Re: [Freesurfer] Question about hippocampal sub-volume extraction

[Wei Shao]

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Hi, Abdalla Z Mohamed

Thanks for your reply, but this is code is for T1 scan only according to
the instruction, I want to extract the volume from the T2 (for segmentation
based only on the additional scan )

Best,
Wei

On Mon, May 3, 2021 at 7:55 PM  wrote:

> External Email - Use Caution
>
> Hi Wei,
>
> You can directly extract the volumes from all subjects within your
> Freesurfer Analysis folder by using the following command
>
> quantifyHAsubregions.sh hippoSf T1 result.txt
>
>
>
> Best regards,
>
> Abdalla Z Mohamed.
>
>
>
>
>
> *From: *Wei Shao 
> *Sent: *Tuesday, 4 May 2021 5:22 AM
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Question about hippocampal sub-volume extraction
>
>
>
> *External Email - Use Caution*
>
> Hello,Dear Freesurfer exports
>
>
>
> I have a question about the pipeline of hippocampal sub-volume extraction:
>
> quantifyHAsubregions.sh hippoSf -  
> 
>
> Let's say I have two different groups of analysisID such as sub-AVP
> and sub-BAY
>
>
>
> I can pass a wildcard to extract the data of T2 scan from all sub-BAY
> subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt
>
>
>
> But Is there any way that I can extract the sub-volume from all the two
> different group subjects at one time? Thanks.
>
>
>
> Best,
>
> Wei
>
>
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Re: [Freesurfer] Question about hippocampal sub-volume extraction

[bio.abdallah2012]

External Email - Use CautionHi Wei, You can directly extract the volumes from all subjects within your Freesurfer Analysis folder by using the following command quantifyHAsubregions.sh hippoSf T1 result.txt Best regards, Abdalla Z Mohamed.   From: Wei ShaoSent: Tuesday, 4 May 2021 5:22 AMTo: Freesurfer support listSubject: [Freesurfer] Question about hippocampal sub-volume extraction External Email - Use CautionHello,Dear Freesurfer exports  I have a question about the pipeline of hippocampal sub-volume extraction:quantifyHAsubregions.sh hippoSf -  Let's say I have two different groups of analysisID such as sub-AVP and sub-BAY I can pass a wildcard to extract the data of T2 scan from all sub-BAY subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt But Is there any way that I can extract the sub-volume from all the two different group subjects at one time? Thanks. Best,Wei 
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[Freesurfer] mri_ribbon does not return the ribbon

[Caspar M. Schwiedrzik]

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Hi!
I am trying to make a ribbon.mgz from a non-human primate surface recon
that does not have an aseg. Following this prior discussion: Re:
[Freesurfer] ribbon.mgz Without aseg.mgz (mail-archive.com)

I tried mri_ribbon:

mri_ribbon ./surf/rh.white ./surf/rh.pial ./mri/orig.mgz
rh.ribbon.mgz

Attached is the output. It looks like it roughly follows the grey matter,
but especially the sulci seem to be filled. Unfortunately, there is no help
for mri_ribbon. Any advice on how to proceed? The above mentioned
discussion did not lead to a conclusion on how to get a ribbon without
aseg.
Thank you! Caspar
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[Freesurfer] Question about hippocampal sub-volume extraction

[Wei Shao]

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Hello,Dear Freesurfer exports

I have a question about the pipeline of hippocampal sub-volume extraction:

quantifyHAsubregions.sh hippoSf - 


Let's say I have two different groups of analysisID such as sub-AVP and
sub-BAY

I can pass a wildcard to extract the data of T2 scan from all sub-BAY
subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt

But Is there any way that I can extract the sub-volume from all the two
different group subjects at one time? Thanks.

Best,
Wei
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[Freesurfer] PET seeding with hippocampal subfields

[Mohammad Akradi]

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Dear Freesurfer Development Team

I've used freesurfer with hippocampal subfields module to get GM and
Thickness in this region in detail. but now I need this subfields' mask to
use it on my PET data. So I'll appreciate it if you tell me how I can get
this regions' mask. Or which atlas I should use to achieve them? so I can
calculate FDG uptake in these regions too.

best regards

-- 
Mohammad Akradi
MSc Student,
Institute of Medical Science and Technology,
Shahid Beheshti University, Tehran, Iran
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Re: [Freesurfer] QA in longitudinal processing

[Fischl, Bruce]

Was the aseg correct in the cross? If you can upload this subject (all the 
cross and long timepoints) we can take a look

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Malo Gaubert
Sent: Monday, May 3, 2021 10:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] QA in longitudinal processing


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Hello,

Any idea on how to correct pial & white matters segmentation splitting out on 
lateral ventricle while aseg is correct (see previous message below)?
Thank you.



Le lun. 26 avr. 2021 à 08:38, Malo Gaubert 
mailto:malogaub...@gmail.com>> a écrit :
Hello,

Any idea on how to fix these longitudinal issues?



Le jeu. 15 avr. 2021 à 09:44, Malo Gaubert 
mailto:malogaub...@gmail.com>> a écrit :
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 preprocessing: MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial
Thus I launched the creation of BASE followed by the LONGITUDINAL. Everything 
went well for recon-all for these 3 steps.
Now, I want to do the QA on the data and I have two questions regarding this QA:

1/ For one subject, for the two timepoints, the white and pial surface are 
entering in the left lateral ventricle as displayed in figure 1 (session 1 of 
the subject; cross-sectional), while the aseg is fine (this area is considered 
as Lateral ventricle, see figure 2 attached).
What correction could I apply for this case ?

2/ For some subjects, there is a small shift between the pial of the two 
sessions (or the white; see figure 3=display of the norm of my norm and 
pial/white for the two timepoints (long)) and/or some weird/non straight lines 
for pial or white (see figure 3, especially between temporal pole and the rest 
of the brain). What could be the error in this case? Could it be related to 
some bad quality of T1w images?

1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz
2) Platform: Ubuntu 18 (Virtual Machine on remote server)
3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu SMP 
Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Any help would be appreciated.

Best,
Malo
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Re: [Freesurfer] QA in longitudinal processing

[Malo Gaubert]

External Email - Use Caution

Hello,

Any idea on how to correct pial & white matters segmentation splitting out
on lateral ventricle while aseg is correct (see previous message below)?
Thank you.



Le lun. 26 avr. 2021 à 08:38, Malo Gaubert  a écrit :

> Hello,
>
> Any idea on how to fix these longitudinal issues?
>
>
>
> Le jeu. 15 avr. 2021 à 09:44, Malo Gaubert  a
> écrit :
>
>> 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 preprocessing:
>> https://secure-web.cisco.com/1tX5fu_Ax9KbuzA3-e77cyR3x9mZzkFLtWRrRWH3fyTUdv1WD_ki1GLxZ82DWLz_teRZ96w91IMHTeGHi2gjEZuR8iVAPBgg-swudBYPvMSn1FhP5yr5BFToH-M7L0nM8NjsUmp5kMiCY4ixrdU8PxaZtgFJlZylT0Oo9Ce6lvex-XFnKUOXKmAAoMiFNmwbX0hfUIydiJuyPMboMY2V9BdO0nA4L2NJOhjOd5BVjUtdoPv93Rk0pWvVMj-dIE-GiQbspTxio-f4qUNKym07mUQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FLongitudinalTutorial
>> Thus I launched the creation of BASE followed by the LONGITUDINAL.
>> Everything went well for recon-all for these 3 steps.
>> Now, I want to do the QA on the data and I have two questions regarding
>> this QA:
>>
>> 1/ For one subject, for the two timepoints, the white and pial surface
>> are entering in the left lateral ventricle as displayed in figure 1
>> (session 1 of the subject; cross-sectional), while the aseg is fine (this
>> area is considered as Lateral ventricle, see figure 2 attached).
>> What correction could I apply for this case ?
>>
>> 2/ For some subjects, there is a small shift between the pial of the two
>> sessions (or the white; see figure 3=display of the norm of my norm and
>> pial/white for the two timepoints (long)) and/or some weird/non straight
>> lines for pial or white (see figure 3, especially between temporal pole and
>> the rest of the brain). What could be the error in this case? Could it be
>> related to some bad quality of T1w images?
>>
>> 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.0.tar.gz
>> 2) Platform: Ubuntu 18 (Virtual Machine on remote server)
>> 3) uname -a: Linux ubuntu18-cbrain-042020 4.15.0-135-generic #139-Ubuntu
>> SMP Mon Jan 18 17:38:24 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>>
>> Any help would be appreciated.
>>
>> Best,
>> Malo
>>
>
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Re: [Freesurfer] Out of memory from longitudinal segmentation of hippocampus

[Iglesias Gonzalez, Juan E.]

Yeah that’s what we do at the Martinos cluster ;-)
I’m glad it’s working!

From:  on behalf of Wei Shao 

Reply-To: Freesurfer support list 
Date: Friday, April 30, 2021 at 19:19
To: Freesurfer support list 
Subject: Re: [Freesurfer] Out of memory from longitudinal segmentation of 
hippocampus


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Hi, E

Thanks for your reply, I used one core and its associated RAM from the 
server,(I guess is not very much) but I have solved it by assigning more RAM 
memory.
Best,
Wei

On Fri, Apr 30, 2021 at 9:35 AM Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
wrote:
Dear Wei,
Sorry for missing your message (it happens sometimes…).
The longitudinal subfield module is very RAM memory hungry.
How much RAM memory do you have (not disk space, these are different things).
Cheers,
/Eugenio






Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wei Shao 
mailto:ws...@research.baycrest.org>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, April 29, 2021 at 22:39
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Out of memory from longitudinal segmentation of 
hippocampus


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Hello, Dear Freesufer experts

I just thought of sending a friendly reminder -

I am wondering if you had the time to go over my question?

Best regards,
Wei

On Sat, Apr 24, 2021 at 2:26 PM Wei Shao 
mailto:ws...@research.baycrest.org>> wrote:
Hello, Dear FreeSurfer expert.

I was tried to use longitudinal segmentation of T1 scans for the longitudinal 
analysis. but there is a problem

making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Error using permute
Out of memory. Type HELP MEMORY for your options.

Error in myMRIread>myMRIread_aux (line 99)
Error in myMRIread (line 63)
Error in SegmentSubfieldsT1Longitudinal (line 904)

MATLAB:nomem
@#@FSTIME  2021:04:24:13:57:21 run_SegmentSubfieldsT1Longitudinal.sh N 17 e 
249.25 S 49.95 U 759.76 P 324% M 1532492 F 249 R 4682496 W 0 c 134624 w 550491 
I 3940880 O 1217536 L 1.24 1.04 1.58
@#@FSLOADPOST 2021:04:24:14:01:30 run_SegmentSubfieldsT1Longitudinal.sh N 17 
4.04 3.43 2.47
Linux gra-login1 3.10.0-1127.8.2.el7.x86_64 #1 SMP Tue May 12 16:57:42 UTC 2020 
x86_64 GNU/Linux

longitudinal subfields exited with ERRORS at Sat Apr 24 14:01:31 EDT 2021

For more details, see the log file 
/home/weishao/long_BAY12019/scripts/long-hippocampal-subfields-T1.log

I have checked the space:

DescriptionSpace   # of files
/home (user weishao)  44G/53G
147k/500k

Could you tell me what I should do? Thanks

Best,
Cheer

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