of large
> tissue defects
>
>External Email - Use Caution
>
> Hi Malte,
>
&
: Hoffmann, Malte,PhD
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal Freesurfer in the presence of large
tissue defects
External Email - Use Caution
Hi Malte,
Thanks for the response, it’s encouraging to hear you think the longitudinal
pipeline will still
here, but this won’t
> necessarily make for a good template.
>
> Malte
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Philip P
>
> Sent: Sunday, February 4, 2024 01:48
> To: freesurfer@nmr.mgh.harva
, but this won’t necessarily make
for a good template.
Malte
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Philip P
Sent: Sunday, February 4, 2024 01:48
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal Freesurfer in the
External Email - Use Caution
Dear Freesurfer Developers,
I am currently running the Longitudinal Pipeline on a cohort with significant
portions of brain tissue removed. The obtained base templates overall look
reasonable, however, when overlaying the transformed session T1ws an
ttp%3A%2F%2Fwww.jeiglesias.com
> >
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> > on behalf of João Ramos
> >
> > Date: Monday, January 29, 2024 at 4:26 PM
> > To: Freesurfer@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] longitudinal hippocampal segmentati
, January 29, 2024 at 4:26
PMTo: Freesurfer@nmr.mgh.harvard.edu
<Freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] longitudinal
hippocampal segmentation error in Mac OS Sonoma + Freesurfer
7.2.0External Email - Use
CautionDear all,I would
appreciate your help in an i
Ramos
Date: Monday, January 29, 2024 at 4:26 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal hippocampal segmentation error in Mac OS
Sonoma + Freesurfer 7.2.0
External Email - Use Caution
Dear all,
I would appreciate your help in an issue I am having and one
External Email - Use Caution
Dear all,
I would appreciate your help in an issue I am having and one that I have not
found a reference to regarding Freesurfer. Basically, I have run all of the
longitudinal Freesurfer pipeline and I am now interested in running the
longitudinal h
External Email - Use Caution
Hi experts,
I have been attempting to analyze a group of subjects through the longitudinal
TRACULA pipeline and have run into many issues regarding the preprocessing step
making use of the thalamic segmentation. I've combed through the archives on
t
External Email - Use Caution
Ah, that makes sense, thanks! We hadn’t really considered feeding them all in
at the cross-sectional step, since to this point for these types of analyses we
have been doing all averaging after freesurfer (on the individual extracted
measures). Bu
You are right that using all the scans will bias toward tp2. I think I
would just run the cross for each time point using all the data you
have. This will not bias the base because an average of the images
within each time point will be used to make the base. If possible, you
will want to make
gh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On
Behalf Of fsbuildSent: Saturday, November 25, 2023 6:43
AMTo: freesur...@nmr.mgh.harvard.eduSubject: Re: [Freesurfer]
Longitudinal LME matlab error - Matrix singular or badly
scaled External Email -
Use Caution Hello
Sophi
nment and only print this email if necessary.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of fsbuild
Sent: Saturday, November 25, 2023 6:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Longitudinal LME matlab error - Matrix singular or
badly scaled
External
External Email - Use Caution
I have a dataset consisting of individuals scanned at two time points 7 years
apart. At the first time point, a single MPRAGE scan was collected for each
individual; at the second, the same MPRAGE scan was collected, as well as an
additional set of
External Email - Use Caution
Hi Sophie,
it's a bit hard to tell, but maybe one option would be to try fitting the model
with just a random-intercept effect instead of both random-intercept and
random-slope effects.
I.e. using [1] instead of [1 2] for the Zcols argument to lme_m
External Email - Use Caution
Hello Sophie,
Just FYI, there is no matlab distribution included in the 7.4.1 release
and we so not support using R2023b. So I presume someone at your site
installed R2023b separately via a Mathworks matlab installer. We do
provide a script
External Email - Use Caution
Hello FreeSurfer experts!
I have carried out some analysis of changes in cortical thickness over time
using the LME Matlab (R23b) Toolbox distributed within Freesurfer (7.4.1) in
line with the instructions on this page:
https://secure-web.cisco.com
External Email - Use Caution
Dear Prof Greeve,
Gentle reminder for this question,
Many thanks
Best wishes
Gabriel
Le lun. 16 oct. 2023 à 09:06, gabriel robert <
gabriel.hadrien.rob...@gmail.com> a écrit :
> Dear Prof Greve,
>
> Many thanks for your reply,
> Could you please c
External Email - Use Caution
Thanks for your email.
-原始邮件-
发件人:"gabriel robert"
发送时间:2023-10-16 15:06:38 (星期一)
收件人: "Freesurfer support list" , "Vaidya,
Nilakshi"
抄送:
主题: Re: [Freesurfer] Longitudinal multimodal processing
External Email - Use Caution
Dear Prof Greve,
Many thanks for your reply,
Could you please confirm also the second part of the sentence ? " [...]
given the sample size this is likely to be marginal compared to the effect
size and results would still be interpretable... "
Sorry but
yes, I think so too
On 9/19/2023 5:07 PM, gabriel robert wrote:
External Email - Use Caution
Dear experts in longitudinal neuroimaging
We carefully read the papers about possible biases introduced by
treating timepoints images differently (Reuter and Fischl NI 2011, for
example) to
External Email - Use Caution
Dear experts in longitudinal neuroimaging
We carefully read the papers about possible biases introduced by treating
timepoints images differently (Reuter and Fischl NI 2011, for example) to
estimate unbiased anatomical and functional changes of brain d
d.edu
Subject: [Freesurfer] Longitudinal Processing Stream Version
External Email - Use Caution
Hello,
I have a question about longitudinal stream processing. On the wiki page
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
External Email - Use Caution
Hello,
I have a question about longitudinal stream processing. On the wiki page (
https://secure-web.cisco.com/1ak_FVO1o5iVON2RkYI_Y4g9zeL4DobzwWVTa4pFlVvLOZsX_otgrcR9pl8LiCuUek5_DaMIuShxR8HZw9Z308Nn-Oea8XuRbsYfnymCNabPqzCdzt84rgttn8r-TZoxD9u2drr8KzKAd
External Email - Use Caution
The argument to -tp should be the cross subject (run earlier with
recon-all), not the input volume
On 8/1/2023 4:58 AM, Bernis SÜTÇÜBAŞI wrote:
External Email - Use Caution
Hello FreeSurfer experts,
I'm attempting to follow the longitudina
External Email - Use Caution
Hello FreeSurfer experts,
I'm attempting to follow the longitudinal pipeline, as described on the
longitudinal processing tutorial
(https://secure-web.cisco.com/1vfvhhwIW62eUqagABMhB_WTdPL428NuWWIuhlLA1wradeuw0s2ojnD8IvCB-0fL80s5FWT9oOODXD26Oz-H13kTK
External Email - Use Caution
Here is the tutorial page for longitudinal pipeline -
https://secure-web.cisco.com/1DcUJ0a_skONZSHVRpSGkgbTHuJUYN0f05kxjKkGh8ULxXW5lqtpzszfBoN-Xtfji8oIhv9vRccou8zbWsrBEOjLdmo0rTMcvCMZxYlfgwwj9WhTkMxZjPQXRIllql_rFkKSHG62EwrEuQ-E69bA0inHgOQJ7ZBwMv0T0u6l4
y 12, 2023 10:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)
External Email - Use Caution
Hi there,
I am hoping to process some longitudinal data using the longitudinal recon-all
pipe
:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Jackson Lee
Sent: Wednesday, July 12, 2023 10:25 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)
External Email - Use Caution
Hi there,
,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Jackson Lee
Sent: Wednesday, July 12, 2023 10:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal pipeline for FreeSurfer (v7.3.2)
External Email - Use Caution
Hi there,
I am hoping to process
External Email - Use Caution
Hi there,
I am hoping to process some longitudinal data using the longitudinal recon-all
pipeline available in FreeSurfer:
https://secure-web.cisco.com/1Y9uqixBqGC2B0XHSMg2zr4QS96oUVSkkZcMdhRqdEkVD1KblmslkRndxPSvHW3LBNES_IqNsfYFPgJ0qwhvc1bNFhpnjhfJbHF
AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal Pipeline Issue
External Email - Use Caution
Hello Freesurfer Team
I'm attempting to create the base for the longitudinal scan process, as
described in the Longitudinal Tutorial (MailScanner has detected a poss
External Email - Use Caution
Hello Freesurfer Team
I'm attempting to create the base for the longitudinal scan process, as
described in the Longitudinal Tutorial
(https://secure-web.cisco.com/1nkZqRPPwsOtKx4RoeA_xG1zIjqnnyVHLQdZ7CBucl4swEGw2yu5tDAEYLYt1W_pGaY29BkceLzhHtS7kbWlwUZ
External Email - Use Caution
Hi Bruce,
Cool! Thank you so much.
Best wishes,
Hamied
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce R.,PHD
Sent: Tuesday, June 27, 2023 8:29 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal
.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Hamied Haroon
Sent: Tuesday, June 27, 2023 11:02 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal structural analysis in FreeSurfer ???
External Email - Use Caution
Thank you so much!
Where
list
Subject: Re: [Freesurfer] Longitudinal structural analysis in FreeSurfer ???
External Email - Use Caution
you can also use our longitudinal stream that improves sensitivity and
reliability. Run it after you have run the cross-sectional - it will improve
your results considerably
...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Tuesday, June 27, 2023 10:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal structural analysis in FreeSurfer ???
External Email - Use Caution
Hi Hamied,
I believe you can use mri_segstats (MailScanner has
AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal structural analysis in FreeSurfer ???
External Email - Use Caution
Hello,
I've run recon-all on patient T1s acquired at different timepoints after a
neurological insult, in FreeSurfer v7.3.2
I want to analys
External Email - Use Caution
Hello,
I've run recon-all on patient T1s acquired at different timepoints after a
neurological insult, in FreeSurfer v7.3.2
I want to analyse any change in the volume, surface area and average thickness
of specific regions across time in each patien
--reg tp1_FLAIRtoT1.lta --o tp1_flair_reg.mgz
--targ tp1_t1_reg.mgz
for time-point 1, etcetera.
Stefano
[Freesurfer] Longitudinal SAMSEG with multi-contrast
data<https://secure-web.cisco.com/1wqAljGN-HfqNgjoB_GLYISZdkqc0_9NrBWKfoyXxioxHK0i086v_G7kb-EdcMGoIPUAEHSdvP
External Email - Use Caution
Hi:
How can I generate "tp1_flair_reg.mgz" image appeared in command
"run_samseg_long --timepoint tp0_t1_reg.mgz tp0_flair_reg.mgz --timepoint
tp1_t1_reg.mgz tp1_flair_reg.mgz --timepoint tp2_t1_reg.mgz
tp2_flair_reg.mgz --output outputDir/" ?
Sin
External Email - Use Caution
Hello FreeSurfer devs,
I am attempting to run a Longitudinal TRACULA analysis on 3 timepoints per
subject using an HCP server. I have used the example dmrirc page
(https://secure-web.cisco.com/1JykEBcpM6vAD_4qy69NGW33wNc83B-TuXM37yVrgXaTHoNwBQkiBWLQw
: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Hemond, Christopher
Sent: Wednesday, March 29, 2023 2:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal processing of single time point data
External Email - Use Caution
Dear Freesurfer experts,
I am processing
External Email - Use Caution
Dear Freesurfer experts,
I am processing longitudinal data from subjects participating in a pre-post
analysis; a few subjects do not have follow-up data. I'd like to still include
these subjects and plan on using mixed effects analysis methods given
In theory you could, but you'd have to map the tp1 brainmask to tp2.
Note that it might not matter that much because the cross surfaces are
not used during the base creation. I would see how things look in the
base, then edit the brainmask in the base if needed. The base brainmask
will then be
External Email - Use Caution
Hello all,
I'm wondering if I can use brainmask or pial surface of timepoint1 as a
reference for the skullstrip of timepoint2. TP2 is being problematic during
skullstrip. I've tried -wsthresh and -gcut. Any option to use brainmask1 as a
reference poi
No, it does not matter.
On 11/16/2022 2:33 PM, Julie Ottoy wrote:
External Email - Use Caution
Hi FS team,
I just wanted to double check if, for the longitudinal pipeline, it
matters which time point is being read first? For example, in the
command below, should -tp -tp in the ord
External Email - Use Caution
Hi FS team,
I just wanted to double check if, for the longitudinal pipeline, it matters
which time point is being read first? For example, in the command below,
should -tp -tp in the order of the scans being acquired?
recon-all -base -tp -tp ...
messed things up, maybe.
Have a nice day!
Lauri
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lauri Tuominen
Sent: November-03-22 2:39 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal stream bug ?
CAUTION: External Mail. Do
External Email - Use Caution
Hi FreeSurfer Developers,
I am trying to run a longitudinal analysis on Ubuntu 20.04.1 LTS,
freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551, and Python 3.8.5.
I use the following command:
long_mris_slopes --qdec ../tables/long.all.table.dat \
External Email - Use Caution
One way we’ve seen recon-all eventually fail running on Linux hosted on Windows
is whatever is virtualizing Linux to run on top of the Windows OS - simply runs
out of memory at some point in the processing pipeline. That can result
in a message in t
You may be able to use one of the paired diff options in mris_preproc.
Run it with --help. I also put some info on it below. QDEC has been
deprecated
--paired-diff
After concatenating all the inputs together, create a new output file by
computing paired differences, ie, Input1-Input2, Input3
External Email - Use Caution
Hello Freesurfer developers,
I am interested in analyzing PET data following a longitudinal design.
I have co-registered each PET image to the closest MRI in time processed
through the longitudinal stream.
I have sampled each co-registered PET image t
Best,
Andrew
*From:* Greve, Douglas N.,Ph.D.
*Sent:* Wednesday, February 16, 2022 10:37 AM
*To:* Willett, Andrew Sunday ; Freesurfer
support list
*Subject:* Re: [Freesurfer] Longitudinal Stream Error
Does that file exist?
ps. Please remember to post to the list. Thanks!
?
Best,
Andrew
From: Greve, Douglas N.,Ph.D.
Sent: Wednesday, February 16, 2022 10:37 AM
To: Willett, Andrew Sunday ; Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal Stream Error
Does that file exist?
ps. Please remember to post to the list. Thanks!
On
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
h the community's conventions.
I am encountering errors when processing Freesurfer longitudinal
stream (Freesurfer v6.0). Cross-sectional streams proceeded and
completed without error, but base template creation and all following
longitudinal steps failed.
*I created a txt script for the bas
This is my first time seeking support here so I apologize if I am not familiar
with the community's conventions.
I am encountering errors when processing Freesurfer longitudinal stream
(Freesurfer v6.0). Cross-sectional streams proceeded and completed without
error, but base template cre
External Email - Use Caution
Good evening Martin,
Thank you for the quick reply and for the considerations.
Much appreciated,
Jacob
Message: 9
Date: Wed, 15 Dec 2021 06:55:48 +
From: "Reuter, Martin,Ph.D."
Subject: Re: [
Hi Jacob,
whenever there is is systematic difference, there is also potential for a bias.
In your specific situation no one knows how large this bias could be. I would
think it will not really be measurable, as the base is only used for
initialisation and within such a small time frame, the met
External Email - Use Caution
Dear Freesurfer friends,
It seems that prior messages* on longitudinal recon with missing timepoints
have suggested that it is okay for a subset of participants to include
different numbers of timepoints into the longitudinal pipeline, so long as
External Email - Use Caution
Dear FreeSurfer Team,
I am working with a longitudinal design (before and after treatment), and
based on the website's recommendation (
https://secure-web.cisco.com/1zrVKA2yLWZKJu8t_xqtLsDY49D7WzDkL9DDKJIkf-aD-ta0MoxVsjvpA3mU7AatuLy2HhTTrGBfLjCwCV1vfWz
External Email - Use Caution
Hello FreeSurfer developers,
I have created the "subjects" folder, and I included a large sample of
participants inside the folder.
I have performed transversal analysis (CROSS), all successfully.
I am now performing a longitudinal analysis with the
Dear Walker,
We currently don’t have a longitudinal pipeline for the hypothalamic subunits.
We are currently working on a longitudinal version for our deep learning
segmentation tools, but we don’t have anything available yet.
You can always run the module on the timepoints independently for no
I see that generating the hippocampal subfields in the longitudinal pipeline
has its own script (segmentHA_T1_long.sh), but am not seeing a corresponding
script or command to do the same for the hypothalamic subunits. Would simply
running mri_segment_hypothalamic_subunits on my subject_session
On 8/11/2021 1:17 PM, Erik O'Hanlon wrote:
External Email - Use Caution
External Email - Use Caution
Dear FS experts,
I have run the longitudinal pipeline on a dataset with three
timepoints. I am particularly interested in the longitudinal
hippocampal and amygdala data and
External Email - Use Caution
Dear FS experts,
I have run the longitudinal pipeline on a dataset with three timepoints. I am
particularly interested in the longitudinal hippocampal and amygdala data and
want to run LME on these.
I've made the qdec table with the id age, sex and t
Try running it without the -parallel flag. If you want to use multiple
cores, then add -threads N (N= number of cores)
On 7/6/2021 4:29 AM, Susanne Gellißen wrote:
External Email - Use Caution
Dear FreeSurfer Developers,
I am processing MRI data using the freesurfer processing stream w
External Email - Use Caution
Many thanks.
Best regards
On Thu, Jun 24, 2021, 10:07 Douglas N. Greve wrote:
> If you are going to compare the volume across subject, then it does need
> to be corrected with eTIV
>
> On 6/15/2021 8:06 AM, AJ wrote:
>
> External Email - Use
If you are going to compare the volume across subject, then it does need
to be corrected with eTIV
On 6/15/2021 8:06 AM, AJ wrote:
External Email - Use Caution
Hi,
After running longitudinal processing and creating base and long runs,
When looking at volumes of various structures ov
External Email - Use Caution
Hi,
After running longitudinal processing and creating base and long runs, When
looking at volumes of various structures over time of the same subject, are
the volumes not need to be corrected by eTIV since head size does not vary
overtime?
Many thank
External Email - Use Caution
Hello FreeSurfer developers,
I am trying to apply longitudinal processing on T1w MRI data for two
timepoints (~8 months between the two TP) in adolescents in order to
perform vertex-based analyses.
I am following the online tutorial here for the prepro
Date: Tuesday, March 23, 2021 at 07:31
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] longitudinal hippocampal subfield
External Email - Use Caution
Dear Freesurfer team,
I'm studying in longitudinal hippocampal changes. Currently I have output from
recon-all
External Email - Use Caution
Dear Freesurfer team,
I'm studying in longitudinal hippocampal changes. Currently I have output from
recon-all with T1 and T2-FLAIR across each subject for each time point and
output from the longitudinal pipeline for each subject.
Now, I want to run
External Email - Use Caution
Thanks a lot Martin.
Regards
Suzan
On Thu, 18 Mar 2021 at 9:09 pm, Reuter, Martin,Ph.D. <
mreu...@mgh.harvard.edu> wrote:
>
> Hi Suzan,
>
> actually it uses rigid within-subject registration.
> The transformation files should be in ./mri/transforms (i
Hi Suzan,
actually it uses rigid within-subject registration.
The transformation files should be in ./mri/transforms (in long and in base).
Best, Martin
On 17. Mar 2021, at 23:05, Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:
Where is the non-linear registration coming from? Our lo
Where is the non-linear registration coming from? Our long stream uses
affine.
On 3/11/2021 2:59 PM, Suzan Maleki wrote:
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Hi FS experts,
I appreciate it if you help me with a question on your
longitudinal processing pipeline. If I use FreeSurfer to genera
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Hi FS experts,
I appreciate it if you help me with a question on your
longitudinal processing pipeline. If I use FreeSurfer to generate an
unbiased T1 image template from N time points (non-linear registration),
then how can I apply the within subject
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Thank you very much Douglas.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology
Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las U
On 2/26/2021 9:41 AM, Agurne Sampedro Calvete wrote:
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Dear Douglas,
And is there a recommended way to compute a z value from the cluster
p-value?
You can use a p-to-z conversion; I'/m not sure it means much though
With voxel-wise measure of z value, do y
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Dear Douglas,
And is there a recommended way to compute a z value from the cluster
p-value?
With voxel-wise measure of z value, do you mean a z value of a particular
voxel, for instance, the voxel with the maximum p value in a cluster?
Thank you very
There is no z value for the cluster itself, but you could take the
cluster p-value and use it to compute a z value. Or do you want a
voxel-wise measure of z value?
On 2/24/2021 4:00 AM, Agurne Sampedro Calvete wrote:
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Dear Freesurfer experts,
In relation
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Dear Freesurfer experts,
In relation to the previous question, could I obtain a Z value of the
significant cluster obtained by opening in freeview the z.mgh and place the
cursor on the point with the highest value? Is there another way to obtain
a Z v
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Hi Vittal,
please see my response from Nov 30th on this list.
Best,
Kersten.
Am 04.12.2020 um 08:16 schrieb vittal korann
mailto:vittalkor...@gmail.com>>:
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Dear FreeSurfer experts
This is just a gentle remind
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Dear FreeSurfer experts
This is just a gentle reminder of my previous mail.
Diers Kersten has replied to my query. He asked me to send a few details
pertaining to my issue.
I shared all the necessary details with you people and waiting for your
respons
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Hello VIttal,
thanks for the info about the design.
You wrote before that the Matlab variable X (i.e., the design matrix) has a
dimension of 47x6. X is a translation of the study design into a numerical
matrix, which is part of the statistical model
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No problem, thanks!
So I shall send an email only to freesurfer or would it fine if I put you
in cc?
With regards
Vittal
On Mon, Nov 30, 2020 at 4:25 PM Diers, Kersten /DZNE
wrote:
> Hi Vittal,
>
> Sorry, I can only help on the public freesurfer l
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