Re: [Freesurfer] recon-all error

[Yeseul Kim]

It works now!
Thank you :)



On 15 August 2017 at 03:30, Douglas N Greve 
wrote:

> first, run it with -subject sbj1_rec (ie, don't give it the full path).
> There is something wrong with the dash before the "i". It looks like a
> dash, but it is really something else. Did you cut and paste it from
> somewhere? At the command line, Try deleting it and typing a dash.
>
>
> On 08/14/2017 12:30 PM, Yeseul Kim wrote:
> >
> > Hi
> >
> > I'm beginner of freesurfer and have an error while using recon-all.
> > I'm Mac (Sierra) user.
> >
> >
> > My subject's data is under:
> >
> > /Applications/freesurfer/subjects/yeseul_data
> >
> >
> > After open terminal, I put commands like:
> >
> > export FREESURFER_HOME=/Applications/freesurfer
> >
> > source $FREESURFER_HOME/SetUpFreeSurfer.sh
> >
> > export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_
> data/sbj1
> >
> > recon-all –i $SUBJECTS_DIR/20170720_LHS.MR
> > .HEAD_CNIR_IBS.0017.0001.2017.07.20.
> 16.26.07.667681.198987303.IMA
> > –subject $SUBJECTS_DIR/sbj1_rec -all
> >
> >
> > (My subjects' data is *.IMA format. Filenames are like
> > "20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001..198987303.IMA". I don't
> > think I need to convert IMA format to another, right? Each subject has
> > 192 IMA files and I want to apply recon-all to all of these files.)
> >
> > When I run these commands, I get a messages like:
> >
> >  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
> >
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> >
> > FREESURFER_HOME   /Applications/freesurfer
> >
> > FSFAST_HOME   /Applications/freesurfer/fsfast
> >
> > FSF_OUTPUT_FORMAT nii.gz
> >
> > SUBJECTS_DIR /Applications/freesurfer/subjects
> >
> > MNI_DIR   /Applications/freesurfer/mni
> >
> > Yeseului-MacBook-Pro:~ yeseulkim$
> >
> > Yeseului-MacBook-Pro:~ yeseulkim$ export
> > SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1
> >
> > Yeseului-MacBook-Pro:~ yeseulkim$
> >
> > Yeseului-MacBook-Pro:~ yeseulkim$ recon-all –i
> > $SUBJECTS_DIR/20170720_LHS.MR
> > .HEAD_CNIR_IBS.0017.0001.2017.07.20.
> 16.26.07.667681.198987303
> > –subject $SUBJECTS_DIR/sbj1_rec -all
> >
> > ERROR: Flag i unrecognized.
> >
> > i
> > /Applications/freesurfer/subjects/yeseul_data/sbj1/
> 20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.
> 667681.198987303
> > subject /Applications/freesurfer/subjects/yeseul_data/sbj1/sbj1_rec -all
> >
> > Darwin Yeseului-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0:
> > Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64
> x86_64
> >
> >
> > recon-all -s  exited with ERRORS at Tue Aug 15 01:08:53 KST 2017
> >
> >
> > For more details, see the log file
> >
> > To report a problem, see
> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > 
> >
> >
> >
> > Does it matter with the format of my data files? Or did I set
> > variables incorrectly?
> > Thank you in advance!
> >
> >
> > Best wishes,
> > Yeseul
> > --
> > Yeseul Kim
> > Visual Cognitive Neuroscience Lab
> > Department of Psychology
> > Korea University
> > Seoul, Korea
> >
> >
> > ___
> > 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.
>



-- 
Yeseul Kim
Visual Cognitive Neuroscience Lab
Department of Psychology
Korea University
Seoul, Korea
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[Freesurfer] info on samseg routines

[Antonin Skoch]

Dear experts,

I would like to ask, whether I could obtain a basic general info on samseg 
routines - what specifically are they doing (publication reference) and how to 
use them?

Regards,

Antonin Skoch


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[Freesurfer] obtaining the most recent build of FreeSurfer development version

[Antonin Skoch]

Dear experts,

I would like to download the most recent build of FreeSurfer development 
version (linux 64 bit). 

The origin/dev git repository contains commit up to today (14.8.17), but last 
change of "daily build" of dev version is 28.7.17. 

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Linux-centos6_x86_64-dev.tar.gz

How is the build of dev version sheduled?

Antonin Skoch


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Re: [Freesurfer] mri_binarize/mri_mask command help

[Douglas N Greve]

do the commands on this link get you where you need to be?

https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat


On 08/14/2017 03:04 PM, Yagmur Ozdemir 19 wrote:
> I tried using it both as an input and output and the produced files both 
> seemed wrong, so I was trying different combinations.
>
> The template (a picture of it is attached in my initial email) is a mask for 
> primary visual areas, and to export and use it in a different software I am 
> trying to superimpose it on top of a complete skull stripped volume file like 
> rawavg. I am trying to reconstruct that volume file in that other software 
> hoping to visualize the mask on the software's native surface file.
>
> Thank you for the help,
> Idil
> 
> 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: Monday, August 14, 2017 9:36 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_binarize/mri_mask command help
>
> mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz).
> can you elaborate on what you are trying to do? what do you mean by a
> template?
>
>
> On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
>> Dear FreeSurfer experts,
>>
>> I am trying to use the following command to merge the volume file of a
>> template with original T1 orientation*, with a file like rawavg to get
>> the full brain volume, but the following attached image gets produced
>> and I am pretty sure, as a freesurfer novice, I am using a wrong
>> command line. I have tried mri_mask as well but do not think it is the
>> command to go. I also checked if two volumes are in the same
>> orientation using mri_orient.
>>
>> mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
>>
>> * (I have the native oriented version of this volume template as well,
>> and I attached a photo of the template as well)
>>
>> I would deeply appreciate if someone could help me correct my command
>> line. Thank you all for the time and help
>>
>> Idil
>>
>>
>> ___
>> 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.
>
>
> ___
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> 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] Mean diffusivity on cortex?

[Douglas N Greve]

You will need to run gtmseg --s subject (takes an hour or so), then add 
--seg gtmseg.mgz to the cmd line


On 08/14/2017 04:12 PM, Shane Schofield wrote:
> Hi Dr  Greve,
>
> Are the settings correct to do partial volume correction of my MD images?
>
> mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg 
> subject/dtrecon/register.lta --psf 0 --seg subject/mri/gtmseg.mgz 
> --default-seg-merge --auto-mask PSF .01 --mgx 0.25 --o 
> subject/dtrecon/adc.pvc.mgz --no-rescale
>
> Thank you!
>
>
>
> On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve 
>  wrote:
>
>
> The mri_gtmpvc command will remove volume fraction effects. Look at the
> PETsurfer page. Run it with --psf 0 and use the muller-gartner output.
> The output will only be valid for gray matter
>
>
> On 08/12/2017 10:55 AM, Bruce Fischl wrote:
> > Hi Shane
> >
> > we do have some tools to deal with it like
> > mri_compute_volume_fractions and mri_compute_volume_intensities, or
> > maybe Doug's PET stuff. At the very least you should probably regress
> > thickness out.
> >
> > cheers
> > Bruce
> >
> > On Sat, 12 Aug 2017, Shane Schofield wrote:
> >
> >> Thank you both.
> >>
> >> How can I deal with partial volume in this case? Would it be possible
> >> to use
> >> the partial volume tool for PET on my MD volumes? Sorry if it is a 
> silly
> >> idea.
> >>
> >> Best Wishes,
> >> Shane
> >>
> >>
> >> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia
> >> > wrote:
> >>
> >>
> >> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD
> >> from
> >> a lower-res (diffusion) space to a higher-res (T1) space, so it
> >> should be
> >> smooth already, relatively to measure derived from the T1. And MD 
> varies
> >> pretty smoothly (it¹s a mean of 3 things, after all).
> >>
> >> On 8/11/17, 1:11 PM, "Bruce Fischl"  > wrote:
> >>
> >> >Hi Shane
> >> >
> >> >not really - it totally depends on the size of the effect you are
> >> looking
> >> >for. I would be *very* careful about partial volume effects though
> >> >
> >> >cheers
> >> >Bruce
> >> >On Fri,
> >> >11 Aug 2017, Shane Schofield wrote:
> >> >
> >> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
> >> >>
> >> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a
> >> >>marker
> >> >> of neurodegeneration. The idea is that during the early stages of a
> >> >>disease,
> >> >> cellular microstructure may breakdown before cortical thinning
> >> occurs.
> >> >>This
> >> >> results in "less" barriers against diffusion resulting in an
> >> increase of
> >> >> MD.
> >> >>
> >> >>
> >> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl
> >> >> > 
> wrote:
> >> >>
> >> >>
> >> >> Hi Shane
> >> >>
> >> >> you probably don't need cvs as it is more to extend the 
> surface-based
> >> >> registration to the entire volume. Here you just need the
> >> surface-based
> >> >> registration I believe. Use mri_vol2surf to sample the FA onto the
> >> >>surface.
> >> >> After that it is identical to a thickness study
> >> >>
> >> >> cheers
> >> >> Bruce
> >> >>
> >> >>
> >> >>
> >> >> On Fri, 11 Aug 2017, Shane Schofield
> >> >> wrote:
> >> >>
> >> >> > Thanks Dr Yendiki.
> >> >> >
> >> >> > I am more interested to compare MD in grey matter regions by
> >> putting
> >> >>the
> >> >> MD on the surface, and then do a glmfit type of comparisons. Is
> >> that OK?
> >> >> Would you recommend me
> >> >> > to smooth the data after spatial normalisation? I have also used
> >> the
> >> >> mri_cvs_register as described on the tutorial.
> >> >> >
> >> >> >
> >> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
> >> >> > 
> wrote:
> >> >> >
> >> >> >
> >> >> > Hi DTI Experts,
> >> >> >
> >> >> > Is it sensible to do comparisons of MD on the cortex surface 
> like a
> >> >>normal
> >> >> cortical thickness comparisons between group? If the answer is
> >> yes, are
> >> >> there recommended on
> >> >> > smoothing ?
> >> >> >
> >> >> > DT_RECON has been completed in Freesurfer.
> >> >> >
> >> >> > Thank you.
> >> >> >
> >> >> >
> >> >> >
> >> >> ___
> >> >> 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 

Re: [Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Hi Dr  Greve,
Are the settings correct to do partial volume correction of my MD images?
mri_gtmpvc --i subject/dtrecon/adc.nii.gz --reg subject/dtrecon/register.lta 
--psf 0 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 
--mgx 0.25 --o subject/dtrecon/adc.pvc.mgz --no-rescale 
Thank you!



On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve 
 wrote:

The mri_gtmpvc command will remove volume fraction effects. Look at the 
PETsurfer page. Run it with --psf 0 and use the muller-gartner output. 
The output will only be valid for gray matter


On 08/12/2017 10:55 AM, Bruce Fischl wrote:
> Hi Shane
>
> we do have some tools to deal with it like 
> mri_compute_volume_fractions and mri_compute_volume_intensities, or 
> maybe Doug's PET stuff. At the very least you should probably regress 
> thickness out.
>
> cheers
> Bruce
>
> On Sat, 12 Aug 2017, Shane Schofield wrote:
>
>> Thank you both.
>>
>> How can I deal with partial volume in this case? Would it be possible 
>> to use
>> the partial volume tool for PET on my MD volumes? Sorry if it is a silly
>> idea.
>>
>> Best Wishes,
>> Shane
>>
>>
>> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia
>>  wrote:
>>
>>
>> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD 
>> from
>> a lower-res (diffusion) space to a higher-res (T1) space, so it 
>> should be
>> smooth already, relatively to measure derived from the T1. And MD varies
>> pretty smoothly (it¹s a mean of 3 things, after all).
>>
>> On 8/11/17, 1:11 PM, "Bruce Fischl"  wrote:
>>
>> >Hi Shane
>> >
>> >not really - it totally depends on the size of the effect you are 
>> looking
>> >for. I would be *very* careful about partial volume effects though
>> >
>> >cheers
>> >Bruce
>> >On Fri,
>> >11 Aug 2017, Shane Schofield wrote:
>> >
>> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
>> >>
>> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a
>> >>marker
>> >> of neurodegeneration. The idea is that during the early stages of a
>> >>disease,
>> >> cellular microstructure may breakdown before cortical thinning 
>> occurs.
>> >>This
>> >> results in "less" barriers against diffusion resulting in an 
>> increase of
>> >> MD.
>> >>
>> >>
>> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl
>> >>  wrote:
>> >>
>> >>
>> >> Hi Shane
>> >>
>> >> you probably don't need cvs as it is more to extend the surface-based
>> >> registration to the entire volume. Here you just need the 
>> surface-based
>> >> registration I believe. Use mri_vol2surf to sample the FA onto the
>> >>surface.
>> >> After that it is identical to a thickness study
>> >>
>> >> cheers
>> >> Bruce
>> >>
>> >>
>> >>
>> >> On Fri, 11 Aug 2017, Shane Schofield
>> >> wrote:
>> >>
>> >> > Thanks Dr Yendiki.
>> >> >
>> >> > I am more interested to compare MD in grey matter regions by 
>> putting
>> >>the
>> >> MD on the surface, and then do a glmfit type of comparisons. Is 
>> that OK?
>> >> Would you recommend me
>> >> > to smooth the data after spatial normalisation? I have also used 
>> the
>> >> mri_cvs_register as described on the tutorial.
>> >> >
>> >> >
>> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
>> >>  wrote:
>> >> >
>> >> >
>> >> > Hi DTI Experts,
>> >> >
>> >> > Is it sensible to do comparisons of MD on the cortex surface like a
>> >>normal
>> >> cortical thickness comparisons between group? If the answer is 
>> yes, are
>> >> there recommended on
>> >> > smoothing ?
>> >> >
>> >> > DT_RECON has been completed in Freesurfer.
>> >> >
>> >> > Thank you.
>> >> >
>> >> >
>> >> >
>> >> ___
>> >> 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
>>
>>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: 

[Freesurfer] Developmental Neuroimaging Postdoc

[emma jane]

The Program for Translational Research on Adversity and Neurodevelopment
 (P-TRAN) at The Pennsylvania State University is seeking a qualified
postdoctoral researcher with expertise in human brain imaging, specifically
magnetic resonance imaging (MRI)) with children and adolescents.  This
position is supported by a recently awarded NICHD Center Grant (i.e., a
CAPSTONE Center for Multidisciplinary Research in Child Abuse and Neglect;
PI: Dr. Jennie Noll) and will be based in the Child Maltreatment Solutions
Network (http://solutionsnetwork.psu.edu/) and the Prevention Research
Center (www.prevention.psu.edu), both of which are located on the
University  Park campus in State College, PA. The primary responsibility of
this position will be to provide neuroimaging research support (e.g.,
experimental design, implementation and data analysis) to a longitudinal
project that will consider the biological embedding of child maltreatment
in multiple biologic systems (e.g., neuroendocrine, autonomic, genetic,
epigenetic, immunologic) and the impact of embedding on health outcomes,
including neurodevelopmental trajectories.  Candidates must have a PhD in
psychology, neuroscience, or an allied field, or have completed all
requirements for a PhD by the time of appointment.  Applicants must have
expertise in human subjects MRI, preferably with developmental cohorts.
Preference will be given to those candidates with experience working with
children who have experienced maltreatment or other high-risk groups.  The
successful candidate will be expected to contribute to experimental design
and co-ordination of the neuroimaging aspects of the project and data
analysis.  Candidates must demonstrate expertise in functional and
structural MRI analysis methods using standard processing packages (e.g.,
SPM, AFNI, FSL, Freesurfer etc.) and experience with longitudinal and
complex datasets would be advantageous.  The postdoctoral researcher will
also be expected to contribute to manuscript preparation and presentation
of study-related outcomes at key scientific meetings.   Extensive
mentorship will be provided to the successful candidate in order to
facilitate transition to an independent research career.  This position
will provide an opportunity to interact with several vibrant research
communities at Penn State, including the Social Sciences Research Institute
(www.ssri.psu.edu) and the Social, Life and Engineering Science Imaging
Center (www.imaging.psu.edu), among others.   The initial appointment will
be for one year, with the possibility of renewal in subsequent years.
Salary and benefits are based on NIH guidelines, commensurate with
experience and qualifications.  Interested candidates should upload a CV,
cover letter, statement of research interests, and 2-3 relevant
publications.  In addition, applicants should arrange for 3 professional
references to be submitted separately to Dr. Emma Jane Rose (Associate
Director for P-TRAN) at emmajaner...@psu.edu. Review of applications will
begin immediately and will continue until the position is filled.   For
further information about this appointment, please contact Dr. Emma Jane
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[Freesurfer] Neuroimaging Postdoc at Penn State

[emma jane]

[image: image.png]
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*Associate Director for the **Program for Translational Research on
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*Edna Bennett Pierce Prevention Research Center*
*The Pennsylvania State University*
*308 Biobehavioral Health Building*
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Re: [Freesurfer] mri_binarize/mri_mask command help

[Yagmur Ozdemir 19]

I tried using it both as an input and output and the produced files both seemed 
wrong, so I was trying different combinations.

The template (a picture of it is attached in my initial email) is a mask for 
primary visual areas, and to export and use it in a different software I am 
trying to superimpose it on top of a complete skull stripped volume file like 
rawavg. I am trying to reconstruct that volume file in that other software 
hoping to visualize the mask on the software's native surface file.

Thank you for the help,
Idil 

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: Monday, August 14, 2017 9:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_binarize/mri_mask command help

mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz).
can you elaborate on what you are trying to do? what do you mean by a
template?


On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to use the following command to merge the volume file of a
> template with original T1 orientation*, with a file like rawavg to get
> the full brain volume, but the following attached image gets produced
> and I am pretty sure, as a freesurfer novice, I am using a wrong
> command line. I have tried mri_mask as well but do not think it is the
> command to go. I also checked if two volumes are in the same
> orientation using mri_orient.
>
> mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
>
> * (I have the native oriented version of this volume template as well,
> and I attached a photo of the template as well)
>
> I would deeply appreciate if someone could help me correct my command
> line. Thank you all for the time and help
>
> Idil
>
>
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Re: [Freesurfer] Freesurfer PIB PET image processing

[Douglas N Greve]

If you use mri_gtmpvc, then the gtm.stats file will have the intensity 
values.


On 08/11/2017 02:37 AM, M Janani wrote:
> Thanks for your support Douglas.
>
> I have processed my PIB PET images using PETSURFER. It works fine.
>
> I have one more query. Could you please help in computing the PiB mean value 
> and intensity value for the ROIs.
>
> Regards,
> Janani
>
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: 10 August 2017 20:06
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>
> do you mean to run the anatomical analysis on them? No.
>
>
> On 08/10/2017 05:23 AM, M Janani wrote:
>> Is it correct to process the PiB images using Freesurfer ?
>>
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: 10 August 2017 03:41
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer PIB PET image processing
>>
>> We do not have any thing to specifically analyze PiB. You can look at
>> the PETsurfer page for more general instructions
>>
>>
>> On 08/09/2017 02:15 AM, M Janani wrote:
>>> Hi Team,
>>>
>>> I apologize, I am new to Freesurfer.
>>>
>>> Currently we are processing PIB PET images.
>>>
>>>   When we compare the SPM data along with FREESURFER
>>> outputs. We were able to see a large variation in the values.
>>>
>>>   Could you please guide us in processing PIB PET
>>> images in Freesurfer?
>>>
>>>   Since the signal of a PET image is very weak, we
>>> used MRI image as a guide to map it to Standard brain.
>>>
>>>   How does Freesurfer process in this case?
>>>
>>>   Your help would be grateful.
>>>
>>> Regards,
>>>
>>> Janani
>>>
>>>
>>>
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
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> Fax: 617-726-7422
>
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Re: [Freesurfer] white matter ROI mask using an fsaverage label

[Douglas N Greve]

you can use mri_aparc2aseg. Look in the recon-all.log file of an 
individual for the command used to generate the wmparc.mgz.



On 08/01/2017 04:43 PM, Eryilmaz, H. Hamdi wrote:
> Hi Anastasia and FS experts,
>
> I am trying to create a white matter ROI mask underneath a cortical 
> ROI label (e.g., 2 mm into the white matter) created in fsaverage 
> space. I will then use this mask to extract values from individual 
> dtifit_FA and dtifit_MD maps generated by trac-all. What would be the 
> easiest way to do this? I thought about using mri_aparc2aseg but I am 
> not quite sure about how to specify a label with this command.
>
> Thanks so much for your help!
>
> Best,
> Hamdi
>
>
>
>
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Re: [Freesurfer] mri_binarize/mri_mask command help

[Douglas N Greve]

mri_binarize needs a mask or segmentation as input (eg, aparc+aseg.mgz). 
can you elaborate on what you are trying to do? what do you mean by a 
template?


On 08/11/2017 03:01 PM, Yagmur Ozdemir 19 wrote:
>
> Dear FreeSurfer experts,
>
> I am trying to use the following command to merge the volume file of a 
> template with original T1 orientation*, with a file like rawavg to get 
> the full brain volume, but the following attached image gets produced 
> and I am pretty sure, as a freesurfer novice, I am using a wrong 
> command line. I have tried mri_mask as well but do not think it is the 
> command to go. I also checked if two volumes are in the same 
> orientation using mri_orient.
>
> mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf
>
> * (I have the native oriented version of this volume template as well, 
> and I attached a photo of the template as well)
>
> I would deeply appreciate if someone could help me correct my command 
> line. Thank you all for the time and help
>
> Idil
>
>
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Re: [Freesurfer] Combining Results of Per-Run GLM?

[Douglas N Greve]

there is not an easy way to do it. Probably the easiest thing to do is 
to create a separate session for each run. You can them analyze them 
under the same analysis name, then combine them together with 
isxconcat-sess, then do a one-sample group mean (--osgm) fixed effects 
analysis in mri_glmfit.


On 08/13/2017 09:53 PM, Taylor, Johnmark wrote:
> Hello,
>
> I am trying to do a GLM analysis for a study in which I scanned each 
> participant twice. Currently, to combine the two scanning sessions I 
> am combining the runs from the two sessions into a single session 
> directory and applying per-session motion correction, essentially 
> treating all the data as though it came from a single session. The 
> issue is that when I do this, the GLM analysis takes prohibitively 
> long (with just 8 subjects, the analysis has already been running for 
> two weeks). To speed things up, I had the idea of doing the runwise 
> GLM (getting the betas and contrast values for each run), then 
> combining the runwise results to get t-values and p-values for the 
> whole session. However, I am not entirely sure how to do this last 
> bit; is there some kind of function that can be used to take all the 
> per-run t-values or effect sizes in a session and combine them to get 
> an aggregate t-value and p-value for the whole session, for a given 
> contrast? I believe FSL follows this analysis strategy (doing runwise 
> analyses then combining them into the whole session), so I was 
> wondering whether FSFAST had a way of doing the same.
>
> Thank you very much,
>
> JohnMark
>
>
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Re: [Freesurfer] recon-all error

[Douglas N Greve]

first, run it with -subject sbj1_rec (ie, don't give it the full path). 
There is something wrong with the dash before the "i". It looks like a 
dash, but it is really something else. Did you cut and paste it from 
somewhere? At the command line, Try deleting it and typing a dash.


On 08/14/2017 12:30 PM, Yeseul Kim wrote:
>
> Hi
>
> I'm beginner of freesurfer and have an error while using recon-all. 
> I'm Mac (Sierra) user.
>
>
> My subject's data is under:
>
> /Applications/freesurfer/subjects/yeseul_data
>
>
> After open terminal, I put commands like:
>
> export FREESURFER_HOME=/Applications/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
> export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1
>
> recon-all –i $SUBJECTS_DIR/20170720_LHS.MR
> 
> .HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303.IMA
> –subject $SUBJECTS_DIR/sbj1_rec -all
>
>
> (My subjects' data is *.IMA format. Filenames are like 
> "20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001..198987303.IMA". I don't 
> think I need to convert IMA format to another, right? Each subject has 
> 192 IMA files and I want to apply recon-all to all of these files.)
>
> When I run these commands, I get a messages like:
>
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>
> FREESURFER_HOME   /Applications/freesurfer
>
> FSFAST_HOME   /Applications/freesurfer/fsfast
>
> FSF_OUTPUT_FORMAT nii.gz
>
> SUBJECTS_DIR /Applications/freesurfer/subjects
>
> MNI_DIR   /Applications/freesurfer/mni
>
> Yeseului-MacBook-Pro:~ yeseulkim$
>
> Yeseului-MacBook-Pro:~ yeseulkim$ export 
> SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1
>
> Yeseului-MacBook-Pro:~ yeseulkim$
>
> Yeseului-MacBook-Pro:~ yeseulkim$ recon-all –i 
> $SUBJECTS_DIR/20170720_LHS.MR 
> .HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303
>  
> –subject $SUBJECTS_DIR/sbj1_rec -all
>
> ERROR: Flag i unrecognized.
>
> i 
> /Applications/freesurfer/subjects/yeseul_data/sbj1/20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303
>  
> subject /Applications/freesurfer/subjects/yeseul_data/sbj1/sbj1_rec -all
>
> Darwin Yeseului-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: 
> Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64
>
>
> recon-all -s  exited with ERRORS at Tue Aug 15 01:08:53 KST 2017
>
>
> For more details, see the log file
>
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
>
>
>
> Does it matter with the format of my data files? Or did I set 
> variables incorrectly?
> Thank you in advance!
>
>
> Best wishes,
> Yeseul
> -- 
> Yeseul Kim
> Visual Cognitive Neuroscience Lab
> Department of Psychology
> Korea University
> Seoul, Korea
>
>
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Re: [Freesurfer] Error when trying to compile the code

[Douglas N Greve]

what is your configure line? You may need to add something to point to 
the mni library

--with-mni-dir="/usr/pubsw/packages/mni/1.5"

On 08/14/2017 10:32 AM, Aziz Nanthaamornphong wrote:
> Dear FreeSurfer Experts,
>
> I was trying to compile the FreeSurfer code by following steps shown 
> in 
> https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page
>
> However, I got this error message after I ran ./configure
>
> configure: error: FATAL: netcdf lib not found. Set LDFLAGS or 
> --with-mni-dir.
>
>
>
> I currently use  OS X El Capitan as the OS.
>
> How can I solve this problem? Thank you in advance.
>
> Aziz.
>
>
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Re: [Freesurfer] Mean diffusivity on cortex?

[Shane Schofield]

Hi Dr Greve,
Thank you very much! I will use the MGX CTX volume for the surface sampling. 
Best Wishes,Shane.

On Monday, August 14, 2017, 4:36:28 PM GMT+1, Douglas N Greve 
 wrote:

The mri_gtmpvc command will remove volume fraction effects. Look at the 
PETsurfer page. Run it with --psf 0 and use the muller-gartner output. 
The output will only be valid for gray matter


On 08/12/2017 10:55 AM, Bruce Fischl wrote:
> Hi Shane
>
> we do have some tools to deal with it like 
> mri_compute_volume_fractions and mri_compute_volume_intensities, or 
> maybe Doug's PET stuff. At the very least you should probably regress 
> thickness out.
>
> cheers
> Bruce
>
> On Sat, 12 Aug 2017, Shane Schofield wrote:
>
>> Thank you both.
>>
>> How can I deal with partial volume in this case? Would it be possible 
>> to use
>> the partial volume tool for PET on my MD volumes? Sorry if it is a silly
>> idea.
>>
>> Best Wishes,
>> Shane
>>
>>
>> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia
>>  wrote:
>>
>>
>> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD 
>> from
>> a lower-res (diffusion) space to a higher-res (T1) space, so it 
>> should be
>> smooth already, relatively to measure derived from the T1. And MD varies
>> pretty smoothly (it¹s a mean of 3 things, after all).
>>
>> On 8/11/17, 1:11 PM, "Bruce Fischl"  wrote:
>>
>> >Hi Shane
>> >
>> >not really - it totally depends on the size of the effect you are 
>> looking
>> >for. I would be *very* careful about partial volume effects though
>> >
>> >cheers
>> >Bruce
>> >On Fri,
>> >11 Aug 2017, Shane Schofield wrote:
>> >
>> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
>> >>
>> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a
>> >>marker
>> >> of neurodegeneration. The idea is that during the early stages of a
>> >>disease,
>> >> cellular microstructure may breakdown before cortical thinning 
>> occurs.
>> >>This
>> >> results in "less" barriers against diffusion resulting in an 
>> increase of
>> >> MD.
>> >>
>> >>
>> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl
>> >>  wrote:
>> >>
>> >>
>> >> Hi Shane
>> >>
>> >> you probably don't need cvs as it is more to extend the surface-based
>> >> registration to the entire volume. Here you just need the 
>> surface-based
>> >> registration I believe. Use mri_vol2surf to sample the FA onto the
>> >>surface.
>> >> After that it is identical to a thickness study
>> >>
>> >> cheers
>> >> Bruce
>> >>
>> >>
>> >>
>> >> On Fri, 11 Aug 2017, Shane Schofield
>> >> wrote:
>> >>
>> >> > Thanks Dr Yendiki.
>> >> >
>> >> > I am more interested to compare MD in grey matter regions by 
>> putting
>> >>the
>> >> MD on the surface, and then do a glmfit type of comparisons. Is 
>> that OK?
>> >> Would you recommend me
>> >> > to smooth the data after spatial normalisation? I have also used 
>> the
>> >> mri_cvs_register as described on the tutorial.
>> >> >
>> >> >
>> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
>> >>  wrote:
>> >> >
>> >> >
>> >> > Hi DTI Experts,
>> >> >
>> >> > Is it sensible to do comparisons of MD on the cortex surface like a
>> >>normal
>> >> cortical thickness comparisons between group? If the answer is 
>> yes, are
>> >> there recommended on
>> >> > smoothing ?
>> >> >
>> >> > DT_RECON has been completed in Freesurfer.
>> >> >
>> >> > Thank you.
>> >> >
>> >> >
>> >> >
>> >> ___
>> >> 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
>>
>>
>
>
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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
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[Freesurfer] recon-all error

[Yeseul Kim]

Hi

I'm beginner of freesurfer and have an error while using recon-all. I'm Mac
(Sierra) user.


My subject's data is under:

 /Applications/freesurfer/subjects/yeseul_data


After open terminal, I put commands like:

export FREESURFER_HOME=/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh



export SUBJECTS_DIR=/Applications/freesurfer/subjects/yeseul_data/sbj1



recon-all –i $SUBJECTS_DIR/20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.
07.20.16.26.07.667681.198987303.IMA –subject $SUBJECTS_DIR/sbj1_rec -all



(My subjects' data is *.IMA format. Filenames are like
"20170720_LHS.MR_HEAR_CNIR_IBS.0017.0001..198987303.IMA". I don't think
I need to convert IMA format to another, right? Each subject has 192 IMA
files and I want to apply recon-all to all of these files.)

When I run these commands, I get a messages like:

 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

Yeseului-MacBook-Pro:~ yeseulkim$

Yeseului-MacBook-Pro:~ yeseulkim$ export SUBJECTS_DIR=/Applications/
freesurfer/subjects/yeseul_data/sbj1

Yeseului-MacBook-Pro:~ yeseulkim$

Yeseului-MacBook-Pro:~ yeseulkim$ recon-all –i $SUBJECTS_DIR/20170720_LHS.MR
.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303 –subject
$SUBJECTS_DIR/sbj1_rec -all

ERROR: Flag i unrecognized.

i /Applications/freesurfer/subjects/yeseul_data/sbj1/
20170720_LHS.MR.HEAD_CNIR_IBS.0017.0001.2017.07.20.16.26.07.667681.198987303
subject /Applications/freesurfer/subjects/yeseul_data/sbj1/sbj1_rec -all

Darwin Yeseului-MacBook-Pro.local 16.7.0 Darwin Kernel Version 16.7.0: Thu
Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Tue Aug 15 01:08:53 KST 2017


For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting


Does it matter with the format of my data files? Or did I set variables
incorrectly?
Thank you in advance!


Best wishes,
Yeseul
-- 
Yeseul Kim
Visual Cognitive Neuroscience Lab
Department of Psychology
Korea University
Seoul, Korea
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Re: [Freesurfer] Mean diffusivity on cortex?

[Douglas N Greve]

The mri_gtmpvc command will remove volume fraction effects. Look at the 
PETsurfer page. Run it with --psf 0 and use the muller-gartner output. 
The output will only be valid for gray matter


On 08/12/2017 10:55 AM, Bruce Fischl wrote:
> Hi Shane
>
> we do have some tools to deal with it like 
> mri_compute_volume_fractions and mri_compute_volume_intensities, or 
> maybe Doug's PET stuff. At the very least you should probably regress 
> thickness out.
>
> cheers
> Bruce
>
> On Sat, 12 Aug 2017, Shane Schofield wrote:
>
>> Thank you both.
>>
>> How can I deal with partial volume in this case? Would it be possible 
>> to use
>> the partial volume tool for PET on my MD volumes? Sorry if it is a silly
>> idea.
>>
>> Best Wishes,
>> Shane
>>
>>
>> On Friday, August 11, 2017, 6:19:45 PM GMT+1, Yendiki, Anastasia
>>  wrote:
>>
>>
>> Agreed, especially so with MD. Keep in mind that you¹re upsampling MD 
>> from
>> a lower-res (diffusion) space to a higher-res (T1) space, so it 
>> should be
>> smooth already, relatively to measure derived from the T1. And MD varies
>> pretty smoothly (it¹s a mean of 3 things, after all).
>>
>> On 8/11/17, 1:11 PM, "Bruce Fischl"  wrote:
>>
>> >Hi Shane
>> >
>> >not really - it totally depends on the size of the effect you are 
>> looking
>> >for. I would be *very* careful about partial volume effects though
>> >
>> >cheers
>> >Bruce
>> >On Fri,
>> >11 Aug 2017, Shane Schofield wrote:
>> >
>> >> Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
>> >>
>> >> Dr Yendiki, I am trying to investigate whether cortical MD can be a
>> >>marker
>> >> of neurodegeneration. The idea is that during the early stages of a
>> >>disease,
>> >> cellular microstructure may breakdown before cortical thinning 
>> occurs.
>> >>This
>> >> results in "less" barriers against diffusion resulting in an 
>> increase of
>> >> MD.
>> >>
>> >>
>> >> On Friday, August 11, 2017, 5:49:40 PM GMT+1, Bruce Fischl
>> >>  wrote:
>> >>
>> >>
>> >> Hi Shane
>> >>
>> >> you probably don't need cvs as it is more to extend the surface-based
>> >> registration to the entire volume. Here you just need the 
>> surface-based
>> >> registration I believe. Use mri_vol2surf to sample the FA onto the
>> >>surface.
>> >> After that it is identical to a thickness study
>> >>
>> >> cheers
>> >> Bruce
>> >>
>> >>
>> >>
>> >> On Fri, 11 Aug 2017, Shane Schofield
>> >> wrote:
>> >>
>> >> > Thanks Dr Yendiki.
>> >> >
>> >> > I am more interested to compare MD in grey matter regions by 
>> putting
>> >>the
>> >> MD on the surface, and then do a glmfit type of comparisons. Is 
>> that OK?
>> >> Would you recommend me
>> >> > to smooth the data after spatial normalisation? I have also used 
>> the
>> >> mri_cvs_register as described on the tutorial.
>> >> >
>> >> >
>> >> > On Friday, August 11, 2017, 7:03:49 AM GMT+1, Shane Schofield
>> >>  wrote:
>> >> >
>> >> >
>> >> > Hi DTI Experts,
>> >> >
>> >> > Is it sensible to do comparisons of MD on the cortex surface like a
>> >>normal
>> >> cortical thickness comparisons between group? If the answer is 
>> yes, are
>> >> there recommended on
>> >> > smoothing ?
>> >> >
>> >> > DT_RECON has been completed in Freesurfer.
>> >> >
>> >> > Thank you.
>> >> >
>> >> >
>> >> >
>> >> ___
>> >> 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
>>
>>
>
>
> ___
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> 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
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Re: [Freesurfer] Question about global mean cortical thickness

[Douglas N Greve]

please send error and all terminal output


On 08/14/2017 12:47 AM, Yi, Hyon-Ah wrote:
> Dear FS experts,
>
>
> I met an error when I try to run mris_preproc. Actually i succeeded 
> this command with my own scripts and fsgd files before.
> There are 2groups with one covariates but I keep getting this error 
> like below.
> mris_preproc --fsgd TESTTEST_age_only.fsgd --hemi lh --meas thickness 
> --target fsaverage --fwhm fwhm10 --o lh.thickness_age.s10.mgh
> ERROR: no subjects specified
> I attached my fsgd file.
> This fsgd file was made using emacs.
> Regards,
> Hyon-Ah Yi.
>
>
>
> ___
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> 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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[Freesurfer] Error when trying to compile the code

[Aziz Nanthaamornphong]

Dear FreeSurfer Experts,

I was trying to compile the FreeSurfer code by following steps shown in
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page

However, I got this error message after I ran ./configure


configure: error: FATAL: netcdf lib not found. Set LDFLAGS or
--with-mni-dir.



I currently use  OS X El Capitan as the OS.

How can I solve this problem? Thank you in advance.

Aziz.
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Re: [Freesurfer] test-retest variability small subcortical regions

[Van Der Deijl, Rosanne]

Hi Bruce,

I mean for the longitudinal analysis.
Forgot to mention this, sorry!

Kind regards,

Rose

Date: Fri, 11 Aug 2017 12:39:58 -0400 (EDT)
From: Bruce Fischl 
Subject: Re: [Freesurfer] Test-retest reliability small subcortical
regions
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Rose

do you mean cross-sectional or longitudinal analysis?

cheers
Bruce

On Fri, 11 Aug 2017,
Van Der Deijl, Rosanne wrote:

> Dear Freesurfer team,
>
> I was wondering what the test-retest reliability is of comparing small
> regions in the subcortical volume, e.g. the amygdala. Has this improved with
> the 6.0 version?
>
> Thank you!
>
> Kind regards,
>
> Rose
>
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Re: [Freesurfer] problem with fsgd glmfit

[Kasper Jessen]

I have found the reason for the error: FSGDF Format Error: file = 
/Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, tag=Input

The class should be 1.0 and 0.0, as stated in the fsgd file.

Otherwise, is the process still correct?

BW
Kasper

>  Original Message 
> Subject: problem with fsgd glmfit
> Local Time: 14 August 2017 10:12 AM
> UTC Time: 14 August 2017 8:12 AM
> From: kas...@brejes.com
> To: freesurfer@nmr.mgh.harvard.edu 
>
> Dear FreeSurfer,
>
> I would like to do the long. two stage model 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel)
>
> Study design: 2 groups (one control group, one patient group) with gender and 
> age as covariates. Each subject was MRI scanned at baseline and 6 weeks 
> follow-up. I would like to test the difference in structural measures between 
> groups over time.
>
> My problem
> 1. Is the process and setup below correct?
> 2. When i pass the above command under 3) i get an error where it says:
>
> FSGDF Format Error: file = /Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, 
> tag=Input
>
> Is there anyone that can help?
>
> I have followed the tutorial:
>
> FIRST STAGE: Preparing the Data - QCACHE is done.
> SECOND STAGE: Option mri_glmfit:
>
> Then i would like to test the difference between groups, and this is were i 
> have a hard time following the tutorial.
>
> I looked at the following guide: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis concerning 
> Group Analysis using mri_glmfit and i understand that i need to use the 
> command below creating my own fsgd file.
>
> 1) Since i have a longitudinal setup, i converted it to a cross-sectional 
> steup as you would do if you used the QDEC option. My fsgd file looks as the 
> one below. 1 = patients and 0 = controls.
>
> GroupDescriptorFile 1
> Title GroupDiff_Lh_Thickness
> Class 1
> Class 0
> Variables age gender
> Input b101_base 1.0 24.0 1.0
> Input b103_base 1.0 41.0 0.0
> Input b105_base 1.0 22.0 1.0
> Input b206_base 0.0 25.0 1.0
> Input b207_base 0.0 23.0 0.0
>
> 2) To test group difference between groups regressing out the effect of age 
> and gender i have made a .mtx file with the following input:
>
> 1 -1 0 0 0 0
>
> 3) Therenext, i ran the following but something is wrong with my fsgd file:
>
> mri_glmfit --y lh.thickness-spc.stack.fwhm15.mgh --fsgd 
> GroupDiffLhThickness.fsgd dods --C group.diff.mtx --surf fsaverage lh 
> --cortex --glmdir lh_thickness_spc_fwhm15_groupdiff
>
> I hoper there is someone who can help.
> Best wishes
> Kasper Jessen___
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[Freesurfer] problem with fsgd glmfit

[Kasper Jessen]

Dear FreeSurfer,

I would like to do the long. two stage model 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel)

Study design: 2 groups (one control group, one patient group) with gender and 
age as covariates. Each subject was MRI scanned at baseline and 6 weeks 
follow-up. I would like to test the difference in structural measures between 
groups over time.

My problem
1. Is the process and setup below correct?
2. When i pass the above command under 3) i get an error where it says:

FSGDF Format Error: file = /Volumes/External/P1_FU/GroupDiffLhThickness.fsgd, 
tag=Input

Is there anyone that can help?

I have followed the tutorial:

FIRST STAGE: Preparing the Data - QCACHE is done.
SECOND STAGE: Option mri_glmfit:

Then i would like to test the difference between groups, and this is were i 
have a hard time following the tutorial.

I looked at the following guide: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis concerning 
Group Analysis using mri_glmfit and i understand that i need to use the command 
below creating my own fsgd file.

1) Since i have a longitudinal setup, i converted it to a cross-sectional steup 
as you would do if you used the QDEC option. My fsgd file looks as the one 
below. 1 = patients and 0 = controls.

GroupDescriptorFile 1
Title GroupDiff_Lh_Thickness
Class 1
Class 0
Variables age gender
Input b101_base 1.0 24.0 1.0
Input b103_base 1.0 41.0 0.0
Input b105_base 1.0 22.0 1.0
Input b206_base 0.0 25.0 1.0
Input b207_base 0.0 23.0 0.0

2) To test group difference between groups regressing out the effect of age and 
gender i have made a .mtx file with the following input:

1 -1 0 0 0 0

3) Therenext, i ran the following but something is wrong with my fsgd file:

mri_glmfit --y lh.thickness-spc.stack.fwhm15.mgh --fsgd 
GroupDiffLhThickness.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex 
--glmdir lh_thickness_spc_fwhm15_groupdiff

I hoper there is someone who can help.
Best wishes
Kasper Jessen___
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