[Freesurfer] Incorporating hi-res T2w image in longitudinal pipeline

[Raikes, Adam C - (adamraikes)]

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Good afternoon,

We are collecting hi-resolution T1w and T2w images (0.8mm3) in a pre-/post- 
design. I am using Freesurfer 7.4.1 to process the data and have been 
successful in ingressing the T2w images in the cross-sectional recon-all runs 
with -T2  and -T2pial.

Two questions:

  1.
When creating the base image, is there any value to using the T2s and, if so, 
is there a way to do that?
  2.
When running the -long step, I know that -T2pial is an option but do I need to 
pass -T2  with it? If I need the path, should it point to the original 
image or something from the cross/mri folder?

Thanks


Adam C. Raikes, PhD

Imaging Projects Manager

Center for Innovation in Brain Science

University of Arizona


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Re: [Freesurfer] outcome directions of longitudinal two stage model

[L]

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Yes, I was wrong in considering tp1 - tp2 or tp2 - tp1. Actually, my
question is: If the changing rate or % in thickness of a region calculated
using long_mris_slopes is a positive number, does that mean it's an
increase in thickness from baseline (or tp1)?

Thank you,

Lihong

On Wed, May 8, 2024 at 9:35 AM Douglas N. Greve 
wrote:

> not sure what you mean and/or referring to. can  you elaborate?
>
> On 5/7/2024 4:03 PM, L wrote:
>
> External Email - Use Caution
>
> Dear exports,
>
> I am wondering whether the outcomes of the longitudinal two stage model is
> tp1 - tp2 or tp2 - tp1.
>
> Thank you,
>
> Lihong Wang
>
> --
> - Lihong
>
>
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>  .
>


-- 
- Lihong
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Re: [Freesurfer] surface and cortical thickness normalization

[Douglas N. Greve]

The reason I suggested scaling by eTIV is an analogy with a box of 
paper. The surface area of the paper in the box scales linearly with the 
volume in the box (twice the volume, twice the paper, twice the area). I 
vaguely remember doing a test of this, but, if I did, it has been a 
while. probably using eTIV^(2/3) works well too. I don't think it is so 
important that it be unitless (though maybe it is easier at review time).


On 5/3/2024 10:56 AM, Fischl, Bruce R.,PHD wrote:


Hi Yunus

I think typically you would normalize by eTIV^(2/3), which would 
result in a dimensionless scaling


Cheers

Bruce

*From:*freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *yunus soleymani

*Sent:* Friday, May 3, 2024 3:31 AM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] surface and cortical thickness normalization

*External Email - Use Caution *

Hello,

I hope you are doing well. Yesterday, I had some questions regarding 
normalization in Freesurfer. Thanks to Dr. Douglas N. Greve, I 
received answers for all of them. However, I still have one more 
question.


When I normalize brain surfaces to eTIV, they appear to be in two 
different units (mm2 and mm3). Will this be a problem? Additionally, I 
would like to know your thoughts on normalizing cortical thicknesses. 
Do you think they should be normalized to eTIV, or would it be better 
to normalize them to the mean cortical thickness of each subject?


I would greatly appreciate your response.

Thank you,
Yunus


*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
*/Tehran University of Medical Sciences/*
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+98 914 526 9298


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Re: [Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

[Douglas N. Greve]

They are not identical, for  sure. In general, I discourage people from 
modeling categorical variables (eg, Group1/2 below) as continuous 
variables because you make assumptions that might not be reasonable (eg, 
females will have twice the thickness as males). I would use the first 
method.


On 5/2/2024 8:20 PM, Lydia Chung wrote:


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Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which 
regions show differences in cortical thickness between group 1 and 
group 2) and 2) interaction effects (does the relationship between IV 
and DV depend on moderator). Depending on the model, the IV is 
sometimes a binary categorical variable and sometimes a continuous 
variable. The moderator is always continuous. So, interaction effects 
are either continuous x continuous OR categorical x continuous.


One thing I'm trying to understand is whether the two examples below 
are basically two different approaches that answer the SAME question: 
Do people in Group 1 differ from Group 2 on cortical thickness? 
Version 1 is the one provided by FS and Version 2 is an analog of 
another setup I have been provided by colleagues. Are these models 
answering the same or different questions? The freesurfer link below 
also shows an example of how to do an interaction (Group x Age) using 
Version 1 setup; for Version 2 setup of an interaction, I know I would 
multiply the IV and Moderator before this step so that I would have an 
additional "interaction variable" column to add as one of the 
'Variables' listed in the fsgd code.  So, I'm also curious if the two 
different methods of testing an interaction (in addition to the first 
question about the main effect) will get you the identical answer OR 
if there is something conceptually different? Do the nuances of this 
setup have to do with the difference between using DODS or DOSS?


_
_
_Main effect of Group on cortical thickness Version 1 (copied from FS 
example. link here 
)_

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like 
an anova approach?)


_Main effect of Group on cortical thickness Version 2_
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a 
linear regression approach?)


Thank you in advance for your help!

Lydia
--


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 

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Re: [Freesurfer] outcome directions of longitudinal two stage model

[Douglas N. Greve]

not sure what you mean and/or referring to. can  you elaborate?

On 5/7/2024 4:03 PM, L wrote:


External Email - Use Caution


Dear exports,

I am wondering whether the outcomes of the longitudinal two stage 
model is tp1 - tp2 or tp2 - tp1.


Thank you,

Lihong Wang

--
- Lihong


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Re: [Freesurfer] recon-all process still not finishing properly

[Douglas N. Greve]

It should just run the fill step. However, I've been slowly 
reprogramming recon-all to just see what needs to be run and rerun it, 
so you might get more than just the fill.


On 5/3/2024 4:38 PM, Dong, Yilei wrote:


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Hi Freesurfer Developers,

Just to reply to this thread again, if I want to see if recon-all will 
just run the -fill step, do I submit it on the files that have already 
been run? In addition, does this error count as Freesurfer running out 
of RAM or it's more of a cluster issue I have to talk with the staff 
that manage it?


Sincerely,
Yilei

*From:* Dong, Yilei 
*Sent:* Tuesday, April 23, 2024 3:34 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly

Hi Freesurfer support,

I have several questions regarding recon-all -fill and -debug.

If we run recon-all -fill, what is the command set-up for that? From 
the ReconAllDevTable here, *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable 
, 
do we structure the recon-all command to be: recon-all -autorecon2 
-fill -subjid ? I attempted to run recon-all -fill with -debug 
with the structure as follows: recon-all -s $subject -i $1 -fill 
-debug and I was wondering if this was the wrong format. I have also 
attached our recon-all-slurm-apr19.sb cluster submission file for 
reference.


Does recon-all -fill only run the fill step, while ignoring the 
previous steps before that or does recon-all run through all the 
initial steps including the -fill step ideally?


Regarding recon-all -debug, does the stdout file have the huge amounts 
of text specifying what each line is doing? I have included .out and 
.err files from the same recon-all -fill with -debug command for 
reference.


Sincerely,
Yilei

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Thursday, April 18, 2024 2:57 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] recon-all process still not finishing 
properly
not sure what is happening. You can run recon-all with -debug and 
capture the output (both stdout and stderr) into a file. This will 
cause it to print out huge amounts of text specifying what it is doing 
on each line. You should also see if there is some stderr output that 
is not being caught. You can try running recon-all -fill on the 
subject that you created to see if the fill will run at all (this may 
be easier than waiting 4 hours).


On 4/8/2024 3:18 PM, Dong, Yilei wrote:


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Hi Freesurfer Support,

The past few weeks, I've emailed about my recon-all processing stream 
never completely finishing.
We are still encountering the same problem. For context, our 
recon-all job submission script runs recon-all for 1 image. Given a 
folder of 100 MRI images, we have another script that calls upon the 
recon-all script for each image within the folder via a for loop. The 
result is 100 jobs running in parallel on the cluster.


I have attached a screenshot of the parameters we set whenever we 
submit each recon-all job for each image by SLURM to UCSD's cluster. 
The maximum time we are allowed for each job is 48 hours. Our jobs 
are shared-node jobs, which means we run more than 1 job on a single 
node. This time, we increased RAM from 8GB to 16GB in hopes the 
entire recon-all processing stream can fully run through for each 
image, but it still stops at "mri_pretess done" and does not go on to 
the -fill step. Each job submitted to the cluster took around 4 hours 
and 20 minutes each to run in our most recent attempt.


If increasing the RAM did not change anything for us, how else can we 
get more verbose error messages? What other reasons could be why our 
recon-all aborts before finishing? I have attached a recon-all.log 
from one of our subjects for reference and a screenshot of the 
parameters we set for submitting jobs in our cluster for reference.



Freesurfer version: 7.2.0, but already available as module on UCSD's 
cluster system


Platform: Rocky Linux release 8.8 (Green Obsidian)

uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 
28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux


Recon-all log: see attached


Thank you!


Sincerely,

Yilei

Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

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Hi Kersten,

If that's alright with you then that would be great. I completely accept if
my threshold is accurate and leaves no significant findings, I just can't
find a comparable threshold on this forum or elsewhere with such an
elevated threshold value.

I can touch base next week to see what you need from me.

Thanks again,

Dan

On Tue, May 7, 2024 at 3:09 PM Diers, Kersten /DZNE 
wrote:

> Hi Dan,
>
> I can see no obvious issues at the moment, but am happy to take a closer
> look when I am back in office next week.
>
> The fslmer tool ist just an R Implementation of the Matlab scripts, so I
> don't see any need to use them in your case.
>
> Best,
>
> Kersten
>
> Gesendet von Outlook für Android 
> 
>
> --
> *Von:* Dan Levitas 
> *Gesendet:* Dienstag, Mai 7, 2024 7:11:58 PM
> *An:* djlevitas...@gmail.com 
> *Cc:* kersten.di...@dzne.de ;
> mreu...@mgh.harvard.edu ;
> freesurfer@nmr.mgh.harvard.edu 
> *Betreff:* Re: [Freesurfer] Lingering questions for Longitudinal
> spatiotemporal LME analysis
>
> CAUTION: This email originated from outside of DZNE. Do not click links
> or open attachments unless you recognize the sender and know the content is
> safe.
> ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim
> Anklicken von Links oder Öffnen von Anhängen
>
> Hi Kersten & Martin,
>
> I just wanted to ping this thread again, as I'm still unsure about my pcor
> value (4.4) that I'm getting. I've seen other posts where the threshold
> (thmin) value specified in functions such as *mri_surfcluster* are around
> 2 (corresponding to a p-value of 0.01) when threshold *sig.mgh file(s).
> Given that I'm interested in both right and left hemispheres, I'm surprised
> that my single threshold value to account for both hemispheres is so high
> relative to others posts I've come across in the forum. I seem to have
> followed the LME approach correctly (
> https://secure-web.cisco.com/1SQ58WEznZe-ibw3QO19omrHSeej1iX-z28jkMlUtsQ61ntFqO78Z5WsmZPKSefBlApX7ijnNUsVb2PiYTMcLSHgq5Hf73E1qeczBabjq91RDS_J8NHpKFXZcedng6CSw5Dslno59UqFqwqKe0MlynvG0fLgW9CmBvYVyJOMfjqOkUnj-mZQrmtPHn6QGW9EgT6h77RTNNDYi3JzDqC5D-8yvOGOGy_rD2YAqFsyCnmAEdNhiGyU9zP2ii1jchj6eNZzKhgEp6ddY9VNl7yxVdP8JVkPxnFrj87WLBBrvjJrY7zXnrji5tdpZjvFiwVJQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels)
>  but
> I'm unsure if I've done something that has resulted in an elevated pcor
> value.
>
> Martin had recommended the *fslmer* tool (
> https://secure-web.cisco.com/1k8MMiLU-B44BypnewP6obBaoWvRatpcAdkGjbKYO0VGEedf5voupfVkhQXTbs8FThmGd4k5YzTCjcadNDPYbJvVhxCb-iyEmORVnucke7TNUZJKLtAvZmqGquU-VGxTC1N3bTuFZox3yd6f3tKd1Rk37nNQ7paxYwYXE-abGIb4qGHlxAecu3On7dDBTVotVlBChle8YVCs1qrJSKBkOe9Szvup6SomFsZzegV5ZSHpBJnVpNgH6vZYwY_Si4OOvW2M1ZhCLPfN_3zy75ccIM-x39bDlZKH9EWWAEIqYmvpVs6mp4CuDMHgJdI5t19o9rFDy-P4Gw8E3bHc8IJLjSA/https%3A%2F%2Fgithub.com%2Fdeep-mi%2Ffslmer),
>  I'd be happy to use that instead if
> it's more current and the preferred tool for this kind of analysis.
>
> Thanks again,
>
> Dan
>
>
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