[Freesurfer] Email address

[Meysam Ebrahimi]

master.ms...@gmail.com
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Re: [Freesurfer] Fw: recon-all steps question

[miracooloz]

We have already skull stripped and white matter segmented volume ( used lesion 
explorer) . Hence, I want to replace freesurfer 's generated outputs for this 
steps ( brainmask.mgz for skull strip and wm.seg.mgz (not wm.mgz ) for white 
matter)  ‎with ours. I know recon-all -all performs all 31 steps and inserting 
" -nostep " flag tells freesurfer to skip that step. Covering and Creating a 
symbolic link to our files and then, running the remaining steps of recon-all 
might help achieve this ( I believe) . Replacing this freesurfer outputs with 
ours will reduce time spent on pial and white matter edits. 
Best,
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, November 4, 2016 3:37 PM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: recon-all steps question


Hi Paul

can we take a step back. What are you trying to achieve by avoiding these 
steps?

cheers
Bruce


On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:

> Thanks Bruce. Another question, since " -no segmentation " flag skips the 
> white matter segmentation step of recon-all. Can I also use the same 
> logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's, 
> run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then 
> copy/convert my already segmented brain and name it wm.seg.mgz. After
> that, treat it as if I had freesurfer's wm.seg.mgz and finally, run " 
> recon-all -autorecon3 -s " to complete the process. What do you think?   
> Best,  Paul
>
> Sent from my BlackBerry 10 smartphone.
>   Original Message  
> From: Bruce Fischl
> Sent: Friday, November 4, 2016 10:50 AM
> To: Freesurfer support list
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] Fw: recon-all steps question
>
> Hi Paul
>
>
> we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so
> must create them somehow. I think if you copy/convert your already-stripped
> and name it brainmask.mgz we should treat that as if you had edited our
> skull stripping and you should be able to run from their forward
> (autorecon2 and autorecon3 I believe)
>
> cheers
> Bruce
>
>
> On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:
>
>> Please can someone answer this. Thanks 
>> "
>> Hello Freesurfer, I have couple of questions. While going through the
>> frequently asked questions on your
>> pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a
>> question regarding how to integrate a skull stripped from another problem
>> into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
>> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
>> from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
>> of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 
>>
>> First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
>> during skull stripping? why are they present if I included the "-no
>> skullstrip" flag? 
>>
>> Second question, where do I insert my already skull stripped data in the
>> symbolic link? 
>>
>> Last question, the final stages of recon-all ( recon-all -autorecon2
>> -autorecon3)  doesn't include skull stripping, how can I be sure my skull
>> stripped data was incorporated into the freesurfer recon-all process? 
>>
>> Best, 
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>> From: miracoo...@gmail.com
>> Sent: Wednesday, November 2, 2016 9:39 AM
>> To: Freesurfer support list
>> Subject: Fw: recon-all steps question
>>
>>
>>
>> Sent from my BlackBerry 10 smartphone.
>> From: miracle ozzoude 
>> Sent: Monday, October 31, 2016 8:39 AM
>> To: Douglas N Greve
>> Subject: recon-all steps question
>>
>> Hello Freesurfer, I have couple of questions. While going through the
>> frequently asked questions on your
>> page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a
>> question regarding how to integrate a skull stripped from another problem
>> into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
>> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
>> from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
>> of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 
>>
>> First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
>> during skull stripping? why are they present if I included the "-no
>> skullstrip" flag? 
>>
>> Second question, where do I insert my already skull stripped data in the
>> symbolic link? 
>>
>> Last question, the final stages of recon-all doesn't include skull
>> stripping, how can I be sure my skull stripped data was incorporated into
>> the freesurfer recon-all process? 
>>
>> Best, 
>> Paul
>>
>>
>>
>>
>>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

Re: [Freesurfer] Fw: recon-all steps question

[Bruce Fischl]

Hi Paul

can we take a step back. What are you trying to achieve by avoiding these 
steps?


cheers
Bruce


On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:

Thanks Bruce. Another question, since " -no segmentation " flag skips the 
white matter segmentation step of recon-all. Can I also use the same 
logic as the "-noskullstrip" flag to replace the wm.seg.mgz file? That's, 
run " recon-all -autorecon1 -autorecon2 -nosegmentation -s subjid ". Then 
copy/convert my already segmented brain and name it wm.seg.mgz. After 
that, treat it as if I had freesurfer's wm.seg.mgz and finally, run " 
recon-all -autorecon3 -s " to complete the process. What do you think?   
Best,  Paul


Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, November 4, 2016 10:50 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: recon-all steps question

Hi Paul


we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so
must create them somehow. I think if you copy/convert your already-stripped
and name it brainmask.mgz we should treat that as if you had edited our
skull stripping and you should be able to run from their forward
(autorecon2 and autorecon3 I believe)

cheers
Bruce


On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:


Please can someone answer this. Thanks 
"
Hello Freesurfer, I have couple of questions. While going through the
frequently asked questions on your
pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a
question regarding how to integrate a skull stripped from another problem
into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag? 

Second question, where do I insert my already skull stripped data in the
symbolic link? 

Last question, the final stages of recon-all ( recon-all -autorecon2
-autorecon3)  doesn't include skull stripping, how can I be sure my skull
stripped data was incorporated into the freesurfer recon-all process? 

Best, 
Paul

Sent from my BlackBerry 10 smartphone.
From: miracoo...@gmail.com
Sent: Wednesday, November 2, 2016 9:39 AM
To: Freesurfer support list
Subject: Fw: recon-all steps question



Sent from my BlackBerry 10 smartphone.
From: miracle ozzoude 
Sent: Monday, October 31, 2016 8:39 AM
To: Douglas N Greve
Subject: recon-all steps question

Hello Freesurfer, I have couple of questions. While going through the
frequently asked questions on your
page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a
question regarding how to integrate a skull stripped from another problem
into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag? 

Second question, where do I insert my already skull stripped data in the
symbolic link? 

Last question, the final stages of recon-all doesn't include skull
stripping, how can I be sure my skull stripped data was incorporated into
the freesurfer recon-all process? 

Best, 
Paul







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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fw: recon-all steps question

[miracooloz]

Thanks Bruce. Another question, since " -no segmentation " flag skips the white 
matter segmentation step of recon-all. Can I also use the same logic as the 
"-noskullstrip" flag to replace the wm.seg.mgz file? That's, run " recon-all 
-autorecon1 -autorecon2 -nosegmentation -s subjid ". Then copy/convert my 
already segmented brain and name it wm.seg.mgz. After that, treat it as if I 
had freesurfer's wm.seg.mgz and finally, run " recon-all -autorecon3 -s " to 
complete the process. What do you think?  
Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Bruce Fischl
Sent: Friday, November 4, 2016 10:50 AM
To: Freesurfer support list
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] Fw: recon-all steps question

Hi Paul


we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so 
must create them somehow. I think if you copy/convert your already-stripped 
and name it brainmask.mgz we should treat that as if you had edited our 
skull stripping and you should be able to run from their forward 
(autorecon2 and autorecon3 I believe)

cheers
Bruce


On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:

> Please can someone answer this. Thanks 
> "
> Hello Freesurfer, I have couple of questions. While going through the
> frequently asked questions on your
> pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a
> question regarding how to integrate a skull stripped from another problem
> into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
> from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
> of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 
> 
> First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
> during skull stripping? why are they present if I included the "-no
> skullstrip" flag? 
> 
> Second question, where do I insert my already skull stripped data in the
> symbolic link? 
> 
> Last question, the final stages of recon-all ( recon-all -autorecon2
> -autorecon3)  doesn't include skull stripping, how can I be sure my skull
> stripped data was incorporated into the freesurfer recon-all process? 
> 
> Best, 
> Paul
> 
> Sent from my BlackBerry 10 smartphone.
> From: miracoo...@gmail.com
> Sent: Wednesday, November 2, 2016 9:39 AM
> To: Freesurfer support list
> Subject: Fw: recon-all steps question
> 
> 
> 
> Sent from my BlackBerry 10 smartphone.
> From: miracle ozzoude 
> Sent: Monday, October 31, 2016 8:39 AM
> To: Douglas N Greve
> Subject: recon-all steps question
> 
> Hello Freesurfer, I have couple of questions. While going through the
> frequently asked questions on your
> page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a
> question regarding how to integrate a skull stripped from another problem
> into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
> from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
> of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 
> 
> First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
> during skull stripping? why are they present if I included the "-no
> skullstrip" flag? 
> 
> Second question, where do I insert my already skull stripped data in the
> symbolic link? 
> 
> Last question, the final stages of recon-all doesn't include skull
> stripping, how can I be sure my skull stripped data was incorporated into
> the freesurfer recon-all process? 
> 
> Best, 
> Paul
> 
> 
> 
> 
>

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Pial medial line crossover at hemispheres

[Hampton, Jackie]

Thank you! I uploaded the subject which is labeled as 
SAIS_138_midline_deviation.tar.gz.

On Nov 3, 2016, at 4:46 PM, Bruce Fischl 
> wrote:

Hi Jackie

that's surprising. If you upload the subject we can take a look. You could also 
try relabeling the aseg (i.e. changing left/right labels for thalamic voxels 
that are incorrect)

cheers
Bruce


On Thu, 3 Nov 2016, Hampton, Jackie wrote:

In some of my subjects, the medial pial line crosses over the hemispheres.
It mislabels in both brainmask and aseg. So the part that it crosses too far
over in the left hemisphere is now mislabeled. I have seen this issue in the
forums before, but it didn’t seem that there was a definitive fix to the
issue. I am just hoping someone will be able to give me some direction. I
have tried deleting voxels to no avail. Thank you!
I have attached screenshots of the issue that I am having.
Jackie Hampton
Clinical Research Study Assistant
Nico Dosenbach, MD, PhD & Deanna Greene, PhD
Department of Neurology
Washington University School of Medicine
660 S. Euclid Ave. | Campus Box 8111
St. Louis, MO 63110
Phone: 314-362-4154
jackiehamp...@wustl.edu
[IMAGE][IMAGE]


The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If you
are not the intended recipient, be advised that any unauthorized use,
disclosure, copying or the taking of any action in reliance on the contents
of this information is strictly prohibited. If you have received this email
in error, please immediately notify the sender via telephone or return mail.
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dispose of the e-mail.

Jackie





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] mris_preproc

[Alshikho, Mohamad J.]

Thank you very much Doug!

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, November 4, 2016 12:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc

projfrac = -2 appears to be pointing at the ventricle. It should be 2*thickness 
away from the white surface into the white matter


On 11/04/2016 12:11 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> I am sorry for sending multiple emails. I wanted to be sure that I understand 
> it properly. Kindly:
> My question is regarding "projfrac = -1" and "projfrc=-2" are the pointers in 
> the figure located correctly where the analysis will be carried out?
>
> Thanks again
>
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 4, 2016 12:09 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc
>
> Do you have a question about the image?
>
>
> On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
>> Thank you Doug!
>> Kindly in the attached figure are the "projfrac" values for #4 and #5 
>> correct for at which level the analysis will be carried out.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Friday, November 4, 2016 10:29 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mris_preproc
>>
>>
>>
>> On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote:
>>>Dear FS experts,
>>>
>>>I ran surface based analysis using PET maps, and the pipeline
>>> reported, in FS list, by multiple colleagues as  the following:
>>>
>>> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
>>>
>>> ·mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii
>>> subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
>>>
>>> ·mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval
>>> lh.mgh --tval lh.sm6.mgh
>>>
>>> ·mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage
>>> lh --cortex --glmdir lh.glmdir//
>>>
>>> ·then mri_glmfit-sim to correct for multiple comparison.
>>>
>>> I wanted to know the correct usage of the flag "*_projfrac_*" in the
>>> command "*_mris_preproc_*":
>>>
>>> My understanding is that this flag control running the surface based
>>> analysis far from the surface (i.e. close to the surface or deep in
>>> the white matter)
>>>
>>> ·If it is 0.5 èthat means the surface based analysis is running in
>>> the middle area between white and pial
>>>
>>> ·if it is zero èthe surface based analysis is running close to white
>>> matter
>>>
>>> ·if it is +1 èthat means the surface based analysis is running close
>>> to the pial
>>>
>>> ·if it is -1 èthat means the surface based analysis is running deep
>>> in the white matter
>>>
>>> Kindly:
>>>
>>> 1.Is this correct?
>>>
>> Yes
>>> 2.Can I  use values like -2 or -3 ... etc to run the analysis deep in
>>> the white matter. I aim to run surface based analysis on multiple
>>> layers of the brain deep from the pial to investigate how the PET
>>> signal is going to change between these layers?
>>>
>> In principle, yes, but often what happens is that when you follow the normal 
>> vector into the white matter that far, you end up in GM or CSF and not WM.
>>> 3.What is the difference between the flag "*_projfrac_*" and the flag
>>> "*_projdis_*"
>>>
>> projdist will project an absolute distance (in mm). projfrac will
>> project a fraction of the thickness (as you describe above)
>>> 4.If I replace the PET maps in the previous pipeline by diffusion
>>> maps? Is it keep valid for diffusion data?
>>>
>> I guess it depends on what you mean by "valid". As I mention above, it
>> will not necessarily sample WM, and that probably invalidates it
>> somewhat
>>> Many Thank!
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR 

Re: [Freesurfer] mris_preproc

[Douglas N Greve]

projfrac = -2 appears to be pointing at the ventricle. It should be 
2*thickness away from the white surface into the white matter


On 11/04/2016 12:11 PM, Alshikho, Mohamad J. wrote:
> Hi Doug,
> I am sorry for sending multiple emails. I wanted to be sure that I understand 
> it properly. Kindly:
> My question is regarding "projfrac = -1" and "projfrc=-2" are the pointers in 
> the figure located correctly where the analysis will be carried out?
>
> Thanks again
>
>
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 4, 2016 12:09 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc
>
> Do you have a question about the image?
>
>
> On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
>> Thank you Doug!
>> Kindly in the attached figure are the "projfrac" values for #4 and #5 
>> correct for at which level the analysis will be carried out.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Friday, November 4, 2016 10:29 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mris_preproc
>>
>>
>>
>> On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote:
>>>Dear FS experts,
>>>
>>>I ran surface based analysis using PET maps, and the pipeline
>>> reported, in FS list, by multiple colleagues as  the following:
>>>
>>> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
>>>
>>> ·mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii
>>> subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
>>>
>>> ·mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval
>>> lh.mgh --tval lh.sm6.mgh
>>>
>>> ·mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage
>>> lh --cortex --glmdir lh.glmdir//
>>>
>>> ·then mri_glmfit-sim to correct for multiple comparison.
>>>
>>> I wanted to know the correct usage of the flag "*_projfrac_*" in the
>>> command "*_mris_preproc_*":
>>>
>>> My understanding is that this flag control running the surface based
>>> analysis far from the surface (i.e. close to the surface or deep in
>>> the white matter)
>>>
>>> ·If it is 0.5 èthat means the surface based analysis is running in
>>> the middle area between white and pial
>>>
>>> ·if it is zero èthe surface based analysis is running close to white
>>> matter
>>>
>>> ·if it is +1 èthat means the surface based analysis is running close
>>> to the pial
>>>
>>> ·if it is -1 èthat means the surface based analysis is running deep
>>> in the white matter
>>>
>>> Kindly:
>>>
>>> 1.Is this correct?
>>>
>> Yes
>>> 2.Can I  use values like -2 or -3 ... etc to run the analysis deep in
>>> the white matter. I aim to run surface based analysis on multiple
>>> layers of the brain deep from the pial to investigate how the PET
>>> signal is going to change between these layers?
>>>
>> In principle, yes, but often what happens is that when you follow the normal 
>> vector into the white matter that far, you end up in GM or CSF and not WM.
>>> 3.What is the difference between the flag "*_projfrac_*" and the flag
>>> "*_projdis_*"
>>>
>> projdist will project an absolute distance (in mm). projfrac will
>> project a fraction of the thickness (as you describe above)
>>> 4.If I replace the PET maps in the previous pipeline by diffusion
>>> maps? Is it keep valid for diffusion data?
>>>
>> I guess it depends on what you mean by "valid". As I mention above, it
>> will not necessarily sample WM, and that probably invalidates it
>> somewhat
>>> Many Thank!
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 

Re: [Freesurfer] mris_preproc

[Douglas N Greve]

Do you have a question about the image?


On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
> Kindly in the attached figure are the "projfrac" values for #4 and #5 correct 
> for at which level the analysis will be carried out.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Friday, November 4, 2016 10:29 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc
>
>
>
> On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote:
>>   Dear FS experts,
>>
>>   I ran surface based analysis using PET maps, and the pipeline
>> reported, in FS list, by multiple colleagues as  the following:
>>
>> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
>>
>> ·mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii
>> subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
>>
>> ·mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh
>> --tval lh.sm6.mgh
>>
>> ·mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage
>> lh --cortex --glmdir lh.glmdir//
>>
>> ·then mri_glmfit-sim to correct for multiple comparison.
>>
>> I wanted to know the correct usage of the flag "*_projfrac_*" in the
>> command "*_mris_preproc_*":
>>
>> My understanding is that this flag control running the surface based
>> analysis far from the surface (i.e. close to the surface or deep in
>> the white matter)
>>
>> ·If it is 0.5 èthat means the surface based analysis is running in the
>> middle area between white and pial
>>
>> ·if it is zero èthe surface based analysis is running close to white
>> matter
>>
>> ·if it is +1 èthat means the surface based analysis is running close
>> to the pial
>>
>> ·if it is -1 èthat means the surface based analysis is running deep in
>> the white matter
>>
>> Kindly:
>>
>> 1.Is this correct?
>>
> Yes
>> 2.Can I  use values like -2 or -3 ... etc to run the analysis deep in
>> the white matter. I aim to run surface based analysis on multiple
>> layers of the brain deep from the pial to investigate how the PET
>> signal is going to change between these layers?
>>
> In principle, yes, but often what happens is that when you follow the normal 
> vector into the white matter that far, you end up in GM or CSF and not WM.
>> 3.What is the difference between the flag "*_projfrac_*" and the flag
>> "*_projdis_*"
>>
> projdist will project an absolute distance (in mm). projfrac will project a 
> fraction of the thickness (as you describe above)
>> 4.If I replace the PET maps in the previous pipeline by diffusion
>> maps? Is it keep valid for diffusion data?
>>
> I guess it depends on what you mean by "valid". As I mention above, it will 
> not necessarily sample WM, and that probably invalidates it somewhat
>> Many Thank!
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] CUDA 8.0 and error on recon-all nu_correct

[Z K]

On 11/04/2016 07:30 AM, anonymous anonymous wrote:
> Hi all,
>
> I'm new to freesurfer and I'm having some issues.
>
> 1) First of all I tried recon-all in one subject but I got an error on
> nu_correct. This is what the log says:
>
> Can't use 'defined(@array)' (Maybe you should just omit the defined()?)
> at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
> nu_correct: crashed while running nu_estimate_np_and_em (termination
> status=65280)
> ERROR: nu_correct

This is a known issue due to an incompatibility between the mni tools 
shipped with freesurfer 5.3 and the version of perl shipped with ubuntu 
16. The issue is fixed in the upcoming release of freesurfer v6, but in 
the meantime the only known solution is to download and install the 
development version of freesurfer, available from the page (see 
"Development Version"):

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

>
> I searched through the mail list and I found that it may be because my
> data is in an external hard drive... (the hard drive is in FAT32).
> But it's not because the data is in the external hard drive. I copied a
> folder to my computer and I got the same problem. Could it be the data?
>
>
> 2) Then I tried to install CUDA 8.0 ... I don't know if succesfully
> because the command cudadetect shows the following:
>
> cudadetect.bin: error while loading shared libraries: libcudart.so.5.0:
> cannot open shared object file: No such file or directory
>
> Reading as well I'm afraid that freesurfer may not be able to use
> versions of CUDA that are +5? I have an NVIDIA Geforce GTX 950 and using
> NVIDIA binary driver version 370.28.

Freesurfer was compiled against cuda5, so you'll need that version, 
which admittedly is fairly ancient at this point. Its unlikely to change 
in the future because we no longer actively support cuda, as we've 
focused our efforts on openmp.



>
> 3) I think after the installation of CUDA using a .deb I got the paths
> messed up and now I can't even use recon-all on my hard drive. When I
> type recon-all on any other external hard drive or folder, it does show
> the information though. I dont know if it's a permissions problem (I
> also had a blackout earlier...) but the hard disk's files and folders
> seem to have all permissions and the ownership is root:root. I can't
> remount it now because I'm running some things using fsl...

Not sure how to help with this other than to add the location of 
recon-all (which is installed in $FREESURFER_HOME/bin, usually 
/usr/local/freesurfer/bin) to your PATH environment variable.


>
>
>
>
> Please any help would be really appreciated. I've spent a lt of
> hours struggling with all these.
>
>
>
>
> I'm on a ubuntu 16.04 by the way.
>
>
> Thaankius
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mris_preproc

[Alshikho, Mohamad J.]

Hi Doug,
I am sorry for sending multiple emails. I wanted to be sure that I understand 
it properly. Kindly:
My question is regarding "projfrac = -1" and "projfrc=-2" are the pointers in 
the figure located correctly where the analysis will be carried out?

Thanks again




-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Friday, November 4, 2016 12:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc

Do you have a question about the image?


On 11/04/2016 11:09 AM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
> Kindly in the attached figure are the "projfrac" values for #4 and #5 correct 
> for at which level the analysis will be carried out.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Friday, November 4, 2016 10:29 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc
>
>
>
> On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote:
>>   Dear FS experts,
>>
>>   I ran surface based analysis using PET maps, and the pipeline 
>> reported, in FS list, by multiple colleagues as  the following:
>>
>> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
>>
>> ·mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii 
>> subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
>>
>> ·mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval 
>> lh.mgh --tval lh.sm6.mgh
>>
>> ·mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage 
>> lh --cortex --glmdir lh.glmdir//
>>
>> ·then mri_glmfit-sim to correct for multiple comparison.
>>
>> I wanted to know the correct usage of the flag "*_projfrac_*" in the 
>> command "*_mris_preproc_*":
>>
>> My understanding is that this flag control running the surface based 
>> analysis far from the surface (i.e. close to the surface or deep in 
>> the white matter)
>>
>> ·If it is 0.5 èthat means the surface based analysis is running in 
>> the middle area between white and pial
>>
>> ·if it is zero èthe surface based analysis is running close to white 
>> matter
>>
>> ·if it is +1 èthat means the surface based analysis is running close 
>> to the pial
>>
>> ·if it is -1 èthat means the surface based analysis is running deep 
>> in the white matter
>>
>> Kindly:
>>
>> 1.Is this correct?
>>
> Yes
>> 2.Can I  use values like -2 or -3 ... etc to run the analysis deep in 
>> the white matter. I aim to run surface based analysis on multiple 
>> layers of the brain deep from the pial to investigate how the PET 
>> signal is going to change between these layers?
>>
> In principle, yes, but often what happens is that when you follow the normal 
> vector into the white matter that far, you end up in GM or CSF and not WM.
>> 3.What is the difference between the flag "*_projfrac_*" and the flag 
>> "*_projdis_*"
>>
> projdist will project an absolute distance (in mm). projfrac will 
> project a fraction of the thickness (as you describe above)
>> 4.If I replace the PET maps in the previous pipeline by diffusion 
>> maps? Is it keep valid for diffusion data?
>>
> I guess it depends on what you mean by "valid". As I mention above, it 
> will not necessarily sample WM, and that probably invalidates it 
> somewhat
>> Many Thank!
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] mapping ROI to surface space

[Andrews, Derek]

Hello Freesurfer Developers,

I have gotten ahold of the dev version of mri_label2label.

Currently I have a .w file that I need to “fill in the holes” on. Could
you please specify the steps I will need to take to make my .w file an
acceptable input for mri_label2label, and any recommendations you may have
for the value of N for the —close flag.

Thank you.

Best, Derek 




Derek Sayre Andrews, MSc
PhD Candidate

The Sackler Institute for Translational Neurodevelopment
Department of Forensic and Neurodevelopmental Sciences
Institute of Psychiatry, Psychology & Neuroscience, King's College London

Telephone: +44 (0)20 7848 5701
Email: derek.andr...@kcl.ac.uk





> On 28/10/2016 15:53, "Bruce Fischl"  wrote:
> 
> Hi Derek
> 
> I think the dev version of mri_label2label supports
> open/close/dilate/erode
> operations:
> 
> mri_label2label --help
> USAGE: mri_label2label.bin
> 
>   --srclabel input label file
> 
>   --erode  N erode the label N times before writing
>   --open   N open the label N times before writing
>   --close  N close the label N times before writing
>   --dilate  Ndilate the label N times before writing
> .
> .
> .
> 
> if your version doesn't have these operations let us know and we can get
> you an updated one
> 
> cheers
> Bruce
> 
> 
> 
> On Fri, 28 Oct 2016,
> Andrews, Derek wrote:
> 
>> Hi Bruce,
>> 
>> As always thank you for your prompt reply.
>> 
>> For the morphological close operation, would you suggest using mris_fill
>> on the surface ROI I created and then running mri_vol2surf again on the
>> volume output by mris_fill?
>> 
>> Best, Derek
>> 
>> 
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>> 
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>> London
>> 
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>> 
>> 
>> 
>> 
>> 
>>> On 28/10/2016 14:54, "Bruce Fischl"  wrote:
>>> 
>>> p.s. you could remove many/most of these holes using a morphological
>>> close operation
 On Fri, 28 Oct 2016, Andrews, Derek wrote:
 
 Hello Freesurfer Developers and Community,
 
 I am looking to map a ROI.nii based on the MNI152 template to the
 fsaverage
 pial surface.
 
 I have used the following commands
 
 Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl
 ‹12
 ‹t1
 
 Then
 
 mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh
 
 The ROI appears to be in the right place however is very blotchy.
 Have I
 missed a step? Or is this correct?
 
 See bellow a picture of the ROI highlighted in FSL and in tksurfer
 after
 mapped using the above.
 
 Thank you for your support,
 
 Best, Derek
 
 [IMAGE]
 
 
 
 
 
 ___
 __
 ___
 
 Derek Sayre Andrews, MSc
 PhD Candidate
 
 The Sackler Institute for Translational Neurodevelopment
 
 Department of Forensic and Neurodevelopmental Sciences
 
 Institute of Psychiatry, Psychology & Neuroscience, King's College
 London
 
 Telephone: +44 (0)20 7848 5701
 Email: derek.andr...@kcl.ac.uk
 
 
 
 ___
>>> Freesurfer mailing list
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>>> nm
>>> 
>>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer=01%7C01%7Cderek
>>> .a
>>> 
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>>> b8
>>> 
>>> 3c724071654356%7C0=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D&
>>> re
>>> served=0
>>> 
>>> 
>>> The information in this e-mail is intended only for the person to whom
>>> it
>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> 
>>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa
>>> rt
>>> 
>>> ners.org%2Fcomplianceline=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e
>>> f7
>>> 
>>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0
>>> =%
>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D=0 . If the
>>> e-mail was sent to you in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>> 
>> 
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>> 
>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n
>> 

Re: [Freesurfer] Fw: recon-all steps question

[Bruce Fischl]

Hi Paul


we required the T1.mgz, brainmask.auto.mgz and brainmask.mgz volumes so 
must create them somehow. I think if you copy/convert your already-stripped 
and name it brainmask.mgz we should treat that as if you had edited our 
skull stripping and you should be able to run from their forward 
(autorecon2 and autorecon3 I believe)


cheers
Bruce


On Fri, 4 Nov 2016, miracoo...@gmail.com wrote:


Please can someone answer this. Thanks 
"
Hello Freesurfer, I have couple of questions. While going through the
frequently asked questions on your
pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a
question regarding how to integrate a skull stripped from another problem
into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag? 

Second question, where do I insert my already skull stripped data in the
symbolic link? 

Last question, the final stages of recon-all ( recon-all -autorecon2
-autorecon3)  doesn't include skull stripping, how can I be sure my skull
stripped data was incorporated into the freesurfer recon-all process? 

Best, 
Paul

Sent from my BlackBerry 10 smartphone.
From: miracoo...@gmail.com
Sent: Wednesday, November 2, 2016 9:39 AM
To: Freesurfer support list
Subject: Fw: recon-all steps question



Sent from my BlackBerry 10 smartphone.
From: miracle ozzoude 
Sent: Monday, October 31, 2016 8:39 AM
To: Douglas N Greve
Subject: recon-all steps question

Hello Freesurfer, I have couple of questions. While going through the
frequently asked questions on your
page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a
question regarding how to integrate a skull stripped from another problem
into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid >
create a symbolic link from T1.mgz to brainmask.auto.mgz and another like
from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages
of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). 

First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created
during skull stripping? why are they present if I included the "-no
skullstrip" flag? 

Second question, where do I insert my already skull stripped data in the
symbolic link? 

Last question, the final stages of recon-all doesn't include skull
stripping, how can I be sure my skull stripped data was incorporated into
the freesurfer recon-all process? 

Best, 
Paul




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Re: [Freesurfer] ROI NumVert

[Douglas N Greve]

You should be able to apply the mris_preproc command on the xhemi page

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

substituting your average subject for fsaverage_sym



On 11/04/2016 10:41 AM, Daya P wrote:
> I went to the shell script and changed the input for aparc+aseg and 
> aseg. and managed to make it work.
>
> My other question is that now that I have it running, after it is done 
> I would like to run a vertex wise analysis.
>
> Is there a tutorial/help or command that I should apply to do 
> asymmetry analysis.
> I was looking at the group analysis and setting GLM for thickness and 
> age.
> How could I do that with the results of xhemi for asymmetry in left 
> and right hemisphere?
>
> Thank you for you help!
>
>> On Nov 4, 2016, at 10:31 AM, Douglas N Greve 
>> > wrote:
>>
>> Try adding --zilles --reg
>>
>> It is a hack, but it might just work
>>
>>
>> On 11/04/2016 07:34 AM,daianapu...@gmail.com 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your reply, when I run xhemireg I get an error for
>>> cannot find aseg. is there any way to avoid that?  in the way there is
>>> a noaseg flag for other commmands. I built a cortical Atlas and dont
>>> have subcortical labels
>>>
>>> Thank you ,
>>> Daiana
>>> Daiana Pur
>>>
>>>
>>>
>>>
>>> On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve"
>>> >> > 
>>> wrote:
>>>
>>>oh, sorry, it does assume that you have pbsubmit, I had forgotten 
>>> that.
>>>You can actually follow the instructions for building your own 
>>> atlas at
>>>the bottom of the xhemi web page
>>>
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>>>
>>>This does the same thing as make_folding_atlas. It takes a long 
>>> time if
>>>you don't have a computational cluster to submit it to, which is 
>>> why I
>>>wrote make_folding_atlas
>>>
>>>doug
>>>
>>>
>>>On 11/02/2016 01:15 PM, Daya P wrote:
 Hi,

 When i try running make_folding_atlas I get

 xhemireg Trout2016 Wed Nov  2 13:11:23 EDT 2016
  #@# xhemireg --s Trout2016
 pbsubmit: Command not found.
 Launched 9 xhemireg processes
 #%# Waiting for 9 xhemireg processes Wed Nov  2 13:11:33 EDT 2016
 #%# Waiting for 9 xhemireg processes Wed Nov  2 13:12:33 EDT 2016

 I do not have access to a cluster. is there any way to bypass this?

 Thank  you,

 Daiana

 On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
> wrote: > > I've written a script that will come out with version
>>>6, but I've > put it > here > >
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
>> I think it should work in 5.3, but I'm not sure. If not, you
>>>can > download the dev version and make the atlas using that. Run
>>>it with > --help to get info on how to run it. > > > > On
>>>10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed
>>>to make a registration template and an cortical atlas > because >
 I am trying to measure cortical thickness, GM and surface area >
>>>on cat > > brains. > > > > What would be the necessary changes? >
 Would it be possible (and appropriate) to use just > >
>>>mris_left_right_register instead? > > > > Daiana > > > > On Fri,
>>>Oct 28, 2016 at 11:34 AM, Douglas Greve > > > >> wrote: > > > > A
>>>difference of 10 out of 500 or 1000 does not both me at > all. Why
> do you need to create your own atlas? It is doable for the
>>>cross > > hemi stuff, it is just difficult. > > > > > > On
>>>10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your
>>>help! > >> > >> I created a registration template and atlas from
>>>scratch > could I > >> input that in the interhemispheric
>>>registration analysis? > >> > >> The ROIs for the diffrerent
>>>regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct
>>>24, 2016 5:03 PM, "Douglas N Greve" > >> > >> wrote: > >> > >> It
>>>would depend on how big the ROI is to begin with. Do you > >> know
>>>that we > >> have our own interhemispheric analysis that might be
>>>better > >> for this? > >> Check out > >> > >>
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> > >> > > >> > >>
>> On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> >
>>> I drew ROIs on an initial subject and then after > >>
>>>registering all other > >> > subjects to the initial one, used
>>>mri_label2label to map > >> the ROIs from > >> > the initial
>>>subject to subsequent ones. > >> > I am interested in looking at
>>>asymmetry between left and > >> right regions. > >> > > >> > I had
>>>two concerns, one that the ROIs have different # > >> vertices on
>>> different subjects, but as you mentioned the nonlinear > >>
>>>process makes > >> > sense, since each subject 

Re: [Freesurfer] ROI NumVert

[Daya P]

I went to the shell script and changed the input for aparc+aseg and aseg. and 
managed to make it work.

My other question is that now that I have it running, after it is done I would 
like to run a vertex wise analysis.

Is there a tutorial/help or command that I should apply to do asymmetry 
analysis.  
I was looking at the group analysis and setting GLM for thickness and age. 
How could I do that with the results of xhemi for asymmetry in left and right 
hemisphere?

Thank you for you help!

> On Nov 4, 2016, at 10:31 AM, Douglas N Greve  
> wrote:
> 
> Try adding --zilles --reg
> 
> It is a hack, but it might just work
> 
> 
> On 11/04/2016 07:34 AM, daianapu...@gmail.com  
> wrote:
>> 
>> Hi,
>> 
>> Thank you for your reply, when I run xhemireg I get an error for 
>> cannot find aseg. is there any way to avoid that?  in the way there is 
>> a noaseg flag for other commmands. I built a cortical Atlas and dont 
>> have subcortical labels
>> 
>> Thank you ,
>> Daiana
>> Daiana Pur
>> 
>> 
>> 
>> 
>> On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" 
>>  
>> >> wrote:
>> 
>>oh, sorry, it does assume that you have pbsubmit, I had forgotten that.
>>You can actually follow the instructions for building your own atlas at
>>the bottom of the xhemi web page
>> 
>>http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi 
>> 
>> 
>>This does the same thing as make_folding_atlas. It takes a long time if
>>you don't have a computational cluster to submit it to, which is why I
>>wrote make_folding_atlas
>> 
>>doug
>> 
>> 
>>On 11/02/2016 01:15 PM, Daya P wrote:
>>> Hi,
>>> 
>>> When i try running make_folding_atlas I get
>>> 
>>> xhemireg Trout2016 Wed Nov  2 13:11:23 EDT 2016
>>>  #@# xhemireg --s Trout2016
>>> pbsubmit: Command not found.
>>> Launched 9 xhemireg processes
>>> #%# Waiting for 9 xhemireg processes Wed Nov  2 13:11:33 EDT 2016
>>> #%# Waiting for 9 xhemireg processes Wed Nov  2 13:12:33 EDT 2016
>>> 
>>> I do not have access to a cluster. is there any way to bypass this?
>>> 
>>> Thank  you,
>>> 
>>> Daiana
>>> 
>>> On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
 wrote: > > I've written a script that will come out with version
>>6, but I've > put it > here > >
>>https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas 
>> 
> I think it should work in 5.3, but I'm not sure. If not, you
>>can > download the dev version and make the atlas using that. Run
>>it with > --help to get info on how to run it. > > > > On
>>10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed
>>to make a registration template and an cortical atlas > because >
>>> I am trying to measure cortical thickness, GM and surface area >
>>on cat > > brains. > > > > What would be the necessary changes? >
>>> Would it be possible (and appropriate) to use just > >
>>mris_left_right_register instead? > > > > Daiana > > > > On Fri,
>>Oct 28, 2016 at 11:34 AM, Douglas Greve > > > >> wrote: > > > > A
>>difference of 10 out of 500 or 1000 does not both me at > all. Why
 do you need to create your own atlas? It is doable for the
>>cross > > hemi stuff, it is just difficult. > > > > > > On
>>10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your
>>help! > >> > >> I created a registration template and atlas from
>>scratch > could I > >> input that in the interhemispheric
>>registration analysis? > >> > >> The ROIs for the diffrerent
>>regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct
>>24, 2016 5:03 PM, "Douglas N Greve" > >> > >> wrote: > >> > >> It
>>would depend on how big the ROI is to begin with. Do you > >> know
>>that we > >> have our own interhemispheric analysis that might be
>>better > >> for this? > >> Check out > >> > >>
>>http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi 
>>  > > >> > > >> > >>
> On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> >
>> I drew ROIs on an initial subject and then after > >>
>>registering all other > >> > subjects to the initial one, used
>>mri_label2label to map > >> the ROIs from > >> > the initial
>>subject to subsequent ones. > >> > I am interested in looking at
>>asymmetry between left and > >> right regions. > >> > > >> > I had
>>two concerns, one that the ROIs have different # > >> vertices on
>> different subjects, but as you mentioned the nonlinear > >>
>>process makes > >> > sense, since each subject does not have the
>>exact same > >> brain size and > >> > curvature. > >> > > >> >
>>Another concern was that the ROIs on the left 

[Freesurfer] Fw: recon-all steps question

[miracooloz]

  Please can someone answer this. Thanks "  Hello Freesurfer, I have couple of questions. While going through the frequently asked questions on your pagehttp://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid > create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag? Second question, where do I insert my already skull stripped data in the symbolic link? Last question, the final stages of recon-all ( recon-all -autorecon2 -autorecon3)  doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process? Best, Paul   Sent from my BlackBerry 10 smartphone.From: miracoo...@gmail.comSent: Wednesday, November 2, 2016 9:39 AMTo: Freesurfer support listSubject: Fw: recon-all steps question  Sent from my BlackBerry 10 smartphone.From: miracle ozzoude Sent: Monday, October 31, 2016 8:39 AMTo: Douglas N GreveSubject: recon-all steps questionHello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid > create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz --> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag? Second question, where do I insert my already skull stripped data in the symbolic link? Last question, the final stages of recon-all doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process? Best, Paul


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] ROI NumVert

[Douglas N Greve]

Try adding --zilles --reg

It is a hack, but it might just work


On 11/04/2016 07:34 AM, daianapu...@gmail.com wrote:
>
> Hi,
>
> Thank you for your reply, when I run xhemireg I get an error for 
> cannot find aseg. is there any way to avoid that?  in the way there is 
> a noaseg flag for other commmands. I built a cortical Atlas and dont 
> have subcortical labels
>
> Thank you ,
> Daiana
> Daiana Pur
>
>
>
>
> On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" 
> > wrote:
>
> oh, sorry, it does assume that you have pbsubmit, I had forgotten that.
> You can actually follow the instructions for building your own atlas at
> the bottom of the xhemi web page
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
> This does the same thing as make_folding_atlas. It takes a long time if
> you don't have a computational cluster to submit it to, which is why I
> wrote make_folding_atlas
>
> doug
>
>
> On 11/02/2016 01:15 PM, Daya P wrote:
> > Hi,
> >
> > When i try running make_folding_atlas I get
> >
> > xhemireg Trout2016 Wed Nov  2 13:11:23 EDT 2016
> >   #@# xhemireg --s Trout2016
> > pbsubmit: Command not found.
> > Launched 9 xhemireg processes
> > #%# Waiting for 9 xhemireg processes Wed Nov  2 13:11:33 EDT 2016
> > #%# Waiting for 9 xhemireg processes Wed Nov  2 13:12:33 EDT 2016
> >
> > I do not have access to a cluster. is there any way to bypass this?
> >
> > Thank  you,
> >
> > Daiana
> >
> > On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
> >> wrote: > > I've written a script that will come out with version
> 6, but I've > put it > here > >
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
> > > > I think it should work in 5.3, but I'm not sure. If not, you
> can > download the dev version and make the atlas using that. Run
> it with > --help to get info on how to run it. > > > > On
> 10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed
> to make a registration template and an cortical atlas > because >
> > I am trying to measure cortical thickness, GM and surface area >
> on cat > > brains. > > > > What would be the necessary changes? >
> > Would it be possible (and appropriate) to use just > >
> mris_left_right_register instead? > > > > Daiana > > > > On Fri,
> Oct 28, 2016 at 11:34 AM, Douglas Greve > > > >> wrote: > > > > A
> difference of 10 out of 500 or 1000 does not both me at > all. Why
> > > do you need to create your own atlas? It is doable for the
> cross > > hemi stuff, it is just difficult. > > > > > > On
> 10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your
> help! > >> > >> I created a registration template and atlas from
> scratch > could I > >> input that in the interhemispheric
> registration analysis? > >> > >> The ROIs for the diffrerent
> regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct
> 24, 2016 5:03 PM, "Douglas N Greve" > >> > >> wrote: > >> > >> It
> would depend on how big the ROI is to begin with. Do you > >> know
> that we > >> have our own interhemispheric analysis that might be
> better > >> for this? > >> Check out > >> > >>
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > >> > > >> > >>
> > >> On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> >
> > >> > I drew ROIs on an initial subject and then after > >>
> registering all other > >> > subjects to the initial one, used
> mri_label2label to map > >> the ROIs from > >> > the initial
> subject to subsequent ones. > >> > I am interested in looking at
> asymmetry between left and > >> right regions. > >> > > >> > I had
> two concerns, one that the ROIs have different # > >> vertices on
> > >> > different subjects, but as you mentioned the nonlinear > >>
> process makes > >> > sense, since each subject does not have the
> exact same > >> brain size and > >> > curvature. > >> > > >> >
> Another concern was that the ROIs on the left and right > >>
> hemisphere in > >> > a subject do not have the exact same number
> of vertices. > >> Would a > >> > difference of 10 vertices max
> bias results? > >> > > >> > Thank you for your help, > >> > > >> >
> Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical
> Technologies & Advanced Robotics > >> > Brain and Mind Institute >
> >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada >
> >> > > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > >> >
> > >> > > >> > >> >>> wrote: > >> > > >> > Hi Daiana > >> > > >> >
> yes, that is to be expected given the nonlinear > nature > >> of
> the > >> > cross-subject registration. It shouldn't bias things, >
> >> although > >> > you'll need to give us more details if you want
> a > 

Re: [Freesurfer] mris_preproc

[Douglas N Greve]

On 11/04/2016 07:25 AM, Alshikho, Mohamad J. wrote:
>
>  Dear FS experts,
>
>  I ran surface based analysis using PET maps, and the pipeline 
> reported, in FS list, by multiple colleagues as  the following:
>
> ·spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
>
> ·mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii 
> subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
>
> ·mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh 
> --tval lh.sm6.mgh
>
> ·mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage 
> lh --cortex --glmdir lh.glmdir//
>
> ·then mri_glmfit-sim to correct for multiple comparison.
>
> I wanted to know the correct usage of the flag “*_projfrac_*” in the 
> command "*_mris_preproc_*":
>
> My understanding is that this flag control running the surface based 
> analysis far from the surface (i.e. close to the surface or deep in 
> the white matter)
>
> ·If it is 0.5 èthat means the surface based analysis is running in the 
> middle area between white and pial
>
> ·if it is zero èthe surface based analysis is running close to white 
> matter
>
> ·if it is +1 èthat means the surface based analysis is running close 
> to the pial
>
> ·if it is -1 èthat means the surface based analysis is running deep in 
> the white matter
>
> Kindly:
>
> 1.Is this correct?
>
Yes
>
> 2.Can I  use values like -2 or -3 ... etc to run the analysis deep in 
> the white matter. I aim to run surface based analysis on multiple 
> layers of the brain deep from the pial to investigate how the PET 
> signal is going to change between these layers?
>
In principle, yes, but often what happens is that when you follow the 
normal vector into the white matter that far, you end up in GM or CSF 
and not WM.
>
> 3.What is the difference between the flag "*_projfrac_*" and the flag 
> "*_projdis_*"
>
projdist will project an absolute distance (in mm). projfrac will 
project a fraction of the thickness (as you describe above)
>
> 4.If I replace the PET maps in the previous pipeline by diffusion 
> maps? Is it keep valid for diffusion data?
>
I guess it depends on what you mean by "valid". As I mention above, it 
will not necessarily sample WM, and that probably invalidates it somewhat
>
> Many Thank!
>
> Mohamad
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

[Douglas N Greve]

oops, sorry,

download these files

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit-sim

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_volcluster

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster

Copy them into $FREESURFER_HOME/bin (after making a backup of the 
previous files).

Edit mri_glmfit-sim to remove

source $FREESURFER_HOME/sources.csh

then hopefully everything should work

doug


On 11/04/2016 06:11 AM, John Anderson wrote:
> Hi Doug,
> I want to use GRF. Will you be willing to share the new versions of 
> the programs? Your help is highly appreciated.
> Thanks!
> Jon
> *on:* Friday, October 28, 2016 at 11:53 AM
> *From:* "Douglas Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Fw: Re: surface based analysis for 
> subcortical structures
>
> If you want to use GRF, then I should get you new versions of some of 
> the programs as the volume-based GRF used the Friston 1994 algorithm 
> that was not as accurate as the Worsley 1996 algorithm. I just updated 
> my code last week (better late than never:). But in the end, you 
> probably want to use permutation if your group analysis allows it.
>
> On 10/23/16 10:25 AM, John Anderson wrote:
>
> Thank you very much Doug,
> The codes worked very well. I was using the wrong command to
> correct the data.
> My command was
> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05
> --3spaces
> and for subcortical structures it must be
>
> mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166
>
> All the bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
> *Sent:* Thursday, October 20, 2016 at 9:20 PM
> *From:* "John Anderson" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis for subcortical
> structures
> Dear Doug,
> Thank you very much for this detailed explaination. I highly
> appreciate your help
> Kindly I have the following question:
> The command mri_vol2vol ran smoothly without any errors
> The command mri_mask output the following :
> mri_mask suvr.tal2mm.nii
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
> suvr.tal2mm.subc.nii
> freadFloat: fread failed
> DoAbs = 0
> Writing masked volume to suvr.tal2mm.subc.nii...done.
> Should I worry about this error ?
> I ignored this error and I continued the following steps. They
> went fine but when I correct for multiple comparisons using the
> command "mri_glmfit-sim" I get the following:
> mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05
> --3spaces
> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat
> --C 2G0C.mtx --glmdir subc.glmdir
> log file is subc.glmdir/cache.mri_glmfit-sim.log
> cd /analyses/pet_scan/SBM/sm
> /usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
> --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> Thu Oct 20 21:10:31 EDT 2016
> Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56
> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
> malshikh
> setenv SUBJECTS_DIR /analyses/recons
> FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
> Original mri_glmfit command line:
> cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat
> --C 2G0C.mtx --glmdir subc.glmdir
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = 10.682767
> ERROR: cannot find
> 
> /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
> I smoothed just fwhm = 1
> Kindly how can I troubleshoo? thank you for any advice
> Bests,
> John
> *Sent:* Thursday, October 20, 2016 at 12:16 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] surface based analysis for subcortical
> structures
>
> After spmregister, you can run
>
> mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
> talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii
>
> # mask out the cortical structures
>
> mri_mask pet.tal2mm.nii
> $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
> pet.tal2mm.subc.nii
>
> # Concatenate all subjects together
>
> mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
> all.pet.tal2mm.subc.nii --prune
>
> # smooth
>
> mri_fwhm --i all.pet.tal2mm.subc.nii --mask
> 

Re: [Freesurfer] ROI NumVert

[daianapur94]

Hi,


Thank you for your reply, when I run xhemireg I get an error for cannot find 
aseg. is there any way to avoid that?  in the way there is a noaseg flag for 
other commmands. I built a cortical Atlas and dont have subcortical labels


Thank you ,

Daiana

Daiana Pur




On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" 
 wrote:










oh, sorry, it does assume that you have pbsubmit, I had forgotten that. 
You can actually follow the instructions for building your own atlas at 
the bottom of the xhemi web page

http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

This does the same thing as make_folding_atlas. It takes a long time if 
you don't have a computational cluster to submit it to, which is why I 
wrote make_folding_atlas

doug


On 11/02/2016 01:15 PM, Daya P wrote:
> Hi,
>
> When i try running make_folding_atlas I get
>
> xhemireg Trout2016 Wed Nov  2 13:11:23 EDT 2016
>   #@# xhemireg --s Trout2016
> pbsubmit: Command not found.
> Launched 9 xhemireg processes
> #%# Waiting for 9 xhemireg processes Wed Nov  2 13:11:33 EDT 2016
> #%# Waiting for 9 xhemireg processes Wed Nov  2 13:12:33 EDT 2016
>
> I do not have access to a cluster. is there any way to bypass this?
>
> Thank  you,
>
> Daiana
>
> On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve 
> > wrote:
>
> I've written a script that will come out with version 6, but I've
> put it
> here
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
> 
>
> I think it should work in 5.3, but I'm not sure. If not, you can
> download the dev version and make the atlas using that. Run it with
> --help to get info on how to run it.
>
>
>
> On 10/28/2016 05:10 PM, Daya P wrote:
> > Hi Doug,
> >
> > I needed to make a registration template and an cortical atlas
> because
> > I am trying to measure cortical thickness, GM and surface area
> on cat
> > brains.
> >
> > What would be the necessary changes?
> > Would it be possible (and appropriate) to use just
> > mris_left_right_register instead?
> >
> > Daiana
> >
> > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve
> > 
>  >> wrote:
> >
> > A difference of 10 out of 500 or 1000 does not both me at
> all. Why
> > do you need to create your own atlas? It is doable for the cross
> > hemi stuff, it is just difficult.
> >
> >
> > On 10/26/16 10:16 AM, Daya P wrote:
> >>
> >> Thank you for your help!
> >>
> >> I created a registration template and atlas from scratch
> could I
> >> input that in the interhemispheric registration analysis?
> >>
> >> The ROIs for the diffrerent regions per hemisphere are 50-100
> >> vertices
> >>
> >> On Oct 24, 2016 5:03 PM, "Douglas N Greve"
> >>  
>  >> wrote:
> >>
> >> It would depend on how big the ROI is to begin with. Do you
> >> know that we
> >> have our own interhemispheric analysis that might be better
> >> for this?
> >> Check out
> >>
> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> 
> >>  >
> >>
> >>
> >> On 10/24/2016 12:33 PM, Daya P wrote:
> >> > Hi Bruce,
> >> >
> >> > I drew ROIs on an initial subject and then after
> >> registering all other
> >> > subjects to the initial one, used mri_label2label to map
> >> the ROIs from
> >> > the initial subject to subsequent ones.
> >> > I am interested in looking at asymmetry between left and
> >> right regions.
> >> >
> >> > I had two concerns, one that the ROIs have different #
> >> vertices on
> >> > different subjects, but as you mentioned the nonlinear
> >> process makes
> >> > sense, since each subject does not have the exact same
> >> brain size and
> >> > curvature.
> >> >
> >> > Another concern was that the ROIs on the left and right
> >> hemisphere in
> >> > a subject do not have the exact same number of vertices.
> >> Would a
> >> > difference of 10 vertices max bias results?
> >> >
> >> > Thank you for your help,
> >> >
> >> > Daiana R. Pur
> >> > Research Assistant
> >> > Canadian Surgical Technologies & Advanced Robotics
> >> > Brain and Mind Institute
> >> > Western University
> >> > London, ON, N6A 5B7
> >> > Canada
> >> >
> >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl
> >> >  
> >>  >
> >>  
> >>  >>> wrote:
> >>   

[Freesurfer] CUDA 8.0 and error on recon-all nu_correct

[anonymous anonymous]

Hi all,

I'm new to freesurfer and I'm having some issues.

1) First of all I tried recon-all in one subject but I got an error on
nu_correct. This is what the log says:

Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at
/usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)
ERROR: nu_correct

I searched through the mail list and I found that it may be because my data
is in an external hard drive... (the hard drive is in FAT32).
But it's not because the data is in the external hard drive. I copied a
folder to my computer and I got the same problem. Could it be the data?


2) Then I tried to install CUDA 8.0 ... I don't know if succesfully because
the command cudadetect shows the following:

cudadetect.bin: error while loading shared libraries: libcudart.so.5.0:
cannot open shared object file: No such file or directory

Reading as well I'm afraid that freesurfer may not be able to use versions
of CUDA that are +5? I have an NVIDIA Geforce GTX 950 and using NVIDIA
binary driver version 370.28.


3) I think after the installation of CUDA using a .deb I got the paths
messed up and now I can't even use recon-all on my hard drive. When I type
recon-all on any other external hard drive or folder, it does show the
information though. I dont know if it's a permissions problem (I also had a
blackout earlier...) but the hard disk's files and folders seem to have all
permissions and the ownership is root:root. I can't remount it now because
I'm running some things using fsl...




Please any help would be really appreciated. I've spent a lt of hours
struggling with all these.




I'm on a ubuntu 16.04 by the way.


Thaankius
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[Freesurfer] mris_preproc

[Alshikho, Mohamad J.]

 Dear FS experts,
 I ran surface based analysis using PET maps, and the pipeline reported, in FS 
list, by multiple colleagues as  the following:

* spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh

* mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii 
subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh

* mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh 
--tval lh.sm6.mgh

* mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage 
lh --cortex --glmdir lh.glmdir//

* then mri_glmfit-sim to correct for multiple comparison.

I wanted to know the correct usage of the flag "projfrac" in the command 
"mris_preproc":

My understanding is that this flag control running the surface based analysis 
far from the surface (i.e. close to the surface or deep in the white matter)


* If it is 0.5 ==> that means the surface based analysis is running in 
the middle area between white and pial

* if it is zero ==> the surface based analysis is running close to 
white matter

* if it is +1 ==> that means the surface based analysis is running 
close to the pial

* if it is -1 ==> that means the surface based analysis is running deep 
in the white matter

Kindly:


1.   Is this correct?

2.   Can I  use values like -2 or -3 ... etc to run the analysis deep in 
the white matter. I aim to run surface based analysis on multiple layers of the 
brain deep from the pial to investigate how the PET signal is going to change 
between these layers?

3.   What is the difference between the flag "projfrac" and the flag 
"projdis"

4.   If I replace the PET maps in the previous pipeline by diffusion maps? 
Is it keep valid for diffusion data?

Many Thank!
Mohamad
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

[John Anderson]

Hi Doug,

I want to use GRF. Will you be willing to share the new versions of the programs? Your help is highly appreciated. 

 

Thanks!

Jon

 

on: Friday, October 28, 2016 at 11:53 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures



If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use permutation if your group analysis allows it.

 
 

On 10/23/16 10:25 AM, John Anderson wrote:



Thank you very much Doug,

The codes worked very well. I was using the wrong command to correct the data.

My command was 

mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

 

and for subcortical structures it must be 


mri_glmfit-sim --glmdir subc.glmdir --grf 3 pos --cwpvalthresh .0166


All the bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Thursday, October 20, 2016 at 9:20 PM
From: "John Anderson" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures



Dear Doug,

Thank you very much for this detailed explaination. I highly appreciate your help

Kindly I have the following question:

The command mri_vol2vol ran smoothly without any errors

The command mri_mask output the following :

 

mri_mask suvr.tal2mm.nii $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz suvr.tal2mm.subc.nii 
freadFloat: fread failed
DoAbs = 0
Writing masked volume to suvr.tal2mm.subc.nii...done.

 

Should I worry about this error ?

 

 

I ignored this error and I continued the following steps. They went fine but when I correct for multiple comparisons using the command "mri_glmfit-sim" I get the following:

 

 


mri_glmfit-sim --glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir
log file is subc.glmdir/cache.mri_glmfit-sim.log

cd /analyses/pet_scan/SBM/sm
/usr/local/freesurfer/stable5_3_0/bin/mri_glmfit-sim
--glmdir subc.glmdir --cache 1.3 pos --cwp 0.05 --3spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu Oct 20 21:10:31 EDT 2016
Linux sven 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
malshikh
setenv SUBJECTS_DIR /analyses/recons
FREESURFER_HOME /usr/local/freesurfer/stable5_3_0

Original mri_glmfit command line:
cmdline mri_glmfit --y all.pet.tal2mm.subc.sm5.nii --fsgd fsgd.dat --C 2G0C.mtx --glmdir subc.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 10.682767
ERROR: cannot find /usr/local/freesurfer/stable5_3_0/average/mult-comp-cor///cortex/fwhm11/pos/th13/mc-z.csd
 


I smoothed just fwhm = 1

 

Kindly how can I troubleshoo? thank you for any advice

 

Bests,
John 


 

Sent: Thursday, October 20, 2016 at 12:16 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] surface based analysis for subcortical structures


After spmregister, you can run

mri_vol2vol --mov pet.nii --reg reg.dat --tal --talres 2 --talxfm
talairach.xfm --nearest --no-save-reg --o pet.tal2mm.nii

# mask out the cortical structures

mri_mask pet.tal2mm.nii
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz
pet.tal2mm.subc.nii

# Concatenate all subjects together

mri_concat s1/pet.tal2mm.subc.nii s2/pet.tal2mm.subc.nii ... --o
all.pet.tal2mm.subc.nii --prune

# smooth

mri_fwhm --i all.pet.tal2mm.subc.nii --mask
$FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz --fwhm X
--smooth-only --o all.pet.tal2mm.subc.smoothed.nii

mri_glmfit --y all.pet.tal2mm.subc.smoothed.nii --fsgd fsgd.txt--C
2gc0.mtx --glmdir subc.glmdir



On 10/19/2016 05:09 PM, John Anderson wrote:
> Dear experts,
> I ran surface based analysis using PET maps. As the following:
> spmregister --s subj --mov pet.nii --reg reg.dat --out pet_t1.mgh
> mris_preproc --target fsaverage --hemi lh --iv subj1/ubject1_pet.nii subject1/pet/pet_2_T1_register.dat . --projfrac 0.5 --out lh.mgh
> mri_surf2surf --hemi lh --s fsaverage --fwhm 6 --cortex --sval lh.mgh --tval lh.sm6.mgh
> mri_glmfit--y lh.sm6.mgh--fsgd fsgd.txt--C 2gc0.mtx --surf fsaverage lh --cortex --glmdir lh.glmdir//
> then mri_glmfit-sim to correct for multiple comparison.
> I want to study the subcortical regions and map it on MNI305. How can
> I resume tha analysis for subcortical structures?
> Thank you for any help!
> Bests,
> John
>
>
>