Re: [Freesurfer] Longitudinal pipeline {Disarmed}

2020-12-03 Thread vittal korann 
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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
response.

Below is the link where I wrote about my query regarding the longitudinal
analysis.
Looking forward to your assistance!

Thanks,
Vittal

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> Today's Topics:
>1. Re: License error on Windows Subsystem for Linux (Shen Lunhao)
>2. smooth longitudinal analysis {Disarmed} (Agurne Sampedro Calvete)
>3. Re: Error in longitudinal pipeline {Disarmed}
>   (Diers, Kersten /DZNE)
>4. Smoothing GWC mgh data (Valentina Meregalli)
>
> --
> Message: 1
> Date: Mon, 23 Nov 2020 06:26:28 +
> From: Shen Lunhao 
> Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux
> To: Freesurfer support list 
> Message-ID:
> <
> dm6pr02mb6493eb25230b280b7dcff288db...@dm6pr02mb6493.namprd02.prod.outlook.com
> >
> Content-Type: text/plain; charset="gb2312"
> External Email - Use Caution
> Hi Andrew,
> The following is the information of four systems. System #3 and #4 are
> same configuration where license error occurred.
> #1  #2  #3  #4
> CoreIntel(R) Xeon(R) CPU E5-2620Intel i7AMD R9 5900X
> AMD R9 5900X
> Mem 32GB16GB32GB32GB
> PlatformLinux version 4.15.0-112-generic (buildd@lcy01-amd64-027)
> (gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)) Window subsystem for
> linux(WSL2) + Ubuntu20.04  Window subsystem for linux(WSL2) + Ubuntu20.04
> Window subsystem for linux(WSL2) + Ubuntu20.04
> Worked  Worked  Didn?t work Didn?t work
> The freesurfer package I used is
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0which downloaded from
> freesurfer website. The license file was four lines type. Hope this
> information is helpful.
> Thanks,
> Lunhao
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> ?? Hoopes, Andrew <
> ahoo...@mgh.harvard.edu>
> Date: 2020?11?21? 1:19
> Reply-To: Freesurfer support list 
> Subject: Re: [Freesurfer] License error on Windows Subsystem for Linux
>
> 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 <
> lunhao0...@hotmail.com>
> 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://secure-web.cisco.com/1gwoaE20Y7b27ULq16GgvwkvDuYOzRdARFYzw1XJCoskz3-oj6huJndWIuxVbk0yVCvgdNi0Oj7GVdtZArfy5iumc2YeEOL6EISaDDZGWxaxL72Jxeq5-rM4PosrAs61L--DGrGQ-qb6mJmz6fxO60OjBUnCaZo11TNmUIUXHBpMTl4hR5bCGLuyCBsEOIcsOAMKVpo5pMFchOkNgp8Uz33jMejFvHUvBttqS1GYSr4rTD6rFCPd5-FxiOBOmu03bHcOZxB8Piql-cfJGw_9i9Q/http%3A%2F%2Fsurfer.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:

Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

2020-12-03 Thread Fischl, Bruce 
Make sure it looks reasonable (that there is a brain in there, and the 
intensities look ok). You can send it to us if you want

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 10:27 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation


External Email - Use Caution
Hi,

What will you be looking in the T1.mgz?
I am quite new to this field so have a very basic understanding of it.

Much appreciated.

Julia Yang


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
Date: Thursday, 3 December 2020 at 12:39 pm
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_watershed error: problem in the COG calcuation
Have you looked at the T1.mgz?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Julia Yang
Sent: Wednesday, December 2, 2020 8:37 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation


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Hi,

While running the recon_all, I bumped into this error message below.
\n mri_watershed -rusage 
/Users/Shared/PD-MCI/Freesurfer/PDMCI107/touch/rusage.mri_watershed.dat -T1 
-brain_atlas 
/Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca 
transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz \n
Mode:  T1 normalized volume
Mode:  Use the information of atlas (default parms, --help for details
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed
*WATERSHED**
Sorting...
mri_watershed Error:
Problem in the COG calculation:
T1.mgz may not contain properly normalized white-matter.
Confirm that T1.mgz has enough white-matter voxels of value 110.
If white-matter contains few if any voxels of value 110,
try adding wm control-points to nu.mgz, and re-run recon-all.
Darwin med-cr-mtm0xv 18.7.0 Darwin Kernel Version 18.7.0: Thu Jan 23 06:52:12 
PST 2020; root:xnu-4903.278.25~1/RELEASE_X86_64 x86_64
recon-all -s PDMCI107 exited with ERRORS at Wed Nov


Recon_all failed without creating the brainmask.mgz.
I have attached files for possible solution.

  *   Recon-all.log
  *   Nu.mgz
  *   Talairach_with_skull.log
  *   Talairach.xfm

Any help would be much appreciated.

Kind Regards,

Julia Yang


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Re: [Freesurfer] flipped_hemisphere

2020-12-03 Thread Mora, Jocelyn S. 
Hi,

If you are interested in checking information on the volume itself, try 
mri_info. If you would like specific examples for reference, I would recommend 
using our wiki pages.

Cheers,
Jocelyn

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Edoardo Pinzuti 

Sent: Thursday, December 3, 2020 10:34 AM
To: Freesurfer support list 
Subject: [Freesurfer] flipped_hemisphere


External Email - Use Caution

Hi,

after performing a segmentation with Freesurfer and making a Bem model it looks 
that some results are flipped between right and left hemispheres. Is there a 
way to check that Freesurfer is interpreting correctly the mri ?

Thanks
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Re: [Freesurfer] recon-all issues debugging

2020-12-03 Thread Fischl, Bruce 
Hi Courtney

Can you send us the recon-all.log file and the full screen output from one job 
that failed?

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Courtney Haswell
Sent: Thursday, December 3, 2020 9:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all issues debugging


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I am trying to debug why all of our T1's are failing Freesurfer recon-all. It 
seems that most of the files are being created but it isn't getting to the 
stats steps to output those files. In the recon-all log it does say "recon-all 
-s 13265 exited with ERRORS."

I looked in the recon-all.error file and the only thing in that is "CMD 
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." 
Would this be the step where the error is happening?

I have checked the T1 thoroughly and it is good quality. What is the best way 
to debug why this is happening with our scans?

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Re: [Freesurfer] segmentHA_T1.sh

2020-12-03 Thread Iglesias Gonzalez, Juan E. 
Hej Olof,
The CA segmentations (along with all the others) are generated when calling 
segmentHA_T1.sh the standard  way:
segmentHA_T1.sh   [SUBJECT_NAME][SUBJECTS_DIR]
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Erik Lindberg 

Reply-To: Freesurfer support list 
Date: Thursday, December 3, 2020 at 10:04
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T1.sh


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Hi,
I am trying to run the segmentHA_T1.sh with the suffix CA but I seem not be 
able to write the call correctly

How should I call this?

best
Olof
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[Freesurfer] flipped_hemisphere

2020-12-03 Thread Edoardo Pinzuti 
External Email - Use Caution

Hi,

after performing a segmentation with Freesurfer and making a Bem model it
looks that some results are flipped between right and left hemispheres. Is
there a way to check that Freesurfer is interpreting correctly the mri ?

Thanks
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[Freesurfer] segmentHA_T1.sh

2020-12-03 Thread Erik Lindberg 
External Email - Use Caution

Hi,
I am trying to run the segmentHA_T1.sh with the suffix CA but I seem not be
able to write the call correctly

How should I call this?

best
Olof
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[Freesurfer] recon-all issues debugging

2020-12-03 Thread Courtney Haswell 
External Email - Use Caution

I am trying to debug why all of our T1's are failing Freesurfer recon-all. It 
seems that most of the files are being created but it isn't getting to the 
stats steps to output those files. In the recon-all log it does say "recon-all 
-s 13265 exited with ERRORS."

I looked in the recon-all.error file and the only thing in that is "CMD 
mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix." 
Would this be the step where the error is happening?

I have checked the T1 thoroughly and it is good quality. What is the best way 
to debug why this is happening with our scans?

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[Freesurfer] Does segmentation depend on input orientation {Disarmed}

2020-12-03 Thread Nederpelt, D. van (David) 
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Hi,

I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and 
once on this image converted to LAS orientation
I would expect the output (especially in volume) to be equal, because 
freesurfer reconverts it to its own orientation if I understood correctly. 
However, I found that the segmentation and output volumes differed depending on 
the input orientation.

So while in fact both images are actually the same, the output differs. What 
would be the reason for this difference in output?

Any help would be much appreciated

Kind regards,


[cid:image002.png@01D40E30.3E299A80]

David van Nederpelt, MSc.  | PhD Candidate
Radiology and Nuclear Medicine
Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ 
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