Re: [Freesurfer] Special image protocol

[mustafa amin]

External Email - Use Caution

I am going to use Phillips Achieva 1.5 Tesla by the way. Thank you in advance.

Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara

> On 26 Mar 2019, at 21.24, Bruce Fischl  wrote:
> 
> Hi Mustafa
> 
> what type of scanner are you using? A normal mprage should be fine. 
> Typically we acquire sagittaly as that is the shortest air-to-air 
> direction. Make sure that the acquisition is 3D and around 1mm isotropic. 
> We may have a protocol you can use depending on your scanner hardware and 
> software
> cheers
> Bruce
> 
> 
>> On Tue, 26 Mar 2019, mustafa amin wrote:
>> 
>>   External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> I mentioned your suggestion i.e., multiecho mprage at about 1 mm, however 
>> the radiologist and operator of the MRI did not understand with the term. 
>> Can you explain it further please? We never done it before, here in Medan 
>> Indonesia. This is the first time we are going to do it. And, do you have 
>> suggestion for the MRI slice? Coronal, sagittal or else? Thank you in 
>> advance.
>> 
>> Yours faithfully,
>> 
>> Mustafa M. Amin
>> Consultant Psychiatrist in Biological Psychiatry
>> Department of Psychiatry
>> Faculty of Medicine
>> Universitas Sumatera Utara
>> 
>>> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.  
>>> wrote:
>>> 
>>> I highly recommend the multiecho mprage at about 1mm.
>>> 
 On 2/21/19 10:30 AM, Bruce Fischl wrote:
 Hi Mustafa
 
 FreeSurfer should work fine with many image protocols. If you have the
 freedom to choose one, Andre van der Kouwe (ccd) can point you at the
 sequence he developed for Siemens. If you are using a different scanner
 give us the details and we can recommend something
 
 cheers
 Bruce
 
 
 On Thu, 21 Feb
 2019, mustafa amin wrote:
 
>   External Email - Use Caution
> 
> Dear member,
> 
> I am really new with this freesurfer, just need to ask 1 question. Is 
> there a special image protocol before running the MRI and then upload it 
> to freesurfer? Please share your thoughts. Thank you for your kind 
> attention and cooperation.
> 
> Yours faithfully,
> 
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
> 
> 
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Re: [Freesurfer] Special image protocol

[mustafa amin]

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Thank you Douglas. I have showed it to the radiologist and the operator. They 
said it needs contrast that will be injected to the patients. Is it true? 
Please confirm. Thank you in advance.

Yours faithfully,

Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara

> On 27 Mar 2019, at 05.12, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> If you're scanner is on this list, then use the given protocol
> http://adni.loni.usc.edu/methods/documents/mri-protocols/
> 
> 
>> On 3/26/19 1:56 AM, mustafa amin wrote:
>> External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> I mentioned your suggestion i.e., multiecho mprage at about 1 mm, however 
>> the radiologist and operator of the MRI did not understand with the term. 
>> Can you explain it further please? We never done it before, here in Medan 
>> Indonesia. This is the first time we are going to do it. And, do you have 
>> suggestion for the MRI slice? Coronal, sagittal or else? Thank you in 
>> advance.
>> 
>> Yours faithfully,
>> 
>> Mustafa M. Amin
>> Consultant Psychiatrist in Biological Psychiatry
>> Department of Psychiatry
>> Faculty of Medicine
>> Universitas Sumatera Utara
>> 
>>> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.  
>>> wrote:
>>> 
>>> I highly recommend the multiecho mprage at about 1mm.
>>> 
 On 2/21/19 10:30 AM, Bruce Fischl wrote:
 Hi Mustafa
 
 FreeSurfer should work fine with many image protocols. If you have the
 freedom to choose one, Andre van der Kouwe (ccd) can point you at the
 sequence he developed for Siemens. If you are using a different scanner
 give us the details and we can recommend something
 
 cheers
 Bruce
 
 
 On Thu, 21 Feb
 2019, mustafa amin wrote:
 
>External Email - Use Caution
> 
> Dear member,
> 
> I am really new with this freesurfer, just need to ask 1 question. Is 
> there a special image protocol before running the MRI and then upload it 
> to freesurfer? Please share your thoughts. Thank you for your kind 
> attention and cooperation.
> 
> Yours faithfully,
> 
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
> 
> 
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> 
> 
> 
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>> 
>> 
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Re: [Freesurfer] Special image protocol

[mustafa amin]

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Hi Bruce,

I mentioned and showed the MP-RAGE protocol along with 3D acquisition, sagittal 
and 1 mm isotropic. According to the radiologist and the operator it needs 
contrast that will be injected to the patient. Is it true? Please confirm and 
share some thoughts with me. Thank you in advance.

Yours faithfully,

Mustafa M. Amin
Consultant Psychiatrist in Biological Psychiatry
Department of Psychiatry
Faculty of Medicine
Universitas Sumatera Utara

> On 26 Mar 2019, at 21.24, Bruce Fischl  wrote:
> 
> Hi Mustafa
> 
> what type of scanner are you using? A normal mprage should be fine. 
> Typically we acquire sagittaly as that is the shortest air-to-air 
> direction. Make sure that the acquisition is 3D and around 1mm isotropic. 
> We may have a protocol you can use depending on your scanner hardware and 
> software
> cheers
> Bruce
> 
> 
>> On Tue, 26 Mar 2019, mustafa amin wrote:
>> 
>>   External Email - Use Caution
>> 
>> Dear Douglas,
>> 
>> I mentioned your suggestion i.e., multiecho mprage at about 1 mm, however 
>> the radiologist and operator of the MRI did not understand with the term. 
>> Can you explain it further please? We never done it before, here in Medan 
>> Indonesia. This is the first time we are going to do it. And, do you have 
>> suggestion for the MRI slice? Coronal, sagittal or else? Thank you in 
>> advance.
>> 
>> Yours faithfully,
>> 
>> Mustafa M. Amin
>> Consultant Psychiatrist in Biological Psychiatry
>> Department of Psychiatry
>> Faculty of Medicine
>> Universitas Sumatera Utara
>> 
>>> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.  
>>> wrote:
>>> 
>>> I highly recommend the multiecho mprage at about 1mm.
>>> 
 On 2/21/19 10:30 AM, Bruce Fischl wrote:
 Hi Mustafa
 
 FreeSurfer should work fine with many image protocols. If you have the
 freedom to choose one, Andre van der Kouwe (ccd) can point you at the
 sequence he developed for Siemens. If you are using a different scanner
 give us the details and we can recommend something
 
 cheers
 Bruce
 
 
 On Thu, 21 Feb
 2019, mustafa amin wrote:
 
>   External Email - Use Caution
> 
> Dear member,
> 
> I am really new with this freesurfer, just need to ask 1 question. Is 
> there a special image protocol before running the MRI and then upload it 
> to freesurfer? Please share your thoughts. Thank you for your kind 
> attention and cooperation.
> 
> Yours faithfully,
> 
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
> 
> 
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> 
> 
> 
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> 
>>> 
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>> 
>> 
>> 
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Re: [Freesurfer] Longitudinal Two Stage Model Question

[Arsenije Subotic]

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Hi Doug,


Thanks for getting back to me so quickly. Just to confirm, I can proceed to use 
the mri_glmfit analysis as shown on the group level tutorial?


I'm not sure I can do the paired analysis since my subjects in one group are 
not matched with those from the other and one group has more participants than 
the other. I will however use the the link you gave me to compute the 
difference within one of my groups.


Best,

Arsenije



---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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Re: [Freesurfer] Left and right pial surfaces crossing in medial cortex

[Matthieu Vanhoutte]

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Dear Experts,

Would you have any advice?

Best,
Matthieu

Le mar. 26 mars 2019 à 13:54, Matthieu VANHOUTTE <
matthieuvanhou...@gmail.com> a écrit :

> Dear FS' experts,
>
> Using both T1 and FLAIR in recon-all to improve pial surfaces, I often
> have the case where pial surfaces from the left and right hemisphere are
> crossing in medial cortex (see attached images).
>
> Is it anormal and bad ? If so, How could I fix it ?
>
> Best,
>
> Matthieu
>
>
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Re: [Freesurfer] Special image protocol

[Greve, Douglas N.,Ph.D.]

If you're scanner is on this list, then use the given protocol
http://adni.loni.usc.edu/methods/documents/mri-protocols/


On 3/26/19 1:56 AM, mustafa amin wrote:
>  External Email - Use Caution
>
> Dear Douglas,
>
> I mentioned your suggestion i.e., multiecho mprage at about 1 mm, however the 
> radiologist and operator of the MRI did not understand with the term. Can you 
> explain it further please? We never done it before, here in Medan Indonesia. 
> This is the first time we are going to do it. And, do you have suggestion for 
> the MRI slice? Coronal, sagittal or else? Thank you in advance.
>
> Yours faithfully,
>
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
>
>> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.  
>> wrote:
>>
>> I highly recommend the multiecho mprage at about 1mm.
>>
>>> On 2/21/19 10:30 AM, Bruce Fischl wrote:
>>> Hi Mustafa
>>>
>>> FreeSurfer should work fine with many image protocols. If you have the
>>> freedom to choose one, Andre van der Kouwe (ccd) can point you at the
>>> sequence he developed for Siemens. If you are using a different scanner
>>> give us the details and we can recommend something
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 21 Feb
>>> 2019, mustafa amin wrote:
>>>
 External Email - Use Caution

 Dear member,

 I am really new with this freesurfer, just need to ask 1 question. Is 
 there a special image protocol before running the MRI and then upload it 
 to freesurfer? Please share your thoughts. Thank you for your kind 
 attention and cooperation.

 Yours faithfully,

 Mustafa M. Amin
 Consultant Psychiatrist in Biological Psychiatry
 Department of Psychiatry
 Faculty of Medicine
 Universitas Sumatera Utara


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>
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Re: [Freesurfer] Longitudinal Two Stage Model Question

[Greve, Douglas N.,Ph.D.]

basically yes. The full instructions for a paired analysis are here
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis


On 3/26/19 5:56 PM, Arsenije Subotic wrote:
>
> External Email - Use Caution
>
> Sorry,
>
>
> I was actually able to compile a FSGD file that has a single line for 
> each subject (containing the fsid base) along with gender and age at 
> baseline. I ran this through the mris_preproc command 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) 
> in order to stack the spc files which were previously cached.
>
>
> I guess my question really is can I now simply continue on and use the 
> mri_glmfit instructions on the group analysis tutorial page or is 
> there a special procedure because I am dealing with longitudinal data? 
> I was planning on simply using contrasts i had designed before for my 
> cross-sectional analysis, controlling for age at baseline and gender.
>
>
> Thanks and my apologies for all the questions!
>
> Arsenije
>
>
> ---
>
> *Arsenije Subotic*| MSc Student
>
> Department of Clinical Neurosciences
>
> Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
>
> Tel: (403) 918-6970
>
> arsenije.subot...@ucalgary.ca
>
>
>
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Re: [Freesurfer] Longitudinal Two Stage Model Question

[Arsenije Subotic]

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Sorry,


I was actually able to compile a FSGD file that has a single line for each 
subject (containing the fsid base) along with gender and age at baseline. I ran 
this through the mris_preproc command 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) in order 
to stack the spc files which were previously cached.


I guess my question really is can I now simply continue on and use the 
mri_glmfit instructions on the group analysis tutorial page or is there a 
special procedure because I am dealing with longitudinal data? I was planning 
on simply using contrasts i had designed before for my cross-sectional 
analysis, controlling for age at baseline and gender.


Thanks and my apologies for all the questions!

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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Re: [Freesurfer] PetSurfer

[Greve, Douglas N.,Ph.D.]

You should read up on the MRTM2. Basically, when you run MRTM1, it 
computes a separate k2 for each voxel eventhough the k2 should be the 
same across the entire brain (since it actually refers to the reference 
region). With MRTM2, you estimate the single k2 value from high binding 
regions.

On 3/26/19 12:50 PM, Shane Schofield wrote:
>
> External Email - Use Caution
>
> Hello PetSurfer Developers
>
> On the tutorial page, I do not understand this part:
>
> --km-hb 11 12 13 50 51 52 specifies the ROIs to use as the 
> high-binding region if using MRTM2. This creates km.hb.tac.nii.gz with 
> the value for the high-binding region for each time point.
>
> What exactly is a high-binding region and how do these inputs affect 
> the rest of the estimation? If I do not know what the high binding 
> regions for a tracer are, may I leave this blank?
>
> Thank you.
>
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Re: [Freesurfer] How to improve recon all on subjets with hight atrophy level like Alzheymer patients?

[Bruce Fischl]

Hi Barbara

we need to see the inaccuracies in order to help. You can either post 
some images (ideally with arrows), or upload a dataset to our ftp site 
with some voxel coords where you think things should be better.


cheers
Bruce
On Tue, 26 
Mar 2019, Barbara Micaela Duarte Abritta wrote:




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Hello everyone, recently I have started to analyze a new sample of subjets 
which is made up of
people with Alzheimer's, due to this pathology several of my subjects have a 
high level of atrophy
in subcortical and temporal areas of the brain, which causes several errors in 
the pial surface as a
wm surface. So to make both surfaces more accurate I tried to put some control 
points but in many
places this solution was not enough due the level of inaccuracy. Is there any 
solution for this
problem? I will appreciate if you could offer any suggestions to solve this 
problem.

Regards

Bárbara

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Re: [Freesurfer] mkanalysis-sess with a customized HRF

[Greve, Douglas N.,Ph.D.]

No, not easily. You could edit fmri_hemodyn.m, fast_fslgamma.m, or 
fast_spmhrf.m to return your own HRF and then specify the proper one in 
mkanalysis.

On 3/26/19 11:34 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer's experts,
>
> I would like to use a customized HRF with mkanalysis-sess.
> Is there a way to do it?
>
> Thanks!
> Best
> Francesca
>
> -- 
> Francesca Strappini, Ph.D.
> Neurobiology Department
> Weizmann Institute of Science
> 234 Herzl Street, Rehovot 7610001 Israel
> Tel.: +972 58 444 2584
> E-mail: francesca.strapp...@weizmann.ac.il 
> 
>
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[Freesurfer] How to improve recon all on subjets with hight atrophy level like Alzheymer patients?

[Barbara Micaela Duarte Abritta]

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Hello everyone, recently I have started to analyze a new sample of subjets 
which is made up of people with Alzheimer's, due to this pathology several of 
my subjects have a high level of atrophy in subcortical and temporal areas of 
the brain, which causes several errors in the pial surface as a wm surface. So 
to make both surfaces more accurate I tried to put some control points but in 
many places this solution was not enough due the level of inaccuracy. Is there 
any solution for this problem? I will appreciate if you could offer any 
suggestions to solve this problem.

Regards

Bárbara
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[Freesurfer] Longitudinal Two Stage Model Question

[Arsenije Subotic]

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Hello,


I am doing a longitudinal analysis for which I have already qcached my data 
using the long_mris_slopes command.


I am having issues figuring out how to run the mri_glmfit command for my 
longitudinal two stage model. I'm interested in comparing the spc over time 
between two groups after controlling for age and gender. The tutorial on the 
longitudinal two stage model however only shows how to do it for one sample.


Am I still expected to use contrasts and make glm directories like the 
cross-sectional group analysis tutorial suggests? I was just confused because 
the code is different. I have a longitudinal table so I assumed that would be 
enough, but do I still need to make a FSGD file that is basically the same as 
the longitudinal file?


Thank you for your help,

Arsenije



---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] PetSurfer

[Shane Schofield]

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Hello PetSurfer Developers
On the tutorial page, I do not understand this part:
--km-hb 11 12 13 50 51 52 specifies the ROIs to use as the high-binding region 
if using MRTM2. This creates km.hb.tac.nii.gz with the value for the 
high-binding region for each time point.
What exactly is a high-binding region and how do these inputs affect the rest 
of the estimation? If I do not know what the high binding regions for a tracer 
are, may I leave this blank?
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Re: [Freesurfer] mris_fix_topology stuck running

[Bruce Fischl]

overlay the orig.nofix on the data and see if it includes the non-brain 
tissue. You can also tar and gzip your entire subject dir and ftp it to us 
if you want us to take a look

cheers
Bruce

On Tue, 26 Mar 2019, Soichi Hayashi wrote:



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Bruce,
I am still going through the wiki, but I found the mri/brainmask.mgz contains a 
lot of non brain
voxels like these..

Screenshot from 2019-03-26 11-56-48.png

Could this be the cause of the problem? Maybe Freesurfer had a problem 
generating a good brainmask?
Does this create the high number of vertices that needs to be corrected?

Soichi

On Tue, Mar 26, 2019 at 10:46 AM Bruce Fischl  
wrote:
  Hi Soichi

  look at the inflated.nofix in the 3D view, not the  orig.nofix. You can
  check out our tutorial here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview?highlight=%28topolo
  gy%29%7C%28tutorial%29


  although there may be a better one (hopefully someone else will chime in 
if
  so)

  cheers
  Bruce



  On Tue, 26 Mar 2019, Soichi Hayashi wrote:

  >
  > External Email - Use Caution
  >
  > Bruce,
  > Thank you for your help. I'd very much appreciate it. 
  >
  > I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really 
find anything
  out of
  > ordinary.. from my layman's eyes. 
  >
  > Screenshot from 2019-03-26 10-35-42.png
  >
  > Could you point me to the wiki you mentioned?
  >
  > Soichi
  >
  > On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl 
 wrote:
  >       Hi Soichi
  >
  >       that is too big a defect to expect it to fix - more than half the 
number
  >       of vertices in a typical hemisphere. It means something is badly 
wrong
  >       that you need to correct prior to the topo fixer. You can look at 
our
  >       wiki for this kind of thing, but I would start by looking at the
  >       rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, 
like large
  >       parts of the skull attached to the surface or something like that
  >
  >       cheers
  >       Bruce
  >
  >
  >       On Sun, 24 Mar 2019, Soichi Hayashi wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hello.
  >       > I am trying to troubleshoot an issue where recon_all is not 
finishing after
  >24 hours.
  >       It's getting
  >       > stuck when it tries to run the following command.
  >       >
  >       > $ mris_fix_topology -rusage 
./output/touch/rusage.mris_fix_topology.rh.dat
  -mgz
  >       -sphere
  >       > qsphere.nofix -ga -seed 1234 output rh 
  >       > INFO: assuming .mgz format
  >       > reading spherical homeomorphism from 'qsphere.nofix'
  >       > using genetic algorithm with optimized parameters
  >       > setting seed for random number genererator to 1234
  >       >
  >       > *
  >       > Topology Correction Parameters
  >       > retessellation mode:           genetic search
  >       > number of patches/generation : 10
  >       > number of generations :        10
  >       > surface mri loglikelihood coefficient :         1.0
  >       > volume mri loglikelihood coefficient :          10.0
  >       > normal dot loglikelihood coefficient :          1.0
  >       > quadratic curvature loglikelihood coefficient : 1.0
  >       > volume resolution :                             2
  >       > eliminate vertices during search :              1
  >       > initial patch selection :                       1
  >       > select all defect vertices :                    0
  >       > ordering dependant retessellation:              0
  >       > use precomputed edge table :                    0
  >       > smooth retessellated patch :                    2
  >       > match retessellated patch :                     1
  >       > verbose mode :                                  0
  >       >
  >       > *
  >       > $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 
zkaufman Exp $
  >       >   $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  >       > reading input surface 
/home/hayashis/Downloads/output/surf/rh.qsphere.nofix...
  >       > before topology correction, eno=-696 (nv=191488, nf=384368, 
ne=576552, g=349)
  >       > reading brain volume from brain...
  >       > reading wm segmentation from wm...
  >       > using quasi-homeomorphic spherical map to tessellate cortical 
surface...
  >       >
  >       > Correction of the Topology
  >       > Finding true center and radius of S

[Freesurfer] BrainHack Donostia 2nd edition, 5-8 May 2019, San Sebastian

[Stefano Moia]

External Email - Use Caution

Dear all, 

At the Basque Center on Cognition, Brain and Language (BCBL), we are organizing 
the second edition of Brainhack Donostia ( 
https://brainhackdonostia.pages.bcbl.eu ), an event focused on neuroimaging and 
the promotion of open-source resources in an accessible way across disciplines 
and experience levels. 

This edition will take place on May 5 -8 at BCBL, where two invited speakers 
(Prof. Dimitri Van De Ville, EPFL, and Matteo Bastiani, University of 
Nottingham) and other scientists from BCBL will give talks and develop hands-on 
tutorials on data handling from several neuroimaging techniques. In particular, 
we will cover three techniques: Diffusion-Weighted Imaging (DWI), 
Magnetoencephalography (MEG) and functional Magnetic Resonance Imaging (fMRI). 
To know more about it, you can c heck the schedule here: 
https://brainhackdonostia.pages.bcbl.eu/sites/timeline.html 
We are also going to host a hackaton in parallel, in which the attendants will 
propose and collaborate on neuroimaging-related projects (e.g., data 
acquisition, visualization, etc.). Check the project page for more info: 
https://brainhackdonostia.pages.bcbl.eu/sites/projects.html 

We encourage you to come and enjoy such an experience with us! Feel free to 
register here https://brainhackdonostia.pages.bcbl.eu/sites/register.html 

For any inquiries, please email us at info.bhg-donos...@bcbl.eu 

We hope to see you in May! 

Stefano Moia 

--- 
PhD student @ BCBL 
www.bcbl.eu 

Tel: +34 943 309 300 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 
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[Freesurfer] mkanalysis-sess with a customized HRF

[Francesca Strappini]

External Email - Use Caution

Dear Freesurfer's experts,

I would like to use a customized HRF with mkanalysis-sess.
Is there a way to do it?

Thanks!
Best
Francesca

-- 
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strapp...@weizmann.ac.il
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Re: [Freesurfer] mris_fix_topology stuck running

[Bruce Fischl]

Hi Soichi

look at the inflated.nofix in the 3D view, not the  orig.nofix. You can 
check out our tutorial here:


https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview?highlight=%28topology%29%7C%28tutorial%29


although there may be a better one (hopefully someone else will chime in if 
so)


cheers
Bruce



On Tue, 26 Mar 2019, Soichi Hayashi wrote:



External Email - Use Caution

Bruce,
Thank you for your help. I'd very much appreciate it. 

I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really find 
anything out of
ordinary.. from my layman's eyes. 

Screenshot from 2019-03-26 10-35-42.png

Could you point me to the wiki you mentioned?

Soichi

On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl  wrote:
  Hi Soichi

  that is too big a defect to expect it to fix - more than half the number
  of vertices in a typical hemisphere. It means something is badly wrong
  that you need to correct prior to the topo fixer. You can look at our
  wiki for this kind of thing, but I would start by looking at the
  rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, like 
large
  parts of the skull attached to the surface or something like that

  cheers
  Bruce


  On Sun, 24 Mar 2019, Soichi Hayashi wrote:

  >
  > External Email - Use Caution
  >
  > Hello.
  > I am trying to troubleshoot an issue where recon_all is not finishing 
after >24 hours.
  It's getting
  > stuck when it tries to run the following command.
  >
  > $ mris_fix_topology -rusage 
./output/touch/rusage.mris_fix_topology.rh.dat -mgz
  -sphere
  > qsphere.nofix -ga -seed 1234 output rh 
  > INFO: assuming .mgz format
  > reading spherical homeomorphism from 'qsphere.nofix'
  > using genetic algorithm with optimized parameters
  > setting seed for random number genererator to 1234
  >
  > *
  > Topology Correction Parameters
  > retessellation mode:           genetic search
  > number of patches/generation : 10
  > number of generations :        10
  > surface mri loglikelihood coefficient :         1.0
  > volume mri loglikelihood coefficient :          10.0
  > normal dot loglikelihood coefficient :          1.0
  > quadratic curvature loglikelihood coefficient : 1.0
  > volume resolution :                             2
  > eliminate vertices during search :              1
  > initial patch selection :                       1
  > select all defect vertices :                    0
  > ordering dependant retessellation:              0
  > use precomputed edge table :                    0
  > smooth retessellated patch :                    2
  > match retessellated patch :                     1
  > verbose mode :                                  0
  >
  > *
  > $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
  >   $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
  > reading input surface 
/home/hayashis/Downloads/output/surf/rh.qsphere.nofix...
  > before topology correction, eno=-696 (nv=191488, nf=384368, ne=576552, 
g=349)
  > reading brain volume from brain...
  > reading wm segmentation from wm...
  > using quasi-homeomorphic spherical map to tessellate cortical surface...
  >
  > Correction of the Topology
  > Finding true center and radius of Spherical Surface...done
  > Surface centered at (0,0,0) with radius 100.0 in 9 iterations
  > marking ambiguous vertices...
  > 133741 ambiguous faces found in tessellation
  > segmenting defects...
  > 63 defects found, arbitrating ambiguous regions...
  > analyzing neighboring defects...
  >       -merging segment 16 into 0
  >       -merging segment 23 into 0
  >       -merging segment 48 into 0
  >       -merging segment 32 into 22
  >       -merging segment 49 into 47
  >       -merging segment 54 into 51
  > 57 defects to be corrected 
  > 0 vertices coincident
  > Computing Initial Surface Statistics
  >       -face       loglikelihood: -9.3123  (-4.6561)
  >       -vertex     loglikelihood: -6.5427  (-3.2713)
  >       -normal dot loglikelihood: -3.5794  (-3.5794)
  >       -quad curv  loglikelihood: -6.0564  (-3.0282)
  >       Total Loglikelihood : -25.4907
  >
  > CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517)
  >
  > ---
  >
  > After displaying the last line, the process seems to be stuck running 
with 100%
  cpu (single core)
  > for >24 hours until our batch scheduler kills it. I think the issue is 
with my input
  data, but it
  > looks clean and well ACPC aligned, and I don't know what

Re: [Freesurfer] Special image protocol

[Bruce Fischl]

Hi Mustafa

what type of scanner are you using? A normal mprage should be fine. 
Typically we acquire sagittaly as that is the shortest air-to-air 
direction. Make sure that the acquisition is 3D and around 1mm isotropic. 
We may have a protocol you can use depending on your scanner hardware and 
software
cheers
Bruce


On Tue, 26 Mar 2019, mustafa amin wrote:

>External Email - Use Caution
>
> Dear Douglas,
>
> I mentioned your suggestion i.e., multiecho mprage at about 1 mm, however 
> the radiologist and operator of the MRI did not understand with the term. 
> Can you explain it further please? We never done it before, here in Medan 
> Indonesia. This is the first time we are going to do it. And, do you have 
> suggestion for the MRI slice? Coronal, sagittal or else? Thank you in 
> advance.
>
> Yours faithfully,
>
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
>
>> On 22 Feb 2019, at 00.10, Greve, Douglas N.,Ph.D.  
>> wrote:
>>
>> I highly recommend the multiecho mprage at about 1mm.
>>
>>> On 2/21/19 10:30 AM, Bruce Fischl wrote:
>>> Hi Mustafa
>>>
>>> FreeSurfer should work fine with many image protocols. If you have the
>>> freedom to choose one, Andre van der Kouwe (ccd) can point you at the
>>> sequence he developed for Siemens. If you are using a different scanner
>>> give us the details and we can recommend something
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Thu, 21 Feb
>>> 2019, mustafa amin wrote:
>>>
External Email - Use Caution

 Dear member,

 I am really new with this freesurfer, just need to ask 1 question. Is 
 there a special image protocol before running the MRI and then upload it 
 to freesurfer? Please share your thoughts. Thank you for your kind 
 attention and cooperation.

 Yours faithfully,

 Mustafa M. Amin
 Consultant Psychiatrist in Biological Psychiatry
 Department of Psychiatry
 Faculty of Medicine
 Universitas Sumatera Utara


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>>
>>
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>
>
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Re: [Freesurfer] recon from 7T data

[Jonathan Polimeni]

thanks falk! and valeria, as for the SPM-based normalization, we also
often use this for bias correction of 7 Tesla data, and natalia posted the
parameters we use for 7T MPRAGEs here:

https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon


-jon



On Tue, 26 Mar 2019, falk.luesebr...@med.ovgu.de wrote:

> External Email - Use Caution
>
> Hi Valeria,
>
> you can account for the inhomogeneities Bruce was talking about by either 
> using SPMs or FreeSurfers inhomogeneity correction. Personally, I prefer SPM 
> over FreeSurfer, but if you supply a brainmask to the FreeSurfer tool, it 
> gives reasonable results around the temporal lobes, too.
>
> I haven't used an MEMPRAGE sequence, however, using an MPRAGE you can use a 
> FWHM of 30 and a regularization of 0.001 in SPMs segmentation tool, setting 
> the sample distance to 2 improves the correction further. Using the N3 
> implemented in FreeSurfer you could run (from the subject's directory) 
> mri_nu_correct.mni --n 2 --uchar transforms/talairach.xfm --mask 
> brainmask.mgz --stop 0.0001 --distance 15 --fwhm 0.15 --shrink 2 
> --proto-iters 1 --i orig.mgz --o nu.mgz. Then proceed with the 
> normalization of autorecon1. Both correction methods take quite some time.
>
> In case of MP2RAGE or if the MPRAGE was divided by a GRE manually you will 
> need to adjust these settings accordingly. The N4 algorithm of ANTs works 
> fine also if a brainmask is supplied. In case someone wants to have some 
> parameters to run an inhomogeneity with that tool or on MP2RAGE/Division 
> data, let me know.
>
> Best,
> Falk
>
> -Ursprüngliche Nachricht-
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
>  Im Auftrag von Bruce Fischl
> Gesendet: Montag, 25. März 2019 20:27
> An: Freesurfer support list 
> Cc: freesurfer-boun...@nmr.mgh.harvard.edu; Andre van der Kouwe 
> ; Jonathan Polimeni 
> Betreff: Re: [Freesurfer] recon from 7T data
>
> Hi Valeria
>
> Jon Polimeni and Andre van der Kouwe put together a specific acquisition and 
> set of preprocessing steps for 7T (mp2rage I believe). You need to account 
> for the transmit inhomogeneities, which are what is causing you to lose the 
> temporal lobes.
>
> cheers
> Bruce
>
>
> On Mon, 25 Mar 2019, Barletta, Valeria wrote:
>
> >
> >
> >  
> >
> > Dear Freesurfers,
> >
> > I am trying to perform the FreeSurfer cortical reconstruction process
> > from my 7 Tesla MEMPRAGE, but am getting very bad results (see first
> > attachment) compared to what I had using the 3 Tesla images (second 
> > attachment).
> >
> > Before launching the "recon-all ... -all" command, I applied the
> > FreeSurfer Gradient non-linearity correction.
> >
> >
> > What can have been the problem?
> >
> >
> > Thank you very much for your help,
> >
> > Valeria
> >
> >
> >
>
>
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>
>
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Re: [Freesurfer] regions of Yeo 17 networks in fast

[Thomas Yeo]

External Email - Use Caution

Renumber for visualization purpose.

Do you mean how to re-number in the colortable? Just open the colortable in
a text editing software and edit.

Thanks,
Thomas

On Tue, Mar 26, 2019 at 6:44 PM  wrote:

> Thanks.
>
> Should I renumber for visualization purpose or for fs-fast?
>
> How can I do it?
>
>
> Il 26 marzo 2019 alle 4.01 Thomas Yeo  ha scritto:
>
> Hi Stefano,
>
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001,
> 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
>
> If so, you will just need the right colortable to view the Yeo_17Net.mgz.
> We are currently generating a new colortable that should work for you. This
> might take a while.
>
> If you are in a hurry, you can download the colortable here (
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
> but as you can see the range of values are not in the 1000-2000 range. So
> what you need to do is for the left hemisphere structures, you need to
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
>
> Regards,
> Thomas
>
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote:
>
> Hi, my concern is the mri_aparc2aseg command line.
>
> In summary, I have done:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh
> --sval-annot
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
>
>
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000 --annot-table
> /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> The output is correct by the color label is those of aparc.
>
> Probably the error is the match between the annotations and annot-table.
>
> Could you check the command lines, please?
>
> Thanks
>
> Stefano
>
>
>
> Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." <
> dgr...@mgh.harvard.edu> ha scritto:
>
> Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know
> what is in that txt file. You can verify the segids by just bringing up the
> segmentation in freeview and clicking on a voxel. If you load the
> segmentation with that color table and everything looks ok, then the color
> table  is ok.
>
> On 3/10/19 4:05 PM, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> I will use freeview.
>
> Have you any suggestion on the use of fcseed-config option?
>
> Are you agree with the command line listed below?
>
> fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd
> rest -mean -cfg lh.SEED.config -overwrite
>
> My concerns are on -segids. Are the ids included in the file
> 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
>
> How can I select a specific seed (id) to be used in -segids?
>
> Thanks
>
> Stefano
>
>
> Il 10 marzo 2019 alle 17.17 Bruce Fischl 
>  ha scritto:
>
> Hi Stefano
>
> is there a reason you are using tkmedit and not freeview? We deprecated
> tkmedit a long time ago now
>
> cheers
> Bruce
> On Sun, 10 Mar 2019, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> Thanks.
>
> My error is in tkmedit
>
> tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
>
> Il 9 marzo 2019 alle 11.09 Thomas Yeo 
>  ha scritto:
>
> External Email - Use Caution
>
> Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but
> Yeo_17Net.mgz is empty?
> Your tkmedit command seems to assume Yeo_17Net.mgz is in
> /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output
> be in the mri folder?
>
> On Sat, Mar 9, 2019 at 5:47 PM < std...@virgilio.it> wrote:
>
> External Email - Use Caution
>
> I have run:
>
> mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh
> --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20
> 11_17Networks_N1000.annot --tval
> $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
>
> to check the output
>
> tksurfer subj rh inflated -annot
> $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
>
> My concern is here:
>
> mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot
> Yeo2011_17Networks_N1000
>
> --annot-table/Applications/freesurfer/1000

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

mri_aparc2aseg --s subj --o sub/mri/Yeo_17Net.mgz --annot 
Yeo2011_17Networks_N1000 --annot-table 
/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt
freeview subj orig.mgz -ov subj/mri/Yeo_17Net.mgz

I am not sure that the command line sound fine.

When I open the files in freeview, the name of labels is the same of aparc2009.

> Il 26 marzo 2019 alle 4.01 Thomas Yeo  ha scritto:
> 
> Hi Stefano,
> 
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 
> 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
> 
> If so, you will just need the right colortable to view the Yeo_17Net.mgz. 
> We are currently generating a new colortable that should work for you. This 
> might take a while.
> 
> If you are in a hurry, you can download the colortable here ( 
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
>  but as you can see the range of values are not in the 1000-2000 range. So 
> what you need to do is for the left hemisphere structures, you need to 
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere 
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
> 
> Regards,
> Thomas
> 
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Hi, my concern is the mri_aparc2aseg command line.
> > 
> > In summary, I have done:
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
> > 
> >  
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > 
> > The output is correct by the color label is those of aparc.
> > 
> > Probably the error is the match between the annotations and 
> > annot-table.
> > 
> > Could you check the command lines, please?
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > 
> > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < 
> > dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > 
> > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). 
> > > I don't know what is in that txt file. You can verify the segids by just 
> > > bringing up the segmentation in freeview and clicking on a voxel. If you 
> > > load the segmentation with that color table and everything looks ok, then 
> > > the color table  is ok.
> > > 
> > > On 3/10/19 4:05 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > I will use freeview.
> > > > 
> > > > Have you any suggestion on the use of fcseed-config 
> > > > option?
> > > > 
> > > > Are you agree with the command line listed below?
> > > > 
> > > > fcseed-config -segid ... -seg 
> > > > $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg 
> > > > lh.SEED.config -overwrite
> > > > 
> > > > My concerns are on -segids. Are the ids included in the 
> > > > file 
> > > > 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
> > > > 
> > > > How can I select a specific seed (id) to be used in 
> > > > -segids?
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > > > > > > 
> > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl 
> > > > >  mailto:fis...@nmr.mgh.harvard.edu ha 
> > > > > scritto:
> > > > > 
> > > > > Hi Stefano
> > > > > 
> > > > > is there a reason you are using tkmedit and not 
> > > > > freeview? We deprecated
> > > > > tkmedit a long time ago now
> > > > > 
> > > > > cheers
> > > > > Bruce
> > > > > 

Re: [Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Thanks.

Should I renumber for visualization purpose or for fs-fast?

How can I do it?


> Il 26 marzo 2019 alle 4.01 Thomas Yeo  ha scritto:
> 
> Hi Stefano,
> 
> Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 
> 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
> 
> If so, you will just need the right colortable to view the Yeo_17Net.mgz. 
> We are currently generating a new colortable that should work for you. This 
> might take a while.
> 
> If you are in a hurry, you can download the colortable here ( 
> https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt),
>  but as you can see the range of values are not in the 1000-2000 range. So 
> what you need to do is for the left hemisphere structures, you need to 
> renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere 
> structures, you need to renumber them from 58 to 114 to 2001 to 2057.
> 
> Regards,
> Thomas
> 
> On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it 
> mailto:std...@virgilio.it > wrote:
> 
> > > 
> > Hi, my concern is the mri_aparc2aseg command line.
> > 
> > In summary, I have done:
> > 
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh 
> > --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
> > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD 
> > --hemi lh --sval-annot 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot
> >  --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
> > 
> >  
> > 
> > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot 
> > Yeo2011_17Networks_N1000 --annot-table 
> > /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot
> > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
> > 
> > The output is correct by the color label is those of aparc.
> > 
> > Probably the error is the match between the annotations and 
> > annot-table.
> > 
> > Could you check the command lines, please?
> > 
> > Thanks
> > 
> > Stefano
> > 
> > 
> > 
> > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < 
> > dgr...@mgh.harvard.edu mailto:dgr...@mgh.harvard.edu > ha scritto:
> > > 
> > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). 
> > > I don't know what is in that txt file. You can verify the segids by just 
> > > bringing up the segmentation in freeview and clicking on a voxel. If you 
> > > load the segmentation with that color table and everything looks ok, then 
> > > the color table  is ok.
> > > 
> > > On 3/10/19 4:05 PM, std...@virgilio.it 
> > > mailto:std...@virgilio.it wrote:
> > > 
> > > > > > > 
> > > > External Email - Use Caution
> > > > 
> > > > I will use freeview.
> > > > 
> > > > Have you any suggestion on the use of fcseed-config 
> > > > option?
> > > > 
> > > > Are you agree with the command line listed below?
> > > > 
> > > > fcseed-config -segid ... -seg 
> > > > $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg 
> > > > lh.SEED.config -overwrite
> > > > 
> > > > My concerns are on -segids. Are the ids included in the 
> > > > file 
> > > > 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
> > > > 
> > > > How can I select a specific seed (id) to be used in 
> > > > -segids?
> > > > 
> > > > Thanks
> > > > 
> > > > Stefano
> > > > 
> > > > 
> > > > > > > > > 
> > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl 
> > > > >  mailto:fis...@nmr.mgh.harvard.edu ha 
> > > > > scritto:
> > > > > 
> > > > > Hi Stefano
> > > > > 
> > > > > is there a reason you are using tkmedit and not 
> > > > > freeview? We deprecated
> > > > > tkmedit a long time ago now
> > > > > 
> > > > > cheers
> > > > > Bruce
> > > > > On Sun, 10 Mar 2019, std...@virgilio.it 
> > > > > mailto:std...@virgilio.it wrote:
> > > > > 
> > > > > > > > > > > 
> > > > > > External Email - Use Caution
> > > > > > 
> > > > > > Thanks.
> > > > > > 
> > > > > >   

Re: [Freesurfer] recon from 7T data

[falk.luesebr...@med.ovgu.de]

External Email - Use Caution

Hi Valeria,

you can account for the inhomogeneities Bruce was talking about by either using 
SPMs or FreeSurfers inhomogeneity correction. Personally, I prefer SPM over 
FreeSurfer, but if you supply a brainmask to the FreeSurfer tool, it gives 
reasonable results around the temporal lobes, too. 

I haven't used an MEMPRAGE sequence, however, using an MPRAGE you can use a 
FWHM of 30 and a regularization of 0.001 in SPMs segmentation tool, setting the 
sample distance to 2 improves the correction further. Using the N3 implemented 
in FreeSurfer you could run (from the subject's directory) mri_nu_correct.mni 
--n 2 --uchar transforms/talairach.xfm --mask brainmask.mgz --stop 0.0001 
--distance 15 --fwhm 0.15 --shrink 2 --proto-iters 1 --i orig.mgz --o 
nu.mgz. Then proceed with the normalization of autorecon1. Both correction 
methods take quite some time.

In case of MP2RAGE or if the MPRAGE was divided by a GRE manually you will need 
to adjust these settings accordingly. The N4 algorithm of ANTs works fine also 
if a brainmask is supplied. In case someone wants to have some parameters to 
run an inhomogeneity with that tool or on MP2RAGE/Division data, let me know.

Best,
Falk

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von Bruce Fischl
Gesendet: Montag, 25. März 2019 20:27
An: Freesurfer support list 
Cc: freesurfer-boun...@nmr.mgh.harvard.edu; Andre van der Kouwe 
; Jonathan Polimeni 
Betreff: Re: [Freesurfer] recon from 7T data

Hi Valeria

Jon Polimeni and Andre van der Kouwe put together a specific acquisition and 
set of preprocessing steps for 7T (mp2rage I believe). You need to account for 
the transmit inhomogeneities, which are what is causing you to lose the 
temporal lobes.

cheers
Bruce


On Mon, 25 Mar 2019, Barletta, Valeria wrote:

> 
> 
>  
> 
> Dear Freesurfers,
> 
> I am trying to perform the FreeSurfer cortical reconstruction process 
> from my 7 Tesla MEMPRAGE, but am getting very bad results (see first 
> attachment) compared to what I had using the 3 Tesla images (second 
> attachment).
> 
> Before launching the "recon-all ... -all" command, I applied the 
> FreeSurfer Gradient non-linearity correction.
> 
> 
> What can have been the problem?
> 
> 
> Thank you very much for your help,
> 
> Valeria
> 
> 
>


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