Re: [Freesurfer] error in manual edit by freeview

[Ruopeng Wang]

Would it be possible to send use the brain volume file?

Thanks,
Ruopeng

> On Aug 17, 2016, at 9:30 PM, 陈聪 <3110103...@zju.edu.cn> wrote:
> 
> Hi Doug
> Thank you for reply, My problem is shown in picture.
> Regards
> Cong
> 
> 
> ___
> 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


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
dispose of the e-mail.

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

Try using mri_convert to convert one set and see if that fixes it. If 
so, then never use unpack_fsl.sh again. Note that unpack_fsl.sh is not 
part of the FSL suit of tools, so don't blame them ...

On 08/17/2016 01:57 PM, Afzal, Afsana wrote:
> I opened up the functional and anatomical (original and reversed) in freeview 
> and the functional volume is better aligned with the reversed anatomical than 
> with the original anatomical. I realize this is a gross visual check that is 
> probably unreliable but I don't have any other guesses as so why the coreg is 
> failing for over 150 subjects.
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, August 17, 2016 1:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> what do you mean "visual inspection shows that they are actually
> reversed"? Please give details
>
> On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
>> I'm trying to understand why the coregistration for a bunch of subjects are 
>> bad/failing (mincost value > 8).
>>
>> The orientation for the anatomical matches the functional (after FSL 
>> unpacking) but visual inspection shows that they are actually reversed. Then 
>> I used mri_convert to change the orientation of the anatomical but the 
>> coregistration is still failing. So I still have no idea what's causing the 
>> coreg to fail or how to fix it.
>>
>> -Afsana
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, August 16, 2016 5:51 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>
>> I'm still not sure why you are trying to do this. If FSL did not unpack
>> the volumes with the correct orientation, then you need to switch to
>> mri_convert. If they are in the right orientation, then I don't
>> understand what you are trying to do.
>> doug
>>
>> On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>>> Hi Doug,
>>>
>>> After the coregistration failed for the majority of the subjects, I 
>>> visually inspected a handful of the subjects in freeview and it looks like 
>>> the anatomical and the functional are reversed but I could be wrong.
>>>
>>> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
>>> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you 
>>> to a specific subject directory if that would be of any help.
>>>
>>> Might be worth mentioning that the subjects who failed coreg were not 
>>> scanned using siemens scanners but Phillips and GE scanners. Don't know if 
>>> there's some sort of discrepancy between the scanner coordinate frames that 
>>> could potentially lead to this issue.
>>>
>>> Thank you very much for your help,
>>>
>>> Afsana
>>> __
>>> Afsana Afzal
>>> Clinical Research Coordinator
>>> Massachusetts General Hospital
>>> Division of Neurotherapeutics
>>> Department of Psychiatry: Neurosciences
>>> 149 13th St, Room 2612
>>> Charlestown, MA 02129
>>> Phone: 617-643-5129
>>> Fax: 617-726-4078
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, August 16, 2016 3:45 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>>
>>> How do you know that the structural is left-right reversed? Or that the
>>> fMRI is? How did you create the nifti files?
>>>
>>>
>>> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
 Hi,

 I'm having trouble co-registering a bunch of subjects whose T1 is
 left-right reversed. While the orientation of the structural file in
 the NIfTI header is LIA and the orientation of the functional volume
 is LAS, visual inspection shows that the structural is left-right
 reversed. I then followed the steps outlined in
 https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
  to rerun
 the reconstruction and re-registered the subject but the registration
 mincost value is still hovering around 0.9 even with the left-right
 reversed structural.

 I've tried running registration with SPM and FSL; neither method is
 able to register these subjects properly.

 With --init-fsl I get the 

Re: [Freesurfer] malloc_error_break/ can't allocate region

[zkaufman]

Hello Paul,

Doug is essential correct. You can download 5.3 (or the development
version) and just extract it to a different location. Something like:

  $> mkdir /usr/local/freesurfer_5.3
  $> tar -C /usr/local/freesurfer_5.3 -xzvf
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Then you are free to source either version - just make sure you to do in a
separate terminal window. Also, You can download freesurfer 5.3 or the
Development version (see "Development Version") from the following page:

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

Hope this helps.

-Zeke


> Zeke will know better than me, but I think the new version folder name
> will be different, so there should not be any conflict. You will just
> need to reference the new source file
>
> On 08/17/2016 12:23 PM, miracoo...@gmail.com wrote:
>> Sure. Also, do you know how I can upgrade to either without uninstalling
>> FS 5.1?
>>
>> Sent from my BlackBerry 10 smartphone.
>>Original Message
>> From: Douglas N Greve
>> Sent: Tuesday, August 16, 2016 4:01 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Reply To: Freesurfer support list
>> Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region
>>
>> That sounds fishy. I would use the 5.3 or 6.0 version.
>>
>> On 08/16/2016 03:51 PM, miracle ozzoude wrote:
>>> FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
>>>
>>> On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve
>>> > wrote:
>>>
>>> What version of FS (and mri_mcsim) are you using? Does it die if
>>> you run
>>> with just a few reps (eg, 100)?
>>>
>>> On 08/16/2016 01:21 PM, miracle ozzoude wrote:
 Hello FreeSurfer team,
 While running monte carlo correction with 1 reps (mri_mcsim) for
 the whole hemisphere, I received this error at 975 reps for the left
 hemisphere

 " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
>>> failed
 (error code=12)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 Bus error"
 What does this mean and how can I resolve it? Below was my mri_mcsim
 command line " mri_mcsim --o
 wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base
 mc-z --surface fsaverage lh --nreps 1"

 Thank you
 Paul


 ___
 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
>>> 
>>>
>>>
>>> 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
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> ___
>>> 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] Hiring: Cloud and HPC Engineer at NIMH in Bethesda, MD

[Thomas, Adam (NIH/NIMH) [E]]

NIMH is hiring a Cloud and HPC Engineer. Please spread the word!
https://github.com/nih-fmrif/hpc_job_ad


HIRING: CLOUD AND HPC ENGINEER

The National Institute of Mental Health (NIMH) is the lead federal
agency for research on mental disorders. NIMH is one of the 27
Institutes and Centers that make up the National Institutes of Health
(NIH), which is responsible for all federally funded biomedical research
in US. NIH is part of the U.S. Department of Health and Human Services
(HHS). The NIH is a highly rated employer at glassdoor.com with very
competitive salary and benefits packages.

The Data Science and Sharing Team (DSST) is a new group created to
develop and support data sharing and other data-intensive scientific
projects within the NIMH Intramural Research Program (IRP). Working
closely with the Office of Data Science the goal of the DSST is to make
the NIMH IRP a leader in the open science and data sharing practices
mandated by the Open Data Policy released by the White House on 9 May,
2013. We are building a team to make that happen.

What you’ll do…
---

BUILD

You will work with a team of researchers and developers to build and
deploy neuroimaging data processing pipelines for investigators within
the NIMH IRP. You will collaborate with and contribute to other projects
throughout the world that are building standards and tools for open and
reproducible neuroscience (e.g. NiPy, BIDS, Binder, Rstudio). You'll
have the resources of the NIH HPC Cluster at your disposal as well as
additional help from the AWS cloud. All tools and code will be open
source and freely distributed.

TEACH

You will work to bolster data science skills within the NIMH IRP by
teaching courses to scientists on best data practices (e.g., Software
& Data Carpentry) as well as accessing and using specific neuroimaging
repositories (e.g. The Human Connectome Project, OpenfMRI, UK
Biobank).

QUANTIFY

There is no use building tools for open science if no one uses them.
Part of the job of the DSST is to measure data sharing and open science
practices within the NIMH IRP and progress toward their adoption. This
will include bibliometrics for scientific publications from the NIMH IRP
and other measures of data sharing and secondary data utilization. You
will provide crucial systems level support to the team in gauging this
progress.

Who you are…


EXPERIENCED

You should be very comfortable on the command line and have a rock-solid
handle on one or more Unix-based operating systems. You should have some
experience with distributed, high-performance computing tools such as
Spark, OpenStack, Docker/Singularity, and batch processing systems such
as SLURM and SGE. You should also have experience coding in modern
languages currently used in data-intensive, scientific computing such as
Python, R, and Javascript, as well as interfacing with a variety of
APIs.

PROVEN

Ideally we would like to see a recent degree (BS, MS, or PhD) in a STEM
field, but if you can prove you have an equivalent amount of expertise
with your publications, projects, or github/kaggle ranking, we’re all
ears. We are also interviewing students and part-time staff if you’re
still working on your degree.

DRIVEN

Data science is moving fast – we’re looking for someone who can move
faster. You should be a self-learner and a self-starter. Provide some
examples of things you have worked on independently.

How to apply…
-

Email your resume, a cover letter, and a code sample that demonstrates
you are all three of the above to:

datasci-jobsea...@mail.nih.gov

The National Institutes of Health is an equal opportunity employer.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

I opened up the functional and anatomical (original and reversed) in freeview 
and the functional volume is better aligned with the reversed anatomical than 
with the original anatomical. I realize this is a gross visual check that is 
probably unreliable but I don't have any other guesses as so why the coreg is 
failing for over 150 subjects. 

__
Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, August 17, 2016 1:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

what do you mean "visual inspection shows that they are actually
reversed"? Please give details

On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
> I'm trying to understand why the coregistration for a bunch of subjects are 
> bad/failing (mincost value > 8).
>
> The orientation for the anatomical matches the functional (after FSL 
> unpacking) but visual inspection shows that they are actually reversed. Then 
> I used mri_convert to change the orientation of the anatomical but the 
> coregistration is still failing. So I still have no idea what's causing the 
> coreg to fail or how to fix it.
>
> -Afsana
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 5:51 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> I'm still not sure why you are trying to do this. If FSL did not unpack
> the volumes with the correct orientation, then you need to switch to
> mri_convert. If they are in the right orientation, then I don't
> understand what you are trying to do.
> doug
>
> On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>> Hi Doug,
>>
>> After the coregistration failed for the majority of the subjects, I visually 
>> inspected a handful of the subjects in freeview and it looks like the 
>> anatomical and the functional are reversed but I could be wrong.
>>
>> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
>> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
>> a specific subject directory if that would be of any help.
>>
>> Might be worth mentioning that the subjects who failed coreg were not 
>> scanned using siemens scanners but Phillips and GE scanners. Don't know if 
>> there's some sort of discrepancy between the scanner coordinate frames that 
>> could potentially lead to this issue.
>>
>> Thank you very much for your help,
>>
>> Afsana
>> __
>> Afsana Afzal
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, August 16, 2016 3:45 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>
>> How do you know that the structural is left-right reversed? Or that the
>> fMRI is? How did you create the nifti files?
>>
>>
>> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>>> Hi,
>>>
>>> I'm having trouble co-registering a bunch of subjects whose T1 is
>>> left-right reversed. While the orientation of the structural file in
>>> the NIfTI header is LIA and the orientation of the functional volume
>>> is LAS, visual inspection shows that the structural is left-right
>>> reversed. I then followed the steps outlined in
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>>>  to rerun
>>> the reconstruction and re-registered the subject but the registration
>>> mincost value is still hovering around 0.9 even with the left-right
>>> reversed structural.
>>>
>>> I've tried running registration with SPM and FSL; neither method is
>>> able to register these subjects properly.
>>>
>>> With --init-fsl I get the following:
>>> WARNING: initial G-W contrast is negative, but expecting positive.
>>> If the mov data has a T1 contrast, re-run with --T1
>>>
>>> and with --init-spm I get:
>>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>>... continuing.
>>>
>>> At this point I'm out of ideas to try out. This issue is occurring for
>>> over 170 subjects (data collected 

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Douglas N Greve]

what do you mean "visual inspection shows that they are actually 
reversed"? Please give details

On 08/17/2016 01:31 PM, Afzal, Afsana wrote:
> I'm trying to understand why the coregistration for a bunch of subjects are 
> bad/failing (mincost value > 8).
>
> The orientation for the anatomical matches the functional (after FSL 
> unpacking) but visual inspection shows that they are actually reversed. Then 
> I used mri_convert to change the orientation of the anatomical but the 
> coregistration is still failing. So I still have no idea what's causing the 
> coreg to fail or how to fix it.
>
> -Afsana
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 5:51 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> I'm still not sure why you are trying to do this. If FSL did not unpack
> the volumes with the correct orientation, then you need to switch to
> mri_convert. If they are in the right orientation, then I don't
> understand what you are trying to do.
> doug
>
> On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
>> Hi Doug,
>>
>> After the coregistration failed for the majority of the subjects, I visually 
>> inspected a handful of the subjects in freeview and it looks like the 
>> anatomical and the functional are reversed but I could be wrong.
>>
>> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
>> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
>> a specific subject directory if that would be of any help.
>>
>> Might be worth mentioning that the subjects who failed coreg were not 
>> scanned using siemens scanners but Phillips and GE scanners. Don't know if 
>> there's some sort of discrepancy between the scanner coordinate frames that 
>> could potentially lead to this issue.
>>
>> Thank you very much for your help,
>>
>> Afsana
>> __
>> Afsana Afzal
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, August 16, 2016 3:45 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>>
>> How do you know that the structural is left-right reversed? Or that the
>> fMRI is? How did you create the nifti files?
>>
>>
>> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>>> Hi,
>>>
>>> I'm having trouble co-registering a bunch of subjects whose T1 is
>>> left-right reversed. While the orientation of the structural file in
>>> the NIfTI header is LIA and the orientation of the functional volume
>>> is LAS, visual inspection shows that the structural is left-right
>>> reversed. I then followed the steps outlined in
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>>>  to rerun
>>> the reconstruction and re-registered the subject but the registration
>>> mincost value is still hovering around 0.9 even with the left-right
>>> reversed structural.
>>>
>>> I've tried running registration with SPM and FSL; neither method is
>>> able to register these subjects properly.
>>>
>>> With --init-fsl I get the following:
>>> WARNING: initial G-W contrast is negative, but expecting positive.
>>> If the mov data has a T1 contrast, re-run with --T1
>>>
>>> and with --init-spm I get:
>>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>>... continuing.
>>>
>>> At this point I'm out of ideas to try out. This issue is occurring for
>>> over 170 subjects (data collected outside Martinos using non-siemens
>>> scanners).
>>>
>>> Any help would be much appreciated!
>>>
>>> Thanks,
>>>
>>> Afsana
>>>
>>>
>>>
>>> __
>>> *Afsana Afzal*
>>> Clinical Research Coordinator
>>> Massachusetts General Hospital
>>> Division of Neurotherapeutics
>>> Department of Psychiatry: Neurosciences
>>> 149 13th St, Room 2612
>>> Charlestown, MA 02129
>>> Phone: 617-643-5129
>>> Fax: 617-726-4078
>>>
>>>
>>> ___
>>> 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
>> 

Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

[Afzal, Afsana]

I'm trying to understand why the coregistration for a bunch of subjects are 
bad/failing (mincost value > 8). 

The orientation for the anatomical matches the functional (after FSL unpacking) 
but visual inspection shows that they are actually reversed. Then I used 
mri_convert to change the orientation of the anatomical but the coregistration 
is still failing. So I still have no idea what's causing the coreg to fail or 
how to fix it. 

-Afsana


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 16, 2016 5:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed

I'm still not sure why you are trying to do this. If FSL did not unpack
the volumes with the correct orientation, then you need to switch to
mri_convert. If they are in the right orientation, then I don't
understand what you are trying to do.
doug

On 08/16/2016 05:27 PM, Afzal, Afsana wrote:
> Hi Doug,
>
> After the coregistration failed for the majority of the subjects, I visually 
> inspected a handful of the subjects in freeview and it looks like the 
> anatomical and the functional are reversed but I could be wrong.
>
> The nifti files are unpacked from DICOMs using unpack_fsl.sh 
> (/cluster/nrg/tools/0.10.0/code/lib/shell/unpack_fsl.sh). I can point you to 
> a specific subject directory if that would be of any help.
>
> Might be worth mentioning that the subjects who failed coreg were not scanned 
> using siemens scanners but Phillips and GE scanners. Don't know if there's 
> some sort of discrepancy between the scanner coordinate frames that could 
> potentially lead to this issue.
>
> Thank you very much for your help,
>
> Afsana
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, August 16, 2016 3:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Bad Coregistration - Left-Right Reversed
>
> How do you know that the structural is left-right reversed? Or that the
> fMRI is? How did you create the nifti files?
>
>
> On 08/16/2016 01:41 PM, Afzal, Afsana wrote:
>> Hi,
>>
>> I'm having trouble co-registering a bunch of subjects whose T1 is
>> left-right reversed. While the orientation of the structural file in
>> the NIfTI header is LIA and the orientation of the functional volume
>> is LAS, visual inspection shows that the structural is left-right
>> reversed. I then followed the steps outlined in
>> https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal
>>  to rerun
>> the reconstruction and re-registered the subject but the registration
>> mincost value is still hovering around 0.9 even with the left-right
>> reversed structural.
>>
>> I've tried running registration with SPM and FSL; neither method is
>> able to register these subjects properly.
>>
>> With --init-fsl I get the following:
>> WARNING: initial G-W contrast is negative, but expecting positive.
>> If the mov data has a T1 contrast, re-run with --T1
>>
>> and with --init-spm I get:
>> WARNING: bad orientation matrix (determinant = 0) in nifti1 file ...
>>   ... continuing.
>>
>> At this point I'm out of ideas to try out. This issue is occurring for
>> over 170 subjects (data collected outside Martinos using non-siemens
>> scanners).
>>
>> Any help would be much appreciated!
>>
>> Thanks,
>>
>> Afsana
>>
>>
>>
>> __
>> *Afsana Afzal*
>> Clinical Research Coordinator
>> Massachusetts General Hospital
>> Division of Neurotherapeutics
>> Department of Psychiatry: Neurosciences
>> 149 13th St, Room 2612
>> Charlestown, MA 02129
>> Phone: 617-643-5129
>> Fax: 617-726-4078
>>
>>
>> ___
>> 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] opening at the University of Sydney

[Anastasia Yendiki]

-- Forwarded message --
Date: Tue, 16 Aug 2016 22:55:47 +
From: Sasha Klistorner 

Research Fellow - Neuroimaging
Save Sight Institute and Brain and Mind Centre
Sydney Medical School
Reference no. 1332/0816

·   Join a collaborative and supportive research team
·   Bring your expertise in neuroimaging to this important research in 
multiple sclerosis
·   Full-time fixed term for one year, remuneration package: base salary 
$99K-$117K p.a., leave loading and up to 17% superannuation

The University of Sydney is Australia's first university and has an outstanding 
global reputation for academic and research excellence. It employs over 7600 
permanent staff, supporting over 60,000 students.

Save Sight Institute leads research into eye diseases and conditions, 
throughout Australia and internationally.
Our renowned team of laboratory and clinical researchers are at the forefront 
of ophthalmic breakthroughs, and our findings have already saved the sight of 
many people living with eye disease since the institute was formed in 1985.
The Brain and Mind Centre’s multidisciplinary research aims to set new 
standards in brain and mind sciences both in Australia and internationally, is 
dedicated to finding solutions that will lead to generational change. Our 
approach is based on the active collaboration of researchers from basic through 
to translational and clinical brain and mind sciences, students, patients and 
front-line carers.
We are seeking to appoint a Research Fellow to work under the combined 
supervision of Associate Professor Alexander (Sasha) Klistorner at the Save 
Sight Institute and Associate Professor Michael Barnett at the Brain and Mind 
Centre.  These world-class researchers are interested in the development of 
neuroimaging biomarkers of demyelination and axonal loss and the study of the 
mechanisms of axonal degeneration in multiple sclerosis using the visual system 
as a model. You will have the opportunity to actively participate in research 
in this area.
In this role you will:

* work closely with clinical, scientific, imaging and other relevant university 
staff at the Save Sight Institute and the Brain and Mind Centre, and the Sydney 
Neuroimaging Analysis Centre to develop and/or refine magnetic resonance 
imaging protocols and analysis pipelines relevant to the project
* be required to develop and implement a tool for the longitudinal analysis of 
diffusion tensor imaging (DTI) alterations in multiple sclerosis patients
* provide expertise across aspects of magnetic resonance imaging acquisition, 
protocol design and writing, analysis and interpretation of data relevant to 
the project; and contribute to writing peer-reviewed manuscripts
* take responsibility for the supervision of research assistants / image 
analysts working on the project or related projects where relevant

·   undertake administration relating to your own university activities.
You may also have the opportunity to work on other related team projects and to 
supervise postgraduate research students or projects and be involved in 
research training.
To succeed in securing this role you will have:
·   a PhD in neuroimaging or a related discipline
·   knowledge of MRI analytics, physics, mathematical and computational 
modelling
·   strong experience in MRI image processing and analysis
·   solid experience in basic neuroimaging toolboxes such as FSL, 
FreeSurfer or similar analytical packages
·   experience in Diffusion MR data analysis
·   demonstrated experience writing complex analytical reports and papers
·   ability to work both independently and as part of a multidisciplinary 
team
·   programming skills in bash-scripting, Matlab and/or Python
·   sound organisational skills and ability to effectively manage competing 
priorities___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

Re: [Freesurfer] malloc_error_break/ can't allocate region

[Douglas N Greve]

Zeke will know better than me, but I think the new version folder name 
will be different, so there should not be any conflict. You will just 
need to reference the new source file

On 08/17/2016 12:23 PM, miracoo...@gmail.com wrote:
> Sure. Also, do you know how I can upgrade to either without uninstalling FS 
> 5.1?
>
> Sent from my BlackBerry 10 smartphone.
>Original Message
> From: Douglas N Greve
> Sent: Tuesday, August 16, 2016 4:01 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region
>
> That sounds fishy. I would use the 5.3 or 6.0 version.
>
> On 08/16/2016 03:51 PM, miracle ozzoude wrote:
>> FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
>>
>> On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve
>> > wrote:
>>
>> What version of FS (and mri_mcsim) are you using? Does it die if
>> you run
>> with just a few reps (eg, 100)?
>>
>> On 08/16/2016 01:21 PM, miracle ozzoude wrote:
>>> Hello FreeSurfer team,
>>> While running monte carlo correction with 1 reps (mri_mcsim) for
>>> the whole hemisphere, I received this error at 975 reps for the left
>>> hemisphere
>>>
>>> " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
>> failed
>>> (error code=12)
>>> *** error: can't allocate region
>>> *** set a breakpoint in malloc_error_break to debug
>>> Bus error"
>>> What does this mean and how can I resolve it? Below was my mri_mcsim
>>> command line " mri_mcsim --o
>>> wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base
>>> mc-z --surface fsaverage lh --nreps 1"
>>>
>>> Thank you
>>> Paul
>>>
>>>
>>> ___
>>> 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
>> 
>>
>>
>> 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
>> dispose of the e-mail.
>>
>>
>>
>>
>> ___
>> 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

Re: [Freesurfer] FSFAST ROI atlas

[Sabin Khadka]

Hi Michael- Is there anyway I can get those Gordon parcellation annot files?

Cheers,
Sabin Khadka

On Wed, Aug 17, 2016 at 10:59 AM, Harms, Michael  wrote:

>
> FYI: I supplied a version of the “Gordon” parcellation in .annot format to
> Bruce a while back.  He had expressed an interest in possibly including it
> as part of FS 6.0.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From:  on behalf of Doug Greve <
> gr...@nmr.mgh.harvard.edu>
> Reply-To: "freesurfer@nmr.mgh.harvard.edu"  >
> Date: Wednesday, August 17, 2016 at 9:55 AM
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Subject: Re: [Freesurfer] FSFAST ROI atlas
>
> I don't know anything about the Power atlas. For the HCP, if they have it
> in annotation format, then you can run mri_aparc2aseg to map it into the
> anatomical volume, then specify that volume when you run fcseed-config. To
> get the mri_aparc2aseg command line, look in the recon-all to find out how
> aparc+aseg.mgz is created
>
> On 8/17/16 9:28 AM, Sabin Khadka wrote:
>
> Hi Doug- Do you think it is possible to use these atlas? If so could you
> point me to steps that needed to be done.
>
> Thanks for your help!
>
> Cheers,
> Sabin Khadka
>
> On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve  > wrote:
>
>> I have not used them myself.
>>
>> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>>
>> HI all-
>>
>> I am using FSFAST to extract ROI time series values for further
>> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>>
>> However, I was wondering if anyone has used Power et.al 2011 rois and/or
>> HCP's newly defined 180/per hemi rois to extract time series data. If so
>> could you please advise me on how do it (if they are at all possible).
>>
>> Cheers,
>> Sabin Khadka
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___ Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e
>> du/mailman/listinfo/freesurfer 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 dispose of the e-mail.
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
>
> 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.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

Re: [Freesurfer] malloc_error_break/ can't allocate region

[miracooloz]

Sure. Also, do you know how I can upgrade to either without uninstalling FS 5.1?

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Douglas N Greve
Sent: Tuesday, August 16, 2016 4:01 PM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] malloc_error_break/ can't allocate region

That sounds fishy. I would use the 5.3 or 6.0 version.

On 08/16/2016 03:51 PM, miracle ozzoude wrote:
> FS 5.1.0. I tried it with 5000 reps for ROI analysis and it worked.
>
> On Tue, Aug 16, 2016 at 3:46 PM, Douglas N Greve 
> > wrote:
>
> What version of FS (and mri_mcsim) are you using? Does it die if
> you run
> with just a few reps (eg, 100)?
>
> On 08/16/2016 01:21 PM, miracle ozzoude wrote:
> > Hello FreeSurfer team,
> > While running monte carlo correction with 1 reps (mri_mcsim) for
> > the whole hemisphere, I received this error at 975 reps for the left
> > hemisphere
> >
> > " 975 3197.9 0 mri_mcsim(25495) malloc: ***mmap(size=16777216)
> failed
> > (error code=12)
> > *** error: can't allocate region
> > *** set a breakpoint in malloc_error_break to debug
> > Bus error"
> > What does this mean and how can I resolve it? Below was my mri_mcsim
> > command line " mri_mcsim --o
> > wholebrainanalysis/average/mult-comp-cor/fsaverage/lh/cortex --base
> > mc-z --surface fsaverage lh --nreps 1"
> >
> > Thank you
> > Paul
> >
> >
> > ___
> > 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
> 
>
>
> 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
> dispose of the e-mail.
>
>
>
>
> ___
> 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

Re: [Freesurfer] FA/MD.nii to fsaverage space

[Douglas Greve]

First register the DTI to the anatomical with bbregister to create a 
register.dat file for each DTI (you can use the same one for FA and MD; 
for the "mov" volume, use whatever reference you used for motion 
correction). You can then run


mri_vol2surf --mov FA.nii --reg register.dat --projfrac 0.5 --hemi lh 
--trgsubject fsaverage --o subject1.FA.lh.fsaverage.mgh


Run mri_vol2surf with --help to get info about the arguemts


On 8/17/16 6:21 AM, Andrews, Derek wrote:

Dear Freesurfer developers,

I would like to perform an analysis that requires me to have all of my 
subjects surface based and diffusion data in the same space.


I have performed recon-all –qcache so that all my surface based 
measures are in fsaverage space.


I now would like to register the FA.nii and MD.nii images to fsaverage 
space as well.


Could you please provide me some command line examples to perform 
this? I am unsure if I should be using mri_vol2vol or /mri_/cvs_register.


Thank you for your support.

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




___
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


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
dispose of the e-mail.

Re: [Freesurfer] Mixed anisotropic data

[Douglas Greve]

It will have some effect, but it is not clear exactly what. Probably the 
difference in 1.5 and 3T will be bigger. See the paper by Jorge Jovicich 
for more info about the diffs between 1.5 and 3T. You should make sure 
to have a balanced design if you want to publish it.


On 8/16/16 4:52 PM, Mahmoudi, Fariborz wrote:
> Dear Friends,
>
> I have used a mixed set of images from 1.5T and 3.0T scanners with 
> anisotropic voxel size in my study. I used Freesurfer tools for converting 
> them to isotropic voxel size before segmentation and reconvert to initial 
> state after segmentation. It is appreciated if someone let me know using such 
> a mixed anisotropic data causes any side effect in the volume measurement or 
> not. I will be also thankful if you could introduce a reference that 
> discusses the effect.
>
> Best Regards,
> Fari
>
> 
>
> CONFIDENTIALITY NOTICE: This email contains information from the sender that 
> may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected 
> from disclosure. This email is intended for use only by the person or entity 
> to whom it is addressed. If you are not the intended recipient, any use, 
> disclosure, copying, distribution, printing, or any action taken in reliance 
> on the contents of this email, is strictly prohibited. If you received this 
> email in error, please contact the sending party by reply email, delete the 
> email from your computer system and shred any paper copies.
>
> Note to Patients: There are a number of risks you should consider before 
> using e-mail to communicate with us. See our Privacy & Security page on 
> www.henryford.com for more detailed information as well as information 
> concerning MyChart, our new patient portal. If you do not believe that our 
> policy gives you the privacy and security protection you need, do not send 
> e-mail or Internet communications to us.
>
> ___
> 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


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
dispose of the e-mail.

Re: [Freesurfer] FSFAST ROI atlas

[Harms, Michael]

FYI: I supplied a version of the “Gordon” parcellation in .annot format to Bruce a while back.  He had expressed an interest in possibly including it as part of FS 6.0.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From:  on behalf of Doug Greve 
Reply-To: "freesurfer@nmr.mgh.harvard.edu" 
Date: Wednesday, August 17, 2016 at 9:55 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] FSFAST ROI atlas





I don't know anything about the Power atlas. For the HCP, if they have it in annotation format, then you can run mri_aparc2aseg to map it into the anatomical volume, then specify that volume when you run fcseed-config. To get the mri_aparc2aseg command line,
 look in the recon-all to find out how aparc+aseg.mgz is created


On 8/17/16 9:28 AM, Sabin Khadka wrote:


Hi Doug- Do you think it is possible to use these atlas? If so could you point me to steps that needed to be done.


Thanks for your help!




Cheers,

Sabin Khadka




On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
 wrote:


I have not used them myself.



On 8/15/16 10:23 AM, Sabin Khadka wrote:







HI all- 


I am using FSFAST to extract ROI time series values for further connectivity analysis. I've used Desikan, Destriuex and DKT atlas. 


However, I was wondering if anyone has used Power 
et.al 2011 rois and/or HCP's newly defined 180/per hemi rois to extract time series data. If so could you please advise me on how do it (if they are at all possible). 




Cheers,

Sabin Khadka





 


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://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 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 dispose of the e-mail.





___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer






 



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.


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

Re: [Freesurfer] FSFAST ROI atlas

[Douglas Greve]

I don't know anything about the Power atlas. For the HCP, if they have 
it in annotation format, then you can run mri_aparc2aseg to map it into 
the anatomical volume, then specify that volume when you run 
fcseed-config. To get the mri_aparc2aseg command line, look in the 
recon-all to find out how aparc+aseg.mgz is created



On 8/17/16 9:28 AM, Sabin Khadka wrote:
Hi Doug- Do you think it is possible to use these atlas? If so could 
you point me to steps that needed to be done.


Thanks for your help!

Cheers,
Sabin Khadka

On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
> wrote:


I have not used them myself.


On 8/15/16 10:23 AM, Sabin Khadka wrote:

HI all-

I am using FSFAST to extract ROI time series values for further
connectivity analysis. I've used Desikan, Destriuex and DKT atlas.

However, I was wondering if anyone has used Power et.al
 2011 rois and/or HCP's newly defined 180/per hemi
rois to extract time series data. If so could you please advise
me on how do it (if they are at all possible).

Cheers,
Sabin Khadka


___
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
 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 dispose of the e-mail. 


___
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


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
dispose of the e-mail.

Re: [Freesurfer] Recon-all Correcting Defect 0

[Douglas Greve]

Can you send the log file?


On 8/17/16 8:46 AM, Heidi Foo wrote:

Dear FreeSurfer team,

I am currently running recon-all for my subjects but for 2 of them, it 
stops at correcting defect. Do you have any ideas how I can deal with 
this problem?


Thanks.

Regards,
Heidi Foo


___
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


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
dispose of the e-mail.

Re: [Freesurfer] error in manual edit by freeview

[Douglas Greve]

I'm not sure what you are describing. Can you send a picture?


On 8/17/16 8:42 AM, 陈聪 wrote:
> Hi dear all
>  I am using freeview to edit segmentation, I found one slice in coronal 
> view in brainmask.mgz mismatch with other slice, this slice obviously move 
> down.  WM and T1.mgz are normal, I don’t know how to move this wrong slice 
> back.  Any advice will be appreciated.
>
> thanks very much.
> CONG
>  
>
> ___
> 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


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
dispose of the e-mail.

Re: [Freesurfer] recon-all version update not showing in log file

[Douglas Greve]

It will not overwrite the log file so as to retain everything that has 
been done to the data set; new information is appended to the end of it.



On 8/17/16 3:58 AM, Donna Cosgrove wrote:

Hi,

I am updating previously recon'd datasets done with FS versions 4.4 
and 5.2 to v5.3. I'm running the recon-all command on the previously 
done subjects to retain any edits.


However, when I had a look at the recon-all.log, it still has a date 
from the previous recon in 2013.


The pctsurfcon.log contains this info (below) with an updated date, 
but nothing else seems to have updated...

--
Logfile for pctsurfcon
Sun Aug 14 06:12:59 IST 2016
setenv SUBJECTS_DIR /home/psych_lab/Desktop/freesurfer/FREESURFER_
​DONE

cd /home/psych_lab/Desktop/freesurfer/FREESURFER_D
​ONE
/CON9231/scripts
/usr/local/freesurfer/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux nuig-79JP212-Ubuntu 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8 
19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

FREESURFER_HOME /usr/local/freesurfer
Cleaning up
-
T
​he command I'm using ​

recon-all -all -s SUBJ_ID
seems to works fine, even identifying initially in the terminal that 
the build stamps do not match. It does also take much less time than a 
recon from scratch.


Any thoughts would be appreciated.

Thanks for your help!
Donna


___
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


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
dispose of the e-mail.

[Freesurfer] ISMRM diffusion workshop: -1 month!

[Tim Dyrby]

Dear FreeSurfers,

This is just a reminder that the countdown for the ISMRM workshop on 
breaking the barriers of diffusion MRI has started.
The meeting will take place in Lisbon, 11-16 September. Please check 
http://www.ismrm.org/workshops/Diffusion16/ 
 for program and updates.


The registration is still open!

However, please note that accommodation at the Sheraton Lisboa hotel is 
still available *but not at the discounted ISMRM rate* (all the rooms 
have gone!). Alternative options can be found at 
http://www.ismrm.org/workshops/Diffusion16/housing.htm. 



Looking forward seeing you there.

Best,
Tim

--
Tim B. Dyrby
Associate Professor
Danish Research Centre for Magnetic Resonance (DRCMR), section 714
Center for Functional and Diagnostic Imaging and Research
Copenhagen University Hospital Hvidovre
Kettegård Allé 30
2650 Hvidovre
Denmark
Office phone: +45 38626542  Mobile:+45 40790282
web: http://dig.drcmr.dk and www.drcmr.dk
&
Image Analysis and Computer Graphics section
Department of Applied Mathematics and Computer Science
Technical University of Denmark
Richard Petersens Plads, Building 324
2800 Kongens Lyngby
Denmark
Office Phone: +45 45253424

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

Re: [Freesurfer] FSFAST ROI atlas

[Sabin Khadka]

Hi Doug- Do you think it is possible to use these atlas? If so could you
point me to steps that needed to be done.

Thanks for your help!

Cheers,
Sabin Khadka

On Mon, Aug 15, 2016 at 10:39 AM, Douglas Greve 
wrote:

> I have not used them myself.
>
> On 8/15/16 10:23 AM, Sabin Khadka wrote:
>
> HI all-
>
> I am using FSFAST to extract ROI time series values for further
> connectivity analysis. I've used Desikan, Destriuex and DKT atlas.
>
> However, I was wondering if anyone has used Power et.al 2011 rois and/or
> HCP's newly defined 180/per hemi rois to extract time series data. If so
> could you please advise me on how do it (if they are at all possible).
>
> Cheers,
> Sabin Khadka
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://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
>
>
> 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
> dispose of the e-mail.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

[Freesurfer] Recon-all Correcting Defect 0

[Heidi Foo]

Dear FreeSurfer team,

I am currently running recon-all for my subjects but for 2 of them, it
stops at correcting defect. Do you have any ideas how I can deal with this
problem?

Thanks.

Regards,
Heidi Foo
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

[Freesurfer] error in manual edit by freeview

[陈聪]

Hi dear all
I am using freeview to edit segmentation, I found one slice in coronal view 
in brainmask.mgz mismatch with other slice, this slice obviously move down.  WM 
and T1.mgz are normal, I don’t know how to move this wrong slice back.  Any 
advice will be appreciated.

thanks very much.
CONG


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

Re: [Freesurfer] REPOST: problem with Qdecrc file

[Clara Kühn]

Hi Martin,

I tried both. Neither of the options worked, though.
I have created a subdirectory SUBJECTS_DIR/qdec2stage/ where I have my dat 
file, the .Qdecrc, the level files etc. But when I start qdec in that folder, 
load the data table and prepare everything I still can't choose spc (for 
example) from the measures drop down menu.

Is there any other way (e.g. through glmfit) to look at spc or does that only 
work with qdec?

Best, Clara

- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Freitag, 12. August 2016 17:28:52
Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file

Hi Clara, 
Try to start qdec in the same directory. If that fails create a qdec sub 
directory underneath the subjects _dir and put the files there. 
Best Martin 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FA/MD.nii to fsaverage space

[Andrews, Derek]

Dear Freesurfer developers,

I would like to perform an analysis that requires me to have all of my subjects 
surface based and diffusion data in the same space.

I have performed recon-all -qcache so that all my surface based measures are in 
fsaverage space.

I now would like to register the FA.nii and MD.nii images to fsaverage space as 
well.

Could you please provide me some command line examples to perform this? I am 
unsure if I should be using mri_vol2vol or mri_cvs_register.

Thank you for your support.

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.

[Freesurfer] recon-all version update not showing in log file

[Donna Cosgrove]

Hi,

I am updating previously recon'd datasets done with FS versions 4.4 and 5.2
to v5.3. I'm running the recon-all command on the previously done subjects
to retain any edits.

However, when I had a look at the recon-all.log, it still has a date from
the previous recon in 2013.

The pctsurfcon.log contains this info (below) with an updated date, but
nothing else seems to have updated...
--
Logfile for pctsurfcon
Sun Aug 14 06:12:59 IST 2016
setenv SUBJECTS_DIR /home/psych_lab/Desktop/freesurfer/FREESURFER_
​DONE

cd /home/psych_lab/Desktop/freesurfer/FREESURFER_D
​ONE
/CON9231/scripts
/usr/local/freesurfer/bin/pctsurfcon
$Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $
Linux nuig-79JP212-Ubuntu 3.13.0-43-generic #72-Ubuntu SMP Mon Dec 8
19:35:06 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /usr/local/freesurfer
Cleaning up
-
T
​he command I'm using ​

recon-all -all -s SUBJ_ID
seems to works fine, even identifying initially in the terminal that the
build stamps do not match. It does also take much less time than a recon
from scratch.

Any thoughts would be appreciated.

Thanks for your help!
Donna
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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
dispose of the e-mail.