[Freesurfer] Best mesh generation from hippocampus aseg segmentation

[Gonzalo Rojas Costa]

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Hi:

Which is the best library or software to create the hippocampus mesh from
aseg segmentation?

Sincerely


Gonzalo Rojas Costa
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[Freesurfer] mri_surf2vol method one

[Yixin Ma]

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Hi Freesurfer experts,

I'm trying to write the normals of the GM/WM meshes to the entire ribbon.

We usually do it by:
1) Generate normal files from rh.white and lh.white

mris_convert rh.white rh.white.gii

mris_convert -n rh.white rh.white.normals.asc


2) Use matlab 'read_normals' function to read the normals and write
individual directions xyz as a paint format file.

g = gifti([path 'Analysis/' exam '/' subject  '/surf/rh.white.gii']);

norm = read_normals(g,[path 'Analysis/' exam '/' subject
'/surf/rh.white.normals.asc']);

write_wfile([path 'Analysis/' exam '/' subject  '/surf/rh_normx.w'
],norm(:,1));

write_wfile([path 'Analysis/' exam '/' subject  '/surf/rh_normy.w'
],norm(:,2));

write_wfile([path 'Analysis/' exam '/' subject  '/surf/rh_normz.w'
],norm(:,3));


3) Use mri_surf2vol method two to paint the normals into the ribbon. But
the problem is that method two gives me lots of holes in the ribbon.
I'm wondering if it's possible to use mri_surf2vol method one to paint the
normals into the ribbon because method one does not leave holes in the
ribbon. However, it seems like the overlay does not accept paint
file format (rh_normx.w). The overlay in method one accepts rh.thickness as
an input, as shown in the example on the website. I'm wondering how to
convert the painting files to have the same format as rh.thickness?

Thank you in advance,

Yixin
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Re: [Freesurfer] please help me

[saman fouladi]

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 hi Bruce
thank you very very much

On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce 
 wrote:  
 
 #yiv6786467954 #yiv6786467954 -- _filtered {} _filtered {} _filtered 
{}#yiv6786467954 #yiv6786467954 p.yiv6786467954MsoNormal, #yiv6786467954 
li.yiv6786467954MsoNormal, #yiv6786467954 div.yiv6786467954MsoNormal 
{margin:0in;margin-bottom:.0001pt;font-size:11.0pt;font-family:sans-serif;}#yiv6786467954
 a:link, #yiv6786467954 span.yiv6786467954MsoHyperlink 
{color:blue;text-decoration:underline;}#yiv6786467954 p.yiv6786467954msonormal, 
#yiv6786467954 li.yiv6786467954msonormal, #yiv6786467954 
div.yiv6786467954msonormal 
{margin-right:0in;margin-left:0in;font-size:11.0pt;font-family:sans-serif;}#yiv6786467954
 span.yiv6786467954ydp1ac82ctlid-translation {}#yiv6786467954 
span.yiv6786467954ydpe810003dtlid-translation {}#yiv6786467954 
span.yiv6786467954ydpbc4bf220tlid-translation {}#yiv6786467954 
span.yiv6786467954ydp44042622tlid-translation {}#yiv6786467954 
span.yiv6786467954EmailStyle31 
{font-family:sans-serif;color:windowtext;}#yiv6786467954 
.yiv6786467954MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv6786467954 
div.yiv6786467954WordSection1 {}#yiv6786467954 
Nifty is a format that a lot of people use (including us) but it is not needed 
for our processing. Pick *one* file in your dicom series and pass it to 
recon-all:
 
  
 
  
 
recon-all -i  -s  -sdir  -all
 
  
 
cheers
 
Bruce
 
  
 
From: freesurfer-boun...@nmr.mgh.harvard.edu 
On Behalf Of saman fouladi
Sent: Wednesday, October 21, 2020 11:57 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] please help me
 
  
 
External Email - Use Caution
 
hi
 
  
 
Thank you for your response
 
  
 
I have 60 subject MRI that each  contains 174 dcm file. and i want predict age 
of these subjects. in step one i want extract morphology features and in step2 
create a deep learning model that predict age.
 
  
 
According to what I said, what should I do?
 
  
 
If I have to use recon-all with what code can I do this? And what is the use of 
nifty?
 
  
 
On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce 
 wrote:
 
  
 
  
 
Hi Saman
 
 
 
Recon-all will give you a comprehensive assessment of most macroscopically 
visible structures in the brain. You don’t have to convert to nifty first – 
just point recon-all at a single slice in the proper dicom series (for your 3D 
T1-weighted scan), and it will spend a few hours doing stuff
 
 
 
Cheers
 
Bruce
 
 
 
From:freesurfer-boun...@nmr.mgh.harvard.edu 
On Behalf Of saman fouladi
Sent: Tuesday, October 20, 2020 4:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] please help me
 
 
 
External Email - Use Caution
 
hi
 
 
 
I want to process MRI images to extractMorphology features.
 
 
 
I convert my dcm file to nii format by mri-convert command and then I used FSL 
software and BET(Best extraction Tool).
 
  
 
Next I do not know what to do to extract morphological features?
 
 
 
My other question is what is the difference between recon-all and use FEAT( in 
FSL software)? What are the uses of each?
 
 
 
Thank you
 
 
 
 
 
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[Freesurfer] mri_nu_correct error: flar --uchar not recignized

[erbilnurhan]

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Hello FreeSurfer Developers,

I'm trying to compute volumetric data from MPRAGE images by using recon-all as 
decribed athttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

I've got the following message:

mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 
2
ERROR: flag --uchar not recognized

Does anyone have any thoughts on how to trouble-shoot this problem? Also, I've 
attached the recon-all.log in case it's of any use.

FreeSurfer version: freesurfer-darwin-macOS-7.1.1 
(freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0)

macOS high Sierra 10.13.6, x86_64
XQuartz 2.7.11 (xorg-server 1.18.4)

recon-all.log: see attached

Sincerely,

Nurhan ErbilThu Oct 22 12:44:03 +03 2020
/Applications/freesurfer/subjects/nr
/Applications/freesurfer/bin/recon-all
-s nr -i /Applications/freesurfer/subjects/s1.mgz -all -qcache
subjid nr
setenv SUBJECTS_DIR /Applications/freesurfer/subjects
FREESURFER_HOME /Applications/freesurfer
Actual FREESURFER_HOME /Applications/freesurfer
build-stamp.txt: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Darwin Nurhans-MacBook-Pro.local 17.7.0 Darwin Kernel Version 17.7.0: Mon Aug 
31 22:11:23 PDT 2020; root:xnu-4570.71.82.6~1/RELEASE_X86_64 x86_64
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
descriptors  256 
memorylocked unlimited
maxproc  709 

PhysMem: 7245M used (1515M wired), 944M unused.


program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2020/10/22-09:44:05-GMT  BuildTimeStamp: May 25 2011 
22:32:58  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $  
User: nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version 
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2020/10/22-09:44:05-GMT  BuildTimeStamp: May 25 
2011 22:32:58  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
Exp $  User: nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nschmans@W0084482 
(i686-apple-darwin8.8.1) on 2006-10-03 at 21:43:56
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2020/10/22-09:44:06-GMT  BuildTimeStamp: May 25 
2011 22:32:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2020/10/22-09:44:07-GMT  BuildTimeStamp: May 25 2011 
22:32:58  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $  
User: nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2020/10/22-09:44:07-GMT  BuildTimeStamp: May 25 2011 
22:32:58  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $  
User: nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2020/10/22-09:44:07-GMT  BuildTimeStamp: May 25 2011 
22:32:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2020/10/22-09:44:07-GMT  BuildTimeStamp: May 25 2011 
22:32:58  CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $  User: 
nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 
ProgramName: mri_label2label  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2020/10/22-09:44:07-GMT  BuildTimeStamp: May 25 
2011 22:32:58  CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve 
Exp $  User: nurhanerbil  Machine: Nurhans-MacBook-Pro.local  Platform: Darwin  
PlatformVersion: 17.7.0  CompilerName: GCC  CompilerVersion: 4 

Re: [Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

[Fischl, Bruce]

Where did you get the ct from?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of 1248742467
Sent: Thursday, October 22, 2020 7:25 AM
To: freesurfer 
Subject: [Freesurfer] The non-existent field'numEntries' is 
referenced.(write_annotation.m)


External Email - Use Caution

hello, fs

when i use the write_annotation.m, the error message occurs:
`The non-existent field'numEntries' is referenced.

Error write_annotation (line 62)
count = fwrite(fp, int32(ct.numEntries),'int');

Error test_1 (line 13)
write_annotation('rh.aparc.a2009s.annot', c, b, ct)`
How to solve the non-existent field'numEntries' is referenced？By the way, can 
ct change automatically according to the value of label?




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[Freesurfer] There is no view-label option after loading the .annot file

[1248742467]

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Hello, Fs
my freesurfer version is 6, I see others have the view button after load 
.annot file,But my version does not have this option.
Do I need to update the version? And I have installed fs6, can I install fs 7.1 
on the same machine?
What's more, After loading the .annot file in freeview, can I reset its name, 
index, color through view-label?




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[Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

[1248742467]

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hello, fs

when i use the write_annotation.m, the error message occurs:
`The non-existent field'numEntries' is referenced.

Error write_annotation (line 62)
count = fwrite(fp, int32(ct.numEntries),'int');

Error test_1 (line 13)
write_annotation('rh.aparc.a2009s.annot', c, b, ct)`
How to solve the non-existent field'numEntries' is referenced??By the way, can 
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Re: [Freesurfer] longitudinal study

[Martin Reuter]

Hi Ken, 

you should always look at the output from the …long.base directories, those are 
the final outputs. Looks to me that you are looking at the cross sectional 
produced surfaces from the first stage. Those will be 
- in different spaces (as the heads are in different positions in the scanner)
- created independently and therefore will look more different from each other 
than the surfaces from the long stream.

Best, Martin

> On 25. Sep 2020, at 15:55, Douglas N. Greve  wrote:
> 
> What is your command line for visualization? Can you also show the base image 
> as an underlay?
> 
> On 9/24/2020 6:54 PM, KennethSPrice wrote:
>> External Email - Use Caution
>> 
>> Hello,
>> I am running a longitudinal study and am examining the pial surface for my 2 
>> timepoints. The surfaces are slightly offset. Will this effect my 
>> statistical analysis for volume and thickness? I have attached the pial 
>> surface for each time point to this email. Should I be examining 
>> timpoint1.long and timepoint2.long instead?
>> 
>> Thanks,
>> Ken
>> 
>> 
>> Sent with ProtonMail  Secure Email.
>> 
>> 
>> 
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Re: [Freesurfer] starting longitudinal pipeline after mri_robust_template

[Martin Reuter]

Hi Marisa, 

That should be possible. 
You can run the long pipeline up to that step, replace the corresponding files 
with your version and continue from there. 

Best, Martin

> On 1. Oct 2020, at 10:32, Marisa Johanna Nordt  wrote:
> 
> External Email - Use Caution
> Hello, 
>  
> I have a question regarding the longitudinal pipeline: Is it possible to 
> start the longitudinal pipeline after a template (using mri_robust_template) 
> has already been created in a separate step? 
>  
> Thank you so much, 
>  
> Marisa 
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Re: [Freesurfer] lta files longitudinal pipeline

[Martin Reuter]

Hi Marisa, 

the -affine flag was only for some debugging and is currently not supported. It 
may also not do what you think it does. It will remove scaling difference 
between your time points. This makes sense if you have test-retest scans and 
want to remove scanner calibration scaling problems. It will not be the right 
tool, if heads grow (as a longitudinal analysis will only provide measurements 
after global scaling is removed between time points). 

Best, Martin


> On 7. Oct 2020, at 10:54, Marisa Johanna Nordt  wrote:
> 
> External Email - Use Caution
> Hi, 
>  
> I have a question about the lta files from the longitudinal pipeline (using 
> the –affine flag). Instead of just one .lta file from each timepoint to the 
> template 3 different .lta files are saved  
> -tp1_to_templ_norm.lta,  
> -tp1_to_templ_affine.lta,  
> -tp1_to_templ.lta 
>  
> Is the one created last (tp1_to_templ.lta) the final lta-file that I can use 
> to align additional files from tp 1 to the template? 
>  
> Thanks a lot! 
> Marisa 
> 
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Re: [Freesurfer] Question: Longitudinal Edits

[Martin Reuter]

Hi Suzan, 

(sending this also to the FS support list, where these questions fit best, but 
sometimes I miss emails there). 

If edits are necessary or not depends purely on the quality of your data. I.e. 
old scanners, low contrast, motion artefacts etc. 
It also depends on the number of subjects. If you want to quantify small 
changes in only a few subjects, you need to make sure that FS results are clean 
and correct. If you are running a population study with 30.000 people you 
cannot do manual edits at all and have to resort to a quality control paradigm. 

Furthermore, the longitudinal stream additionally benefits from having the 
subject template (aka “base”). Usually it is sufficient to edit that instead of 
all time points (e.g. for skullstrip or surface related problems). 

In short FreeSurfer does not require edits, it allows users to include edits if 
they like. It is recommended to check results. Never trust any automated tool 
blindly. 

Best, Martin


> On 22. Oct 2020, at 03:46, Suzan Maleki  wrote:
> 
> 
> Dear Martin,
> 
> The time and effort of the FreeSurfer team is really appreciated. I would be 
> grateful if you explain to what extent it is necessary to apply manual edits 
> for longitudinal processing ? 
> I have read the FS longitudinal tutorial and noticed so many manual edits 
> need to be done on Cross > Base >Long scans. For example, having two 
> time-points that are 3 months apart, is it really necessary to do manual 
> edits for all the individuals ? 
> I am wondering what are the reasons that necessitate several manual edits for 
> longitudinal pipeline, considering that FreeSurfer is one of the best 
> available and commonly used neuroimaging softwares and supposed to be fully 
> automated. 
> Also, how much those manual edits will affect the reproducibility of the 
> processing ?
> Thanks a lot for your help,
> Kind regards,
> Suzan 
> 
> -- 
> Suzan Maleki
> PhD Student
> 
>  <>Brain, Mind and Society Research Hub
> Turner Institute for Brain and Mental Health
> School of Psychological Sciences
> Monash University
> 770 Blackburn Road
> Clayton VIC 3800 Australia
> 
> E: suzan.mal...@monash.edu 
> W: www.brainmindsociety.com 
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[Freesurfer] Issue with extracted thickness value from significant cluster or peak vertex

[Julian Macoveanu]

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Hi,
I am using FS 7.1.0. After running the surface thickness GLM analysis
I get one cluster after correction for multiple comparison showing a
significant group difference. I want to make a plot illustrating this
group difference. However, when using the mean values from:

cache.th30.abs.y.ocn.dat, I don’t see the expected group difference in
these values.

Question 1)
Are the subjects cluster mean values in y.ocn.dat adjusted for the
covariates I used in the fsgd file? E.g. age, sex and TIV?

Question 2)
I inserted these mean cluster values from y.ocn.dat in SPSS and tried
verify the statistics both with and without adjustment for covariates
and did not get the expected significant group region which I expected
in either case. Why is this?

Question 3)
I moved on to extract the thickness values from peak vertex in my
significant cluster. For this I used mris_convert which I just wanted
to be confirmed that is correct:

mris_convert -c lh.thickness.fwhm15.fsaverage.mgh
$freesurferdir/fsaverage/surf/lh.orig  output.asc

After extracting the thickness value for all subjects from the peak
vertex as reported by the sig.cluster.summary , I still have the same
issue as before, I find no group expected group difference.

Interestingly, the significant cluster I found is part of the
superior_frontal region in aparc2009. When I extract these values it
almost shows significant group differences in the entire region, in
line with the surface GLM findings.

Thanks,
Julian

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[Freesurfer] unpacksdcmdir in version 7: issues with cfg files

[Caspar M. Schwiedrzik]

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Hi!
We are encountering some issues with unpacksdcmdir in version 7.1.1. In
particular, it turns out that the handling of cfg files seems to have
changed, which makes things somewhat impractical.
Old (v5.3) cfg files cannot be used anymore, because only dicom series
names that are actually present in the current session are accepted. This
makes it impossible to have one general cfg file for different experiments,
and also to help structure the cfg files with commented lines. I understand
unpacksdcmdir is being phased out, but the flexibility brought about by cfg
files still makes this a very handy tool. Yet, the current version has lost
much of this flexibility. I suggest reverting to the way unpacksdcmdir
handled cfg files in the past.
Thanks, Caspar
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