Re: [Freesurfer] eddy_correct with DTI {Disarmed}

[Wei Shao]

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Hi,  Douglas

Sorry to bother you again, do you think the problem is the old version of
FSL?

Best,
Wei

On Fri, Nov 13, 2020 at 1:32 PM Wei Shao 
wrote:

> Hi Douglas
>
> I think it's 5.0.11
>
> [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0
> To initialize FreeSurfer,
> do (sh, ash, ksh, and bash)
>   source $EBROOTFREESURFER/FreeSurferEnv.sh
> or (csh, tcsh)
>   $EBROOTFREESURFER/FreeSurferEnv.csh
>
> [weishao@gra-login2 ~]$ module load fsl
> [weishao@gra-login2 ~]$ which fsl
> /cvmfs/
> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/fsl
> [weishao@gra-login2 ~]$
>
> Best,
> Wei
>
> On Fri, Nov 13, 2020 at 10:11 AM Douglas N. Greve 
> wrote:
>
>> What version of FSL are you using?
>>
>> On 11/10/2020 12:19 AM, Wei Shao wrote:
>>
>> External Email - Use Caution
>> Hi, Freesurfer team,
>>
>> My name is Weishao, Here is a problem that bothers me a lot I try to run
>> DTI. I have loaded the FSL module and use the most recent version of
>> Freesurfer. it's appreciated if someone can help. Thanks.
>>
>> Here is the script.
>>
>> dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval
>> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec
>> --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
>> --s /home/weishao/scratch/rawdata/sub-AVP6176/
>> --o /home/weishao/scratch/rawdata/sub-AVP6176/
>>
>> Here is feedback
>>
>> -rw-r- 1 weishao weishao 49041968 Sep  9 11:41
>> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
>> INFO: SUBJECTS_DIR is
>> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects
>> dt_recon logfile
>> Tue Oct 27 16:19:28 EDT 2020
>> VERSION dt_recon 7.1.0
>> setenv SUBJECTS_DIR
>> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects
>> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi
>> /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon
>> --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval
>> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i
>> sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s
>> /home/weishao/scratch/rawdata/sub-AVP6176/ --o
>> /home/weishao/scratch/rawdata/sub-AVP6176/
>> gra95
>> weishao
>> /cvmfs/*MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct
>> 
>> ECRefTP 0
>> #@#---
>> Converting input
>> Tue Oct 27 16:19:28 EDT 2020
>> cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi
>> mri_convert
>> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
>> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
>> mri_convert
>> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz
>> /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
>> reading from
>> /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz...
>> TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.999608, 0.017447, -0.021891)
>> j_ras = (0.0104682, 0.958258, 0.285714)
>> k_ras = (-0.0259621, -0.285373, 0.958065)
>> writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz...
>>
>>
>> #@#---
>> Eddy/Motion Correct
>> Tue Oct 27 16:19:44 EDT 2020
>> cd /scratch/weishao/rawdata/sub-AVP6176/ectmp
>> eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz
>> /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0
>> /cvmfs/*MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct
>> :
>> line 95: /cvmfs/*MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob
>> 

Re: [Freesurfer] License error on Windows Subsystem for Linux

[Hoopes, Andrew]

Hi Lunhao,

Interesting. Can you provide some details on the configurations where this 
worked? Were you using the same linux subsystem and windows versions?

thanks
Andrew

From:  on behalf of Shen Lunhao 

Reply-To: FS Help 
Date: Friday, November 20, 2020 at 2:44 AM
To: FS Help 
Subject: [Freesurfer] License error on Windows Subsystem for Linux


External Email - Use Caution

Hello FreeSurfer Developers,



I'm attempting to use freesurfer 5.3.0 on Windows Subsystem for Linux (Ubuntu 
20.04), but I got license error message as described below:



--

ERROR: Invalid FreeSurfer license key found in license file 
/space/tools/freesurfer/5.3.0/license.txt

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.

--



I tried with the same 5.3.0 packages and same license file on four different 
computers, and two of them work well with the other two got similar license 
error. Does anyone have any thoughts on how to trouble-shoot this one?



1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2) Platform: Windows Subsystem for Linux (Ubuntu 20.04)

3) uname -a: Linux DESKTOP-SJ2K1B2 4.4.0-19041-Microsoft #488-Microsoft Mon Sep 
01 13:43:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux


Best,
Lunhao

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[Freesurfer] PETSurfer

[Boris Rauchmann]

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Dear all,

How can I easily scale the mgx.ctxgm.nii.gz files with the whole brain mean
intensity using PETSufer? Is there a command to use in mri_gtmpvc like
--rescale X?
I know that I can find the mean in  global.gm.dat and I can use that value
for scaling the atlas based results in gtm.stats.dat but how can I easily
scale the image?

Thanks,
Boris
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Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Fischl, Bruce]

Hi Stephanie

I see. Yes, I guess this is ok, you just want to be careful when tossing 
datasets that you aren’t biasing your results. Always better to look at them if 
you can. Big errors are pretty obvious and can be found quite rapidly (e.g. by 
zipping through a bunch of snapshots with nmovie_qt)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Stephanie K
Sent: Friday, November 20, 2020 6:25 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

No, I don’t think that you’ve misunderstood. I was asking about cohorts that 
had not been visually inspected in my first message and then in my last message 
I wanted to check that I didn’t need to also remove people from visually 
inspected data based on statistical outliers (as a further step). In 
conclusion, from what I’ve understood: if there is no visual inspection of 
data, it is best to remove statistical outliers (based on standard deviations) 
even for global measures such estimated intracranial volume, mean thickness 
from left and right hemispheres. When data is visually inspected, there is no 
need to remove any data based on statistical outliers even if those exist as 
these should be good quality.  For the visual inspected data, I have kept all 
participants (which have an acceptable cortical surface reconstruction rating)  
for the regional variables and I also retained all participants for global 
measures (thickness of mean hemisphere, estimated intracranial volume) as the 
data had been processed and removed from further Freesurfer processing if they 
had severe artifacts or irregularities.

Many thanks for your advice.

On Thursday, November 19, 2020, Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

Sorry, I think I misunderstood. If you have visually inspected the analysis 
results and think that they are accurate then you definitely should leave those 
subjects in

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 4:19 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed}


External Email - Use Caution
Hi Bruce,

Is it also necessary to remove outliers (eg. 3 SD from the mean) for  
Freesurfer structural measures of MRI images that have been visually inspected 
as a further data cleaning step?

I really appreciate your help.

Thanks

On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>> wrote:
Hi Stephanie

I think that is always a  good idea, unless for some reason it isn’t possible

Cheers
Bruce

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Stephanie K
Sent: Thursday, November 19, 2020 2:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Mean thickness estimation


External Email - Use Caution
Hi Bruce,

Thanks for the prompt reply. It is my understanding that l_thickness, 
r_thickness and estimated intracranial volume are accurately measured. Would I 
still need to identify and remove outliers if visual inspection of the images 
has not been done?

Many thanks,
Stephanie

On Wed, Nov 18, 2020 at 5:24 PM Stephanie K 
mailto:rklin...@gmail.com>> wrote:
Hi,
I want to estimate the mean cortical thickness. For this I have summed the 
thickness across all 34 regions mapped to the Desikan-Killiany atlas. However, 
I also have the average mean thickness of left and right hemispheres (direct 
output variables of Freesurfer). As there is no visual inspection of the 
imaging in the particular cohort, I remove measures that are 3 standard 
deviations above or below the mean. Hence, I may expect more outliers to be 
removed when I take the average across the regions. I am using these brain 
measures as outcomes in association analyses with the genetic score as the 
exposure. For the mean thickness (averaged across the left and right hemisphere 
thickness variables of freesurfer after removing outliers), the regression 
coefficients have a smaller standard deviation than with thickness averaged 
across the 34 regions. I’m not sure which one to use - which one is more 
accurate? When I look at the mean thickness (which I derived using 34 regions) 
and it’s standard deviation, it is similar to that of the average mean 
thickness across the two hemispheres as well as the standard deviation of that. 
Can you suggest what is most accurate please and what the difference is between 
the mean thickness across the two hemispheres obtained from freesurfer and 
those calculated across the regions? Why does one result in more precision than 
in the other?

Thank you!

[Freesurfer] Time required to run permutations

[Basavaraju, Rakshathi]

External Email - Use Caution

Dear FS team,

Does anyone have any idea how long does the permutation computation to handle 
multiple comparisons take on a surface based analysis? The command is given 
below:

mri_glmfit-sim --glmdir rh.project.glmdir --perm 1000 3 abs --cwp  0.05 
--2spaces --bg 1

Its seems like going on forever, saying
Poll2 Job1..
Poll3 Job1.

I guessed it might stop at 1000 but its going on and on.

Any help on this would be greatly appreciated.

Thanks,
Rakshathi
Post-doc, Columbia.
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[Freesurfer] PETSURFER for AV1451

[Shane Schofield]

External Email - Use Caution

Hi PETSURFERs, 
A quick question to the group: Does any one have experience using PETSURFER on 
dynamic AV1451 scans? How can I know whether the MRTM1 or MRTM2 using midbrains 
(due to off target AV1451 binding) is suitable for my data? 
Thank you!
Best Wishes,Shane
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Re: [Freesurfer] Mean thickness estimation {Disarmed}

[Stephanie K]

External Email - Use Caution

Hi Bruce,

No, I don’t think that you’ve misunderstood. I was asking about cohorts
that had not been visually inspected in my first message and then in my
last message I wanted to check that I didn’t need to also remove people
from visually inspected data based on statistical outliers (as a further
step). In conclusion, from what I’ve understood: if there is no visual
inspection of data, it is best to remove statistical outliers (based on
standard deviations) even for global measures such estimated intracranial
volume, mean thickness from left and right hemispheres. When data is
visually inspected, there is no need to remove any data based on
statistical outliers even if those exist as these should be good quality.
For the visual inspected data, I have kept all participants (which have an
acceptable cortical surface reconstruction rating)  for the regional
variables and I also retained all participants for global measures
(thickness of mean hemisphere, estimated intracranial volume) as the data
had been processed and removed from further Freesurfer processing if they
had severe artifacts or irregularities.

Many thanks for your advice.

On Thursday, November 19, 2020, Fischl, Bruce 
wrote:

> Hi Stephanie
>
>
>
> Sorry, I think I misunderstood. If you have visually inspected the
> analysis results and think that they are accurate then you definitely
> should leave those subjects in
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 4:19 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Mean thickness estimation {Disarmed}
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Is it also necessary to remove outliers (eg. 3 SD from the mean)
> for  Freesurfer structural measures of MRI images that have been visually
> inspected as a further data cleaning step?
>
>
>
> I really appreciate your help.
>
>
>
> Thanks
>
>
>
> On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce 
> wrote:
>
> Hi Stephanie
>
>
>
> I think that is always a  good idea, unless for some reason it isn’t
> possible
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K
> *Sent:* Thursday, November 19, 2020 2:14 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Mean thickness estimation
>
>
>
> *External Email - Use Caution*
>
> Hi Bruce,
>
>
>
> Thanks for the prompt reply. It is my understanding that l_thickness,
> r_thickness and estimated intracranial volume are accurately measured.
> Would I still need to identify and remove outliers if visual inspection of
> the images has not been done?
>
>
>
> Many thanks,
>
> Stephanie
>
>
>
> On Wed, Nov 18, 2020 at 5:24 PM Stephanie K  wrote:
>
> Hi,
>
> I want to estimate the mean cortical thickness. For this I have summed the
> thickness across all 34 regions mapped to the Desikan-Killiany atlas.
> However, I also have the average mean thickness of left and right
> hemispheres (direct output variables of Freesurfer). As there is no visual
> inspection of the imaging in the particular cohort, I remove measures that
> are 3 standard deviations above or below the mean. Hence, I may expect more
> outliers to be removed when I take the average across the regions. I am
> using these brain measures as outcomes in association analyses with the
> genetic score as the exposure. For the mean thickness (averaged across the
> left and right hemisphere thickness variables of freesurfer after removing
> outliers), the regression coefficients have a smaller standard deviation
> than with thickness averaged across the 34 regions. I’m not sure which one
> to use - which one is more accurate? When I look at the mean thickness
> (which I derived using 34 regions) and it’s standard deviation, it is
> similar to that of the average mean thickness across the two hemispheres as
> well as the standard deviation of that. Can you suggest what is most
> accurate please and what the difference is between the mean thickness
> across the two hemispheres obtained from freesurfer and those calculated
> across the regions? Why does one result in more precision than in the other?
>
>
>
> Thank you!
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
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> 

[Freesurfer] Fwd: Error in longitudinal pipeline {Disarmed}

[vittal korann]

External Email - Use Caution

Hi FreeSurfer experts

Recently I started working on the longitudinal data.
I followed the pipeline described in the below link.
Also, I attached my longitudinal table along with freesurfer data.

https://secure-web.cisco.com/10GeKQWbNwmdQQgtn3lkt2V_V6CbZVv7dzOuHKANAfbzRAGomTtlFNhDzA4pY4ZQuLB5OKutRoWZmuTIiRZq8s8dHrF_8jP9_YwiAcYhWc2_nJ1F7j6KtRcLuBUeRd8AEwLty9yAMeJlyYLagWgXBRfs9aYywbcF4h7qbXbfe1Fp6tkTjAhKB7KqEvstqt7f-PV9c2yCvmZdmgnQTe8ZOr5036aKU2v0XgzyYpMep8-97LMopdyYsudhNkLZFuWdv82PEMhJPNLAupP3KrdD04Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels

I got the error while executing the following commands:

CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];

F_lhstats = lme_mass_F(lhstats,CM);

And the Matlab threw an error shown below

>> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1]
> zeros(3,5)];
> >> F_lhstats = lme_mass_F(lhstats,CM);
> Error using lme_mass_F (line 50)
> The number of colums in the contrast matrix CM(1).C is different from the
> corresponding number of fixed effects in stats(1).Bhat


Any help would be appreciated!

With regards
Korann


long.qdec.table.dat.xlsx
Description: MS-Excel 2007 spreadsheet
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Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}

[vittal korann]

External Email - Use Caution

Dear FreeSurfer experts

Just a gentle reminder!
Please do help me to resolve this issue.

With regards
Korann


On Thu, Nov 19, 2020 at 11:54 AM vittal korann 
wrote:

> Dear FreeSurfer experts
>
> This is just a gentle reminder for my query!
> Looking forward to your assistance to resolve the issue.
>
> With regards
> Korann
>
>
> On Tue, Nov 17, 2020 at 1:16 PM vittal korann 
> wrote:
>
>> Hi FreeSurfer experts
>>
>> Recently I started working on the longitudinal data.
>> I followed the pipeline described in the below link.
>> Also, I attached my longitudinal table along with freesurfer data.
>>
>> https://secure-web.cisco.com/1j5IcVQoFutbCXJneW93GE9fueCcZW2QGzUvawnDwu3h_aP7n-Ql_FI7YUupSLhPt3kcF0gGCZdqliXC3LKC4onVM49piES35-4byG-ZbBh7At-UsYZTFWlgqG2Iu_lIjPMnCQm74Tweya37USYVZCoPG99y8EYWsqeLqL_w3x0MLw1Dsy9vGEVExekmgKMRPg8mXrhAuemCFf9moa49hAnMp1KeoaWUMZjCLwRgdowGZYPkKCQ76qf6sRyfcdBnGE-gYl7s16aQfF0enFhCEhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels
>>
>> I got the error while executing the following commands:
>>
>> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];
>>
>> F_lhstats = lme_mass_F(lhstats,CM);
>>
>> And the Matlab threw an error shown below
>>
>> >> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1]
>>> zeros(3,5)];
>>> >> F_lhstats = lme_mass_F(lhstats,CM);
>>> Error using lme_mass_F (line 50)
>>> The number of colums in the contrast matrix CM(1).C is different from
>>> the corresponding number of fixed effects in stats(1).Bhat
>>
>>
>> Any help would be appreciated!
>>
>> With regards
>> Korann
>>
>>
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