Re: [Freesurfer] using T2 for hippo subfields

[Alexopoulos, Dimitrios]

External Email - Use Caution

Yes the output appears ok.
I was under the impression there would be benefits from using the -hires flag 
with submillimeter T1s as input.

If you suggest not having to use the -hires flag in our case (because of little 
benefit from 0.8mm input compared to 1mm), I presume I can still use the 
-hippocampal-subfields-T1 option in the traditional recon-all -all stream?

Jim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, 
Eugenio 
Sent: Thursday, April 19, 2018 1:57:18 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution

Hi Jim,
>From my experience .8 isotropic is on the edge. Did you take a look at the 
>output? You can always send us the data if you want us to take a look.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 19/04/2018, 19:55, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Alexopoulos, Dimitrios"  wrote:

External Email - Use Caution

Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm 
through the standard recon-all -all stream, with the -hires flag (but with no 
experts file). The volumes and surafces look good. Is there any need to be 
concerened with the output since I did not use an experts file?

Jim

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, April 04, 2018 7:52 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] using T2 for hippo subfields

no it is not required

cheers
Bruce
On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote:

> Per an earlier post below, is an 'expert_file' always required when using 
the -hires option?
>
> Jim
>
> __
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Alexopoulos,
> Dimitrios 
> Sent: Sunday, March 25, 2018 9:47:07 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Thanks for the input. I processed a few subjects (T1-mprage, 0.8mm
> isotropic) using the -hires flag, with no expert file, which generated 
nice surfaces.
>
> Is an 'expert_file' required ??
>
>
> Jim
>
> __
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Iglesias
> Gonzalez, Eugenio 
> Sent: Friday, March 23, 2018 11:02:00 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Hi Jim,
>
> In the end it's an empirical question, but my gut feeling is that the
> T1 with hi-res flag will be best.
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> From:  on behalf of "Alexopoulos, 
Dimitrios"
> 
> Reply-To: Freesurfer support list 
> Date: Friday, 23 March 2018 at 16:00
> To: Freesurfer support list 
> Subject: [Freesurfer] using T2 for hippo subfields
>
>
>
> Hi. We are acquiring sequences on a pediatric cohort that include a
> T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd
> like to run the hippocampal subfields module on the subjects using FS 6.0.
>
>
>
> Is it recommended/useful to run the multispectral segmentation mode
> with the additional lower resolution T2 sequence?
>
> I read that you really only benefit if the T2 is of similar or better 
resolution than the T1.
>
>
>
> If that's the case, would it be best to just run with the single T1
> but with the hi-res flag in the recon-all command?
>
>
> Thanks.
>
> Jim
>
>
>
>
>
>
>
>
>
>
>
>
> __
> 

Re: [Freesurfer] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[stdp82]

External Email - Use Caution

> 

Hi,

group analysis.

I would like to perform a simple correlation analysis within group, aiming to 
map the clusters reporting the correlation between the FC and the seed volume 
or neuropsychological test scores (e.g. MMSE). Overall, the morphometric 
measures and NPS test scores do not shown a normal distribution and, thus, 
parametric computation should be discouraged.


Thanks


> 
> Il 19 aprile 2018 alle 18.11 "Douglas N. Greve"  
> ha scritto:
> 
> I'm not sure what you mean. Can you elaborate? Is this an individual
> analysis or a group analysis?
> 
> On 04/18/2018 10:10 AM, std...@virgilio.it wrote:
> >
> 
> > > 
> > Hi list,
> > 
> > which the best way to perform a whole-brain correlation of the FC
> > assessed by FS-FAST with the volumetic or neuropsychological 
> > outcomes?
> > Please note that my question is specifically addressed to those
> > factors (neuropsycholgical scores or volume of seed) did not show a
> > normal distribution and that cannot be trasformed.
> > 
> > Thanks
> > 
> > Kind regards
> > 
> > Stefano
> > 
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > > 
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> 
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> addressed. If you believe this e-mail was sent to you in error and the 
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Re: [Freesurfer] Freesurfer and crypt

[Dicamillo, Robert]

Hi Bennet,

I’m attaching a compressed tar file, chklc_fips.tgz, that is an attempt at 
creating a binary
(chklc_fips) that uses its own local version of crypt.  See the README file 
when you
untar the archive.   This is not officially supported in any way, and while it 
can read
my license file in a non-FIPS environment, I cannot say if it will actually 
work for you.

- -rob


On Apr 19, 2018, at 10:14 AM, Bennet Fauber 
> wrote:


Hi, Rob,

The call to crypt() appears to be in FreeSurfer's license validation routine, 
since it is immediately after reading the license file.  In the sense that 
FreeSurfer cannot run without some sort of license, and that license validation 
is using the native Unix crypt() function to validate, it's not quite 
OpenSource.  I think someone at FreeSurfer would need to replace the single 
call to the crypt() function with some other function that isn't marked as 
'insecure' to bypass this.

I thought I saw something earlier on the mailing list about this, and that 
there was a workaround, but I am unable to locate it again.  Any chance this 
could get passed to the developer who maintains the license validation code?  
Depending on the code and their willingness to share, we might be able to 
contribute an alternative for systems with the elevated security.

This currently may not be a bit issue, but we are seeing increasing strictness 
on our end to comply with federal security guidelines, and it may not just be 
our Medical Center and local VA that are pushing these security measures.

This is what it looks like when it succeeds.

11527 open("/sw/arcts/centos7/freesurfer/6.0.0/license.txt", O_RDONLY) = 3
11527 fstat(3, {st_mode=S_IFREG|0644, st_size=52, ...}) = 0
11527 mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) 
= 0x2b4bcc176000
11527 read(3, "ben...@umich.edu\n6925\n *CpU.rbF6"..., 
8192) = 52
11527 read(3, "", 8192) = 0
11527 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
11527 read(4, "0\n", 31)= 2
11527 close(4)  = 0
11527 close(3)  = 0
11527 munmap(0x2b4bcc176000, 8192)  = 0
11527 getcwd("/home/bennet/tmp/freesurfer", 4096) = 28
11527 open("/home/bennet/tmp/freesurfer/sample-001.mgz", O_RDONLY) = 3

I do not believe that this is something that can be 'whitelisted', as this is 
set in the Linux kernel at boot time.

Thanks,-- bennet


On Thu, Apr 12, 2018 at 11:29 AM, Dicamillo, Robert 
> wrote:
Hello Bennet,

Maybe someone else can chime in on this, as I have not worked on a system
with FIPS, but perhaps there is a way for the FIPS administrator to white list
all the Freesurfer binaries (and the license file), as security exempt.

I know some Enterprise/business applications like Adobe’s Acrobat, etc.,
(closed source) are built with code to work on FIPS compliant systems, but
I don’t see there is currently anything in Freesurfer (essentially open source),
code that knows about cryptographic modules, digital signatures, etc. to work on
a secure system.  Even turning on SElinux for linux OS can be an
issue for some programs.

Another thing to inquire about is if the IT folks maintain any non-secure 
servers,
, i.e., I would not assume that any application will just work in a secure 
environment.

- rob

> On Apr 12, 2018, at 10:51 AM, Bennet Fauber 
> > wrote:
>
> It appears that FreeSurfer is not compatible with systems for which
> FIPS level security is mandated.  In our case, I am told this is part
> of our data use agreement with the VA.
>
> We tried to run it, and I get the following stack trace showing what
> appears to be license validation using the crypt() function, which is
> blacklisted by the Linux kernel by the FIPS configuration.
>
> 28063 open("/opt/apps/freesurfer-6.0/freesurfer/license.txt", O_RDONLY) = 3
> 28063 fstat(3, {st_mode=S_IFREG|0644, st_size=59, ...}) = 0
> 28063 mmap(NULL, 4096, PROT_READ|PROT_WRITE,
> MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fa319883000
> 28063 read(3, 
> "issc-sysad...@umich.edu\n23098\n*C"..., 
> 4096) = 59
> 28063 read(3, "", 4096) = 0
> 28063 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
> 28063 read(4, "1\n", 31)= 2
> 28063 close(4)  = 0
> 28063 write(1, "ERROR: crypt() returned null wit"..., 46) = 46
> 28063 exit_group(1)
>
> Is there a workaround so we can run FreeSurfer FIPS-enabled systems?
>
> Appreciate your consideration of this question,
>
> -- bennet
>
>
>
> On Thu, Mar 29, 2018 at 5:05 PM, Bennet Fauber 
> > wrote:
>> I have a couple of users here who are reporting that on machines with
>> FIPS enabled, which in turn disables certain cryptographic functions,
>> FreeSurfer core dumps with 

Re: [Freesurfer] mni152reg yields bad registration

[Zimmerman, Jared]

External Email - Use Caution

Thanks Doug,

Yeah, I’m confused as to what happened with that registration too.

I just used ANTs to do the warping and that worked well.  Good to know about 
mri_cvs_register though, I will try to use that next time.

-jared

On 4/19/18, 12:12 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Douglas N. Greve"  wrote:

I don't know what might have happened (under the hood, mni152reg uses 
the FSL flirt program). If you want a non-linear registration, then 
you'll need to use CVS (mri_cvs_register) and choose the mni target. If 
you just want the aparc of the aparc+aseg, then don't go into the volume 
at all.


On 04/17/2018 01:57 PM, Zimmerman, Jared wrote:
>
> Hi All,
>
> I’m trying to register the aparc+aseg volumes from subject T1 space to 
> MNI152 space and running into problems.  I’ve taken the following steps
>
> 1.mri152reg –s Subj241
>
> 2.mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz 
> --mov $SUBJECTS_DIR/Subj241/mri/aparc+aseg.mgz --o 
> Subj241_aparc+aseg_mni2mm.nii.gz --reg 
> $SUBJECTS_DIR/Subj241/mri/transforms/reg.mni152.2mm.dat
>
> This yields an image that is rotated and shrunken relative to the 
> MNI152_T1_2mm template as shown in the attached image.
>
> I’m wondering if this is the right way to do what I’d like to do.  The 
> reg.mni152.2mm.dat file is only a linear transform, but I’d like to 
> apply a non-linear transformation to the subject aparc+aseg to get it 
> well matched to the MNI152 template space.  Some of my subjects have 
> atypical head shapes and I really think a non-linear warp will be 
> necessary to achieve a good fit.
>
> I’ve run the MNI152 1mm template through recon-all so I have that as a 
> reference.  Is there a way to map volumes from one subject space to 
> another via fsaverage or sphere sort of like mri_label2label does for 
> labels?
>
> Alternatively, I could just calculate the appropriate T1 to MNI warps 
> with FNIRT or ANTs and apply those to the aparc+aseg, but I figured it 
> would be possible to do with FreeSurfer without calculating any new 
> transforms.
>
> Thanks,
>
> Jared
>
>
>
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[Freesurfer] Brainhack Donostia 2018

[Sanjeev Nara]

External Email - Use Caution


Hello Everyone 

The Basque Center on Cognition Brain and Language (BCBL) will host the first 
edition of the BrainhackDonostia2018. The event aims at bringing together 
students and scientists at all levels of their careers to enjoy science and a 
couple of Cider glasses together.

This year's edition will focus on Neuroimaging techniques, in particular fMRI 
(functional magnetic resonance) MEG (magnetoencephalography, EEG 
(electroencephalogaphy) and fNIRS (functional near infrared spectroscopy). 
Through a combination of lectures and tutorials, participants will be 
introduced on these techniques, and how they can be used to study the mind and 
brain.
For those that have more experience, and have an interest in three days of 
project development, there is also the possibility to propose and develop a 
project related to neuroimaging and/or electrophysiology recruiting 
participants on site.

The event is open to people from different disciplines and backgrounds, with a 
genuine interest in neuroimaging methods, psychology, neuroscience, and more 
generally interdisciplinary research. Feel free to explore our website for 
further information.
http://www.bcbl.eu/events/BrainhackDonostia2018/en/

The event will be hosted on May 2nd-4th 2018 in the Basque Center on Cognition 
Brain and Language in San Sebastian, Spain. The cost is 10€ for Master 
Students, 15€ for PhD and PostDocs, 40€ for Seniors and "Industrials" + 
optional 13€ for the T-shirt. Registration to the event is needed and can be 
done on the website, until the 25th of April. A certificate of attendance will 
be provided to participants.

If you have more questions, we remain at your disposal at the address 
info.bhg-donos...@bcbl.eu

We look forward to see you in May!

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Re: [Freesurfer] QDEC Interaction of Two Covariates

[Douglas N. Greve]

QDEC is mostly depreicated. Use the command-line stream. See the group 
analysis on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial


On 04/19/2018 04:48 PM, David S Lee wrote:
>
>
> Hi FreeSurfer Experts,
>
> I want to test the relationship between cortical thickness and two 
> continuous covariates (interaction) while controlling for one 
> categorical variable. In QDEC, I can only choose one covariate, so I 
> created a new variable that is a dot product (covariate1*covariate2) 
> of the two to represent interaction. After analyzing, when I look at 
> the data points at a single voxel, there is no visual indication of 
> interaction. There also is no fitted line.
>
> Am I utilizing QDEC correctly?
>
> Thank you for your help!
>
> -- 
> David S. Lee
> Associate Research Specialist
> Center for Healthy Minds
> University of Wisconsin - Madison
> (608) 890-1115 
>
>
> ___
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Re: [Freesurfer] Calculation of surface area

[Douglas N. Greve]

We output surface area separately both as a map and as statistics


On 04/19/2018 04:47 PM, Zohar Berman wrote:
> Dear FreeSurfer experts,
>
> Can one use the volume and cortical thickness of a region to calculate 
> the surface area of this region?
>
> Thanks a lot in advance!
> Best,
> Zoi
>
>
>
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[Freesurfer] Calculation of surface area

[Zohar Berman]

External Email - Use Caution

 Dear FreeSurfer experts,

Can one use the volume and cortical thickness of a region to calculate the
surface area of this region?

Thanks a lot in advance!
Best,
Zoi
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[Freesurfer] QDEC Interaction of Two Covariates

[David S Lee]

External Email - Use Caution

Hi FreeSurfer Experts,

I want to test the relationship between cortical thickness and two
continuous covariates (interaction) while controlling for one categorical
variable. In QDEC, I can only choose one covariate, so I created a new
variable that is a dot product (covariate1*covariate2) of the two to
represent interaction. After analyzing, when I look at the data points at a
single voxel, there is no visual indication of interaction. There also is
no fitted line.

Am I utilizing QDEC correctly?

Thank you for your help!

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Thanks for your patience with me. I am really appreciate. : )

Ting
> On Apr 19, 2018, at 3:14 PM, Douglas N. Greve  wrote:
> 
> The wiki and the papers :)
> 
> 
> On 04/19/2018 03:22 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Douglas,
>> 
>> Thanks for your quick response. If I only want the information of cortical 
>> thickness, surface area, volume for various cortical regions and LGI, then 
>> the Freesurfer template is good enough and I don’t need to apply my own 
>> template. This is really helpful. Is there any documents that you will 
>> recommend to get a better understanding about Freesurfer?
>> 
>> Thanks a lot.
>> 
>> Ting
>>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  
>>> wrote:
>>> 
>>> If you want to do a surface-based analysis, then you don't need to have
>>> an accurate volume template. If you want to use a custom volume-based
>>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>>> 
>>> 
>>> On 04/19/2018 01:28 PM, Ting Li wrote:
 External Email - Use Caution
 
 Douglas,
 
 Sorry for bother you again. Our group want to study a cohort children’s 
 brain using Freesurfer. We prefer to register our subjects to a custom 
 children template. The template basically is an average of all the 
 subjects we are going to study. It is constructed by ANTs. The format is 
 nii.gz. My questions is where I should mention this registration template 
 in the command Recon-all?  or how to get the cortical thickness, surface 
 area and volume for various cortical regions for all subjects and perform 
 the GLM analyses?
 
 In Freesurfer, there is a command of making own template for registration. 
 If I generate my template from there, how can I run recon-all for the next 
 to make sure my subjects all register to this template? and how to get the 
 cortical thickness, surface area and volume for various cortical regions 
 for all subjects and perform the GLM analyses?
 
 I really need your help for this. Thanks for your time.
 
 Best,
 Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
> 
> Douglas,
> 
> Thank you so much for your response. My atlas is nii.gz format. What 
> should I do to get the cortical thickness, surface area and volume for 
> various cortical regions? Thanks in advance.
> 
> Best,
> Ting
> 
> 
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>> wrote:
>> 
>> Is the atlas in GCA format? If so, then you can use gca-apply
>> 
>> 
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>> 
>>> We want to run recon-all with a custom atlas which is generated from
>>> ANTs multivariate template construction. What is the right procedure
>>> to run recon-all? Run recon-all to my atlas itself first and them use
>>> this output as a template or I use the custom template directly. I
>>> looked up your email database to search related topic and got lost. I
>>> have sent another email to your group and no response received. Please
>>> help me.
>>> 
>>> Thanks for you time. I look forward to hearing from you.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
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>> 
>> 
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>> it is
>> addressed. If you believe this e-mail was sent to you in error and the 
>> e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
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>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>> 
 ___
 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
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> ___
> Freesurfer mailing list
> 

Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

The wiki and the papers :)


On 04/19/2018 03:22 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Douglas,
>
> Thanks for your quick response. If I only want the information of cortical 
> thickness, surface area, volume for various cortical regions and LGI, then 
> the Freesurfer template is good enough and I don’t need to apply my own 
> template. This is really helpful. Is there any documents that you will 
> recommend to get a better understanding about Freesurfer?
>
> Thanks a lot.
>
> Ting
>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  
>> wrote:
>>
>> If you want to do a surface-based analysis, then you don't need to have
>> an accurate volume template. If you want to use a custom volume-based
>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>>
>>
>> On 04/19/2018 01:28 PM, Ting Li wrote:
>>>  External Email - Use Caution
>>>
>>> Douglas,
>>>
>>> Sorry for bother you again. Our group want to study a cohort children’s 
>>> brain using Freesurfer. We prefer to register our subjects to a custom 
>>> children template. The template basically is an average of all the subjects 
>>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>>> questions is where I should mention this registration template in the 
>>> command Recon-all?  or how to get the cortical thickness, surface area and 
>>> volume for various cortical regions for all subjects and perform the GLM 
>>> analyses?
>>>
>>> In Freesurfer, there is a command of making own template for registration. 
>>> If I generate my template from there, how can I run recon-all for the next 
>>> to make sure my subjects all register to this template? and how to get the 
>>> cortical thickness, surface area and volume for various cortical regions 
>>> for all subjects and perform the GLM analyses?
>>>
>>> I really need your help for this. Thanks for your time.
>>>
>>> Best,
>>> Ting
 On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:

 Douglas,

 Thank you so much for your response. My atlas is nii.gz format. What 
 should I do to get the cortical thickness, surface area and volume for 
 various cortical regions? Thanks in advance.

 Best,
 Ting


> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
> wrote:
>
> Is the atlas in GCA format? If so, then you can use gca-apply
>
>
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>>
>> We want to run recon-all with a custom atlas which is generated from
>> ANTs multivariate template construction. What is the right procedure
>> to run recon-all? Run recon-all to my atlas itself first and them use
>> this output as a template or I use the custom template directly. I
>> looked up your email database to search related topic and got lost. I
>> have sent another email to your group and no response received. Please
>> help me.
>>
>> Thanks for you time. I look forward to hearing from you.
>>
>> Best,
>> Ting
>>
>>
>> ___
>> 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
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

That is, but since that wiki was written, I've written a script called 
make_folding_atlas. It takes quite a while to run through the 10 or so 
iterations. You might not need it as surface-based registration is much 
less sensitive to brain changes than volume-based.


On 04/19/2018 04:05 PM, Ting Li wrote:
>
>
> Douglas,
>
> I have one more question. Do I need an accurate surface template for 
> my surface-based analysis? Does this ( 
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) is 
> the right way to go? Thanks for your time.
>
> Best,
> Ting
>> On Apr 19, 2018, at 2:22 PM, Ting Li > > wrote:
>>
>> Douglas,
>>
>> Thanks for your quick response. If I only want the information of 
>> cortical thickness, surface area, volume for various cortical regions 
>> and LGI, then the Freesurfer template is good enough and I don’t need 
>> to apply my own template. This is really helpful. Is there any 
>> documents that you will recommend to get a better understanding about 
>> Freesurfer?
>>
>> Thanks a lot.
>>
>> Ting
>>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve 
>>> > wrote:
>>>
>>> If you want to do a surface-based analysis, then you don't need to have
>>> an accurate volume template. If you want to use a custom volume-based
>>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>>>
>>>
>>> On 04/19/2018 01:28 PM, Ting Li wrote:
    External Email - Use Caution

 Douglas,

 Sorry for bother you again. Our group want to study a cohort 
 children’s brain using Freesurfer. We prefer to register our 
 subjects to a custom children template. The template basically is 
 an average of all the subjects we are going to study. It is 
 constructed by ANTs. The format is nii.gz. My questions is where I 
 should mention this registration template in the command Recon-all? 
  or how to get the cortical thickness, surface area and volume for 
 various cortical regions for all subjects and perform the GLM analyses?

 In Freesurfer, there is a command of making own template for 
 registration. If I generate my template from there, how can I run 
 recon-all for the next to make sure my subjects all register to 
 this template? and how to get the cortical thickness, surface area 
 and volume for various cortical regions for all subjects and 
 perform the GLM analyses?

 I really need your help for this. Thanks for your time.

 Best,
 Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li  > wrote:
>
> Douglas,
>
> Thank you so much for your response. My atlas is nii.gz format. 
> What should I do to get the cortical thickness, surface area and 
> volume for various cortical regions? Thanks in advance.
>
> Best,
> Ting
>
>
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve 
>> > wrote:
>>
>> Is the atlas in GCA format? If so, then you can use gca-apply
>>
>>
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>>
>>> We want to run recon-all with a custom atlas which is generated from
>>> ANTs multivariate template construction. What is the right procedure
>>> to run recon-all? Run recon-all to my atlas itself first and 
>>> them use
>>> this output as a template or I use the custom template directly. I
>>> looked up your email database to search related topic and got 
>>> lost. I
>>> have sent another email to your group and no response received. 
>>> Please
>>> help me.
>>>
>>> Thanks for you time. I look forward to hearing from you.
>>>
>>> Best,
>>> Ting
>>>
>>>
>>> ___
>>> 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

Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

I have one more question. Do I need an accurate surface template for my 
surface-based analysis? Does this ( 
https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates 
 ) is the 
right way to go? Thanks for your time.

Best,
Ting
> On Apr 19, 2018, at 2:22 PM, Ting Li  wrote:
> 
> Douglas,
> 
> Thanks for your quick response. If I only want the information of cortical 
> thickness, surface area, volume for various cortical regions and LGI, then 
> the Freesurfer template is good enough and I don’t need to apply my own 
> template. This is really helpful. Is there any documents that you will 
> recommend to get a better understanding about Freesurfer? 
> 
> Thanks a lot.
> 
> Ting 
>> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  
>> wrote:
>> 
>> If you want to do a surface-based analysis, then you don't need to have 
>> an accurate volume template. If you want to use a custom volume-based 
>> segmentation atlas, then you'll need to run gcatrain and gca-apply
>> 
>> 
>> On 04/19/2018 01:28 PM, Ting Li wrote:
>>>External Email - Use Caution
>>> 
>>> Douglas,
>>> 
>>> Sorry for bother you again. Our group want to study a cohort children’s 
>>> brain using Freesurfer. We prefer to register our subjects to a custom 
>>> children template. The template basically is an average of all the subjects 
>>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>>> questions is where I should mention this registration template in the 
>>> command Recon-all?  or how to get the cortical thickness, surface area and 
>>> volume for various cortical regions for all subjects and perform the GLM 
>>> analyses?
>>> 
>>> In Freesurfer, there is a command of making own template for registration. 
>>> If I generate my template from there, how can I run recon-all for the next 
>>> to make sure my subjects all register to this template? and how to get the 
>>> cortical thickness, surface area and volume for various cortical regions 
>>> for all subjects and perform the GLM analyses?
>>> 
>>> I really need your help for this. Thanks for your time.
>>> 
>>> Best,
>>> Ting
 On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
 
 Douglas,
 
 Thank you so much for your response. My atlas is nii.gz format. What 
 should I do to get the cortical thickness, surface area and volume for 
 various cortical regions? Thanks in advance.
 
 Best,
 Ting
 
 
> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
> wrote:
> 
> Is the atlas in GCA format? If so, then you can use gca-apply
> 
> 
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>> 
>> We want to run recon-all with a custom atlas which is generated from
>> ANTs multivariate template construction. What is the right procedure
>> to run recon-all? Run recon-all to my atlas itself first and them use
>> this output as a template or I use the custom template directly. I
>> looked up your email database to search related topic and got lost. I
>> have sent another email to your group and no response received. Please
>> help me.
>> 
>> Thanks for you time. I look forward to hearing from you.
>> 
>> Best,
>> Ting
>> 
>> 
>> ___
>> 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
> 

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The information in this e-mail is intended only for the person to whom it is
addressed. If you 

Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Thanks for your quick response. If I only want the information of cortical 
thickness, surface area, volume for various cortical regions and LGI, then the 
Freesurfer template is good enough and I don’t need to apply my own template. 
This is really helpful. Is there any documents that you will recommend to get a 
better understanding about Freesurfer? 

Thanks a lot.

Ting 
> On Apr 19, 2018, at 12:39 PM, Douglas N. Greve  wrote:
> 
> If you want to do a surface-based analysis, then you don't need to have 
> an accurate volume template. If you want to use a custom volume-based 
> segmentation atlas, then you'll need to run gcatrain and gca-apply
> 
> 
> On 04/19/2018 01:28 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> Douglas,
>> 
>> Sorry for bother you again. Our group want to study a cohort children’s 
>> brain using Freesurfer. We prefer to register our subjects to a custom 
>> children template. The template basically is an average of all the subjects 
>> we are going to study. It is constructed by ANTs. The format is nii.gz. My 
>> questions is where I should mention this registration template in the 
>> command Recon-all?  or how to get the cortical thickness, surface area and 
>> volume for various cortical regions for all subjects and perform the GLM 
>> analyses?
>> 
>> In Freesurfer, there is a command of making own template for registration. 
>> If I generate my template from there, how can I run recon-all for the next 
>> to make sure my subjects all register to this template? and how to get the 
>> cortical thickness, surface area and volume for various cortical regions for 
>> all subjects and perform the GLM analyses?
>> 
>> I really need your help for this. Thanks for your time.
>> 
>> Best,
>> Ting
>>> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
>>> 
>>> Douglas,
>>> 
>>> Thank you so much for your response. My atlas is nii.gz format. What should 
>>> I do to get the cortical thickness, surface area and volume for various 
>>> cortical regions? Thanks in advance.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
 On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
 wrote:
 
 Is the atlas in GCA format? If so, then you can use gca-apply
 
 
 On 04/19/2018 10:09 AM, Ting Li wrote:
> Hi Freesurfer Experts,
> 
> We want to run recon-all with a custom atlas which is generated from
> ANTs multivariate template construction. What is the right procedure
> to run recon-all? Run recon-all to my atlas itself first and them use
> this output as a template or I use the custom template directly. I
> looked up your email database to search related topic and got lost. I
> have sent another email to your group and no response received. Please
> help me.
> 
> Thanks for you time. I look forward to hearing from you.
> 
> Best,
> Ting
> 
> 
> ___
> 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


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Re: [Freesurfer] using T2 for hippo subfields

[Iglesias Gonzalez, Eugenio]

External Email - Use Caution

Hi Jim,
>From my experience .8 isotropic is on the edge. Did you take a look at the 
>output? You can always send us the data if you want us to take a look.
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 19/04/2018, 19:55, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Alexopoulos, Dimitrios"  wrote:

External Email - Use Caution

Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm 
through the standard recon-all -all stream, with the -hires flag (but with no 
experts file). The volumes and surafces look good. Is there any need to be 
concerened with the output since I did not use an experts file?

Jim

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, April 04, 2018 7:52 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] using T2 for hippo subfields

no it is not required

cheers
Bruce
On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote:

> Per an earlier post below, is an 'expert_file' always required when using 
the -hires option?
>
> Jim
>
> __
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Alexopoulos,
> Dimitrios 
> Sent: Sunday, March 25, 2018 9:47:07 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Thanks for the input. I processed a few subjects (T1-mprage, 0.8mm
> isotropic) using the -hires flag, with no expert file, which generated 
nice surfaces.
>
> Is an 'expert_file' required ??
>
>
> Jim
>
> __
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Iglesias
> Gonzalez, Eugenio 
> Sent: Friday, March 23, 2018 11:02:00 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Hi Jim,
>
> In the end it's an empirical question, but my gut feeling is that the
> T1 with hi-res flag will be best.
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> From:  on behalf of "Alexopoulos, 
Dimitrios"
> 
> Reply-To: Freesurfer support list 
> Date: Friday, 23 March 2018 at 16:00
> To: Freesurfer support list 
> Subject: [Freesurfer] using T2 for hippo subfields
>
>
>
> Hi. We are acquiring sequences on a pediatric cohort that include a
> T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd
> like to run the hippocampal subfields module on the subjects using FS 6.0.
>
>
>
> Is it recommended/useful to run the multispectral segmentation mode
> with the additional lower resolution T2 sequence?
>
> I read that you really only benefit if the T2 is of similar or better 
resolution than the T1.
>
>
>
> If that's the case, would it be best to just run with the single T1
> but with the hi-res flag in the recon-all command?
>
>
> Thanks.
>
> Jim
>
>
>
>
>
>
>
>
>
>
>
>
> __
> __
>
>
> 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.
>
>
>
>
> __
> __
>
>
> The materials in this message are private 

Re: [Freesurfer] using T2 for hippo subfields

[Alexopoulos, Dimitrios]

External Email - Use Caution

Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm through 
the standard recon-all -all stream, with the -hires flag (but with no experts 
file). The volumes and surafces look good. Is there any need to be concerened 
with the output since I did not use an experts file?

Jim

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, April 04, 2018 7:52 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] using T2 for hippo subfields

no it is not required

cheers
Bruce
On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote:

> Per an earlier post below, is an 'expert_file' always required when using the 
> -hires option?
>
> Jim
>
> __
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Alexopoulos,
> Dimitrios 
> Sent: Sunday, March 25, 2018 9:47:07 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Thanks for the input. I processed a few subjects (T1-mprage, 0.8mm
> isotropic) using the -hires flag, with no expert file, which generated nice 
> surfaces.
>
> Is an 'expert_file' required ??
>
>
> Jim
>
> __
> __
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Iglesias
> Gonzalez, Eugenio 
> Sent: Friday, March 23, 2018 11:02:00 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] using T2 for hippo subfields
>
> Hi Jim,
>
> In the end it's an empirical question, but my gut feeling is that the
> T1 with hi-res flag will be best.
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Translational Imaging Group
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> From:  on behalf of "Alexopoulos, 
> Dimitrios"
> 
> Reply-To: Freesurfer support list 
> Date: Friday, 23 March 2018 at 16:00
> To: Freesurfer support list 
> Subject: [Freesurfer] using T2 for hippo subfields
>
>
>
> Hi. We are acquiring sequences on a pediatric cohort that include a
> T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd
> like to run the hippocampal subfields module on the subjects using FS 6.0.
>
>
>
> Is it recommended/useful to run the multispectral segmentation mode
> with the additional lower resolution T2 sequence?
>
> I read that you really only benefit if the T2 is of similar or better 
> resolution than the T1.
>
>
>
> If that's the case, would it be best to just run with the single T1
> but with the hi-res flag in the recon-all command?
>
>
> Thanks.
>
> Jim
>
>
>
>
>
>
>
>
>
>
>
>
> __
> __
>
>
> 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
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> you are not the intended recipient, be advised that any unauthorized
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Re: [Freesurfer] recon all error mpr2mni305

[Hoopes, Andrew]

Hi Richard, it seems this was caused by a minor update to our mac build 
machine. These libraries should be correctly linked now in the most recent dev 
build (updated a few minutes ago). Let me know if you still have issues

best,
Andrew

On 4/19/18, 2:39 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Jones, Richard"  wrote:

How does the input image look, ie, orig.mg>

The images the look the same as the input DICOM images, no scaling or other 
problems. 


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Re: [Freesurfer] recon all error mpr2mni305

[Jones, Richard]

External Email - Use Caution

Message: 1
Date: Thu, 19 Apr 2018 12:05:03 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] Freesurfer dev version : recon all error
mpr2mni305
To: 
Message-ID: <0b445a3f-8fde-d23e-dab6-442a773c9...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed

How does the input image look, ie, orig.mg>

The images the look the same as the input DICOM images, no scaling or other 
problems. 


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Re: [Freesurfer] LGI for the lobar annotation

[Fernanda Hansen P. de Moraes]

External Email - Use Caution

Thank you!! :D

On Thu, Apr 19, 2018 at 12:57 PM Douglas N. Greve 
wrote:

> yes
>
>
> On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote:
> > Douglas, thank you very much again.
> > So I can assume it is the lGI for the area (in this case the lobe)?
> >
> > Thank you again!
> >
> > On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve  > > wrote:
> >
> > The "intensity" is the mean value of the input (lh.pial_lgi in
> > this case) averaged over vertices. If  you wan the total number,
> > multiply it by the number of vertices or re-run with --accumulate.
> > The area is the surface area of the entire lobe.
> >
> >
> > On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes wrote:
> >> Sorry, my mistake.
> >>
> >> mri_segstats --annot DA011 lh lobesStrict --i
> >> DA011/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats
> >>
> >> On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve
> >> > wrote:
> >>
> >> What is your command line? Also, please remember to post to
> >> the list
> >>
> >>
> >> On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote:
> >> > Dear Douglas,
> >> >
> >> > thank you.
> >> >
> >> >  The code worked, but I didn't understand the result very
> >> well. What
> >> > means intensity? The area, is the ara from the piall_lgi
> >> surface
> >> > (outer surface)?
> >> >
> >> > Thank you again
> >> >
> >> > On Tue, Apr 17, 2018 at 1:07 PM Douglas Greve
> >> 
> >> >  >> >> wrote:
> >> >
> >> > If you run it with --help you will see an example
> >> >
> >> >
> >> > On 4/16/18 7:16 AM, Fernanda Hansen P. de Moraes wrote:
> >> >> Thank you, Douglas,
> >> >>
> >> >> do you have any suggestions on how to make you work?
> >> >>
> >> >> Fernanda
> >> >>
> >> >>
> >> >>
> >> >> On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve
> >> >>  >> 
> >>  >> >> wrote:
> >> >>
> >> >> that should work, except the command line is not
> >> quite right
> >> >>
> >> >>
> >> >> On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes
> >> wrote:
> >> >>> Good night,
> >> >>>
> >> >>> does anyone know if it is possible to calculate
> >> the lGI for
> >> >>> the ?h.lobesStrict.annot? And if it yes, how can
> >> I do it?
> >> >>>
> >> >>> I've already tried to use:
> >> >>>
> >> >>> /mri_segstats --annot
> >> subjxx/label/lh.lobesStrict.annot --i
> >> >>>  $SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum
> >> >>>  lh.lobesStrict.annot.pial_lgi.stats/
> >> >>>
> >> >>> Thank you!
> >> >>> --
> >> >>> Fernanda Hansen P. de Moraes
> >> >>> Física Médica | Instituto D'Or de Pesquisa e
> >> Ensino | Rede
> >> >>> D'Or São Luiz
> >> >>>
> >> >>>
> >> >>>  ___
> >> >>> 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
> >> >> 

Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

No, I think that is it.


On 04/19/2018 02:07 PM, Khoi Mai wrote:
>
> External Email - Use Caution
>
> From what I read in the gctrain --help, does it only require 
> talairach_man.xfm and the manual segmentation files? Does it require 
> anything else for each subject?
>
> On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve 
> > wrote:
>
> If you want to do a surface-based analysis, then you don't need to
> have
> an accurate volume template. If you want to use a custom volume-based
> segmentation atlas, then you'll need to run gcatrain and gca-apply
>
>
> On 04/19/2018 01:28 PM, Ting Li wrote:
> >          External Email - Use Caution
> >
> > Douglas,
> >
> > Sorry for bother you again. Our group want to study a cohort
> children’s brain using Freesurfer. We prefer to register our
> subjects to a custom children template. The template basically is
> an average of all the subjects we are going to study. It is
> constructed by ANTs. The format is nii.gz. My questions is where I
> should mention this registration template in the command
> Recon-all?  or how to get the cortical thickness, surface area and
> volume for various cortical regions for all subjects and perform
> the GLM analyses?
> >
> > In Freesurfer, there is a command of making own template for
> registration. If I generate my template from there, how can I run
> recon-all for the next to make sure my subjects all register to
> this template? and how to get the cortical thickness, surface area
> and volume for various cortical regions for all subjects and
> perform the GLM analyses?
> >
> > I really need your help for this. Thanks for your time.
> >
> > Best,
> > Ting
> >> On Apr 19, 2018, at 11:42 AM, Ting Li  > wrote:
> >>
> >> Douglas,
> >>
> >> Thank you so much for your response. My atlas is nii.gz format.
> What should I do to get the cortical thickness, surface area and
> volume for various cortical regions? Thanks in advance.
> >>
> >> Best,
> >> Ting
> >>
> >>
> >>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve
> > wrote:
> >>>
> >>> Is the atlas in GCA format? If so, then you can use gca-apply
> >>>
> >>>
> >>> On 04/19/2018 10:09 AM, Ting Li wrote:
>  Hi Freesurfer Experts,
> 
>  We want to run recon-all with a custom atlas which is
> generated from
>  ANTs multivariate template construction. What is the right
> procedure
>  to run recon-all? Run recon-all to my atlas itself first and
> them use
>  this output as a template or I use the custom template
> directly. I
>  looked up your email database to search related topic and got
> lost. I
>  have sent another email to your group and no response
> received. Please
>  help me.
> 
>  Thanks for you time. I look forward to hearing from you.
> 
>  Best,
>  Ting
> 
> 
>  ___
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>  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.
> >>>
> >
> > ___
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> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
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> 

Re: [Freesurfer] Recon-all with custom atlas

[Khoi Mai]

External Email - Use Caution

From what I read in the gctrain --help, does it only require
talairach_man.xfm and the manual segmentation files? Does it require
anything else for each subject?

On Thu, Apr 19, 2018 at 12:39 PM, Douglas N. Greve 
wrote:

> If you want to do a surface-based analysis, then you don't need to have
> an accurate volume template. If you want to use a custom volume-based
> segmentation atlas, then you'll need to run gcatrain and gca-apply
>
>
> On 04/19/2018 01:28 PM, Ting Li wrote:
> >  External Email - Use Caution
> >
> > Douglas,
> >
> > Sorry for bother you again. Our group want to study a cohort children’s
> brain using Freesurfer. We prefer to register our subjects to a custom
> children template. The template basically is an average of all the subjects
> we are going to study. It is constructed by ANTs. The format is nii.gz. My
> questions is where I should mention this registration template in the
> command Recon-all?  or how to get the cortical thickness, surface area and
> volume for various cortical regions for all subjects and perform the GLM
> analyses?
> >
> > In Freesurfer, there is a command of making own template for
> registration. If I generate my template from there, how can I run recon-all
> for the next to make sure my subjects all register to this template? and
> how to get the cortical thickness, surface area and volume for various
> cortical regions for all subjects and perform the GLM analyses?
> >
> > I really need your help for this. Thanks for your time.
> >
> > Best,
> > Ting
> >> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
> >>
> >> Douglas,
> >>
> >> Thank you so much for your response. My atlas is nii.gz format. What
> should I do to get the cortical thickness, surface area and volume for
> various cortical regions? Thanks in advance.
> >>
> >> Best,
> >> Ting
> >>
> >>
> >>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve 
> wrote:
> >>>
> >>> Is the atlas in GCA format? If so, then you can use gca-apply
> >>>
> >>>
> >>> On 04/19/2018 10:09 AM, Ting Li wrote:
>  Hi Freesurfer Experts,
> 
>  We want to run recon-all with a custom atlas which is generated from
>  ANTs multivariate template construction. What is the right procedure
>  to run recon-all? Run recon-all to my atlas itself first and them use
>  this output as a template or I use the custom template directly. I
>  looked up your email database to search related topic and got lost. I
>  have sent another email to your group and no response received. Please
>  help me.
> 
>  Thanks for you time. I look forward to hearing from you.
> 
>  Best,
>  Ting
> 
> 
>  ___
>  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
> >>>
> >>>
> >>> 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
>
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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

If you want to do a surface-based analysis, then you don't need to have 
an accurate volume template. If you want to use a custom volume-based 
segmentation atlas, then you'll need to run gcatrain and gca-apply


On 04/19/2018 01:28 PM, Ting Li wrote:
>  External Email - Use Caution
>
> Douglas,
>
> Sorry for bother you again. Our group want to study a cohort children’s brain 
> using Freesurfer. We prefer to register our subjects to a custom children 
> template. The template basically is an average of all the subjects we are 
> going to study. It is constructed by ANTs. The format is nii.gz. My questions 
> is where I should mention this registration template in the command 
> Recon-all?  or how to get the cortical thickness, surface area and volume for 
> various cortical regions for all subjects and perform the GLM analyses?
>
> In Freesurfer, there is a command of making own template for registration. If 
> I generate my template from there, how can I run recon-all for the next to 
> make sure my subjects all register to this template? and how to get the 
> cortical thickness, surface area and volume for various cortical regions for 
> all subjects and perform the GLM analyses?
>
> I really need your help for this. Thanks for your time.
>
> Best,
> Ting
>> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
>>
>> Douglas,
>>
>> Thank you so much for your response. My atlas is nii.gz format. What should 
>> I do to get the cortical thickness, surface area and volume for various 
>> cortical regions? Thanks in advance.
>>
>> Best,
>> Ting
>>
>>
>>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>>> wrote:
>>>
>>> Is the atlas in GCA format? If so, then you can use gca-apply
>>>
>>>
>>> On 04/19/2018 10:09 AM, Ting Li wrote:
 Hi Freesurfer Experts,

 We want to run recon-all with a custom atlas which is generated from
 ANTs multivariate template construction. What is the right procedure
 to run recon-all? Run recon-all to my atlas itself first and them use
 this output as a template or I use the custom template directly. I
 looked up your email database to search related topic and got lost. I
 have sent another email to your group and no response received. Please
 help me.

 Thanks for you time. I look forward to hearing from you.

 Best,
 Ting


 ___
 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.
>>>
>
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Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

I'm not clear on what you are trying to do. Did you apply the atlas to 
an individual and have the atlas ROIs in the individual brain?


On 04/19/2018 12:42 PM, Ting Li wrote:
> 
> Douglas,
>
> Thank you so much for your response. My atlas is nii.gz format. What should I 
> do to get the cortical thickness, surface area and volume for various 
> cortical regions? Thanks in advance.
>
> Best,
> Ting
>
>
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>> wrote:
>>
>> Is the atlas in GCA format? If so, then you can use gca-apply
>>
>>
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>>
>>> We want to run recon-all with a custom atlas which is generated from
>>> ANTs multivariate template construction. What is the right procedure
>>> to run recon-all? Run recon-all to my atlas itself first and them use
>>> this output as a template or I use the custom template directly. I
>>> looked up your email database to search related topic and got lost. I
>>> have sent another email to your group and no response received. Please
>>> help me.
>>>
>>> Thanks for you time. I look forward to hearing from you.
>>>
>>> Best,
>>> Ting
>>>
>>>
>>> ___
>>> 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.
>>
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Sorry for bother you again. Our group want to study a cohort children’s brain 
using Freesurfer. We prefer to register our subjects to a custom children 
template. The template basically is an average of all the subjects we are going 
to study. It is constructed by ANTs. The format is nii.gz. My questions is 
where I should mention this registration template in the command Recon-all?  or 
how to get the cortical thickness, surface area and volume for various cortical 
regions for all subjects and perform the GLM analyses? 

In Freesurfer, there is a command of making own template for registration. If I 
generate my template from there, how can I run recon-all for the next to make 
sure my subjects all register to this template? and how to get the cortical 
thickness, surface area and volume for various cortical regions for all 
subjects and perform the GLM analyses? 

I really need your help for this. Thanks for your time.

Best,
Ting
> On Apr 19, 2018, at 11:42 AM, Ting Li  wrote:
> 
> Douglas,
> 
> Thank you so much for your response. My atlas is nii.gz format. What should I 
> do to get the cortical thickness, surface area and volume for various 
> cortical regions? Thanks in advance. 
> 
> Best,
> Ting
> 
> 
>> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  
>> wrote:
>> 
>> Is the atlas in GCA format? If so, then you can use gca-apply
>> 
>> 
>> On 04/19/2018 10:09 AM, Ting Li wrote:
>>> Hi Freesurfer Experts,
>>> 
>>> We want to run recon-all with a custom atlas which is generated from 
>>> ANTs multivariate template construction. What is the right procedure 
>>> to run recon-all? Run recon-all to my atlas itself first and them use 
>>> this output as a template or I use the custom template directly. I 
>>> looked up your email database to search related topic and got lost. I 
>>> have sent another email to your group and no response received. Please 
>>> help me.
>>> 
>>> Thanks for you time. I look forward to hearing from you.
>>> 
>>> Best,
>>> Ting
>>> 
>>> 
>>> ___
>>> 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.
>> 
> 


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Re: [Freesurfer] unable to open freeview

[Darko Komnenić]

External Email - Use Caution

Hi Andrew,
I did close it and reopen it.
There seem to be two different errors in this output.
If I just run echo $PATH, I get:
"/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
Linuxbrew directory detected, but it seems to be broken. Try to remove
'/home/lisak/.linuxbrew' and try
again./bin:/home/lisak/Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin"

meaning the same error from before, but without the Unmatched ".
whereas, if I cd into Desktop/freesurfer/bin
and then run tcl_setup
I just get the Unmatched ".
I hope this helps.
Best,
Darko

On Thu, Apr 19, 2018 at 7:17 PM, Hoopes, Andrew 
wrote:

> Did you close and open a new terminal window first? Sorry, I forgot to
> mention that the bash_profile needs to be re-sourced if you make changes.
> After this, run “echo $PATH” to make sure that the brew error is no longer
> present
>
> Andrew
>
>
>
> *From: *Darko Komnenić 
> *Date: *Thursday, April 19, 2018 at 1:08 PM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> I commented out the last two lines, and the same error message still
> appears. Please let me know if you have any other suggestions. Thanks!
>
> Best,
>
> Darko
>
>
>
> On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, try commenting out the last two lines and rerunning freeview
> (it’s possible that the error message getting inserted into your PATH is
> the source of these issues):
>
> # export PATH="$HOME/.linuxbrew/bin:$PATH"
>
> # export PATH="$(brew --prefix)/bin:$PATH"
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Thursday, April 19, 2018 at 6:54 AM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> An update,
>
> in the .bash_profile file, there is a line about linuxbrew. Do you
> recommend that I remove it? Sending the file attached.
>
> Best,
>
> Darko
>
>
>
> On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
> wrote:
>
> Hi Andrew,
>
> sorry for the delay. Attached is the hidden bashrc file from my Home
> folder. It doesn't seem to specify anything about linuxbrew, so I don't
> know why this error is showing up. Thanks a lot for any suggestions!
>
> Best,
>
> Darko
>
>
>
> On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
>
> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks a lot for your feedback!
>
> I renamed the original fine, so it is now called just tcl_setup, and here
> is the output I got after typing "freeview"
>
> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> Unmatched ".
>
> So this looks pretty much like the error I got when using Human Connectome
> Project pipelines (to answer your earlier question, the only time I got
> this error before was while running FreeSurferPipelineBatch.sh in HCP
> pipelines, specifically after the start of FreeSurferHighResWhite script).
> I don't use FreeSurfer for anything else on this computer, since this is
> the special 5.3-HCP version, and I use FS6 on a different computer. Also,
> the Unmatched quote error does not appear when running FSL or other
> programs.
>
> (Not sure if you're familiar with HCP pipelines, but they are used (among
> other things) to estimate cortical myelin content, and have 3 main
> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
> Unmatched ". error in the FS one. When writing to their mailing list, I was
> told that it seems like an error unique to my computer, and they have not
> encountered it before.)
>
>
>
> Anyway, the Linuxbrew 

Re: [Freesurfer] unable to open freeview

[Hoopes, Andrew]

Did you close and open a new terminal window first? Sorry, I forgot to mention 
that the bash_profile needs to be re-sourced if you make changes. After this, 
run “echo $PATH” to make sure that the brew error is no longer present
Andrew

From: Darko Komnenić 
Date: Thursday, April 19, 2018 at 1:08 PM
To: "Hoopes, Andrew" 
Cc: FS Help 
Subject: Re: [Freesurfer] unable to open freeview

Hi Andrew,
I commented out the last two lines, and the same error message still appears. 
Please let me know if you have any other suggestions. Thanks!
Best,
Darko

On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew 
> wrote:
Hi Darko, try commenting out the last two lines and rerunning freeview (it’s 
possible that the error message getting inserted into your PATH is the source 
of these issues):
# export PATH="$HOME/.linuxbrew/bin:$PATH"
# export PATH="$(brew --prefix)/bin:$PATH"


From: Darko Komnenić >
Date: Thursday, April 19, 2018 at 6:54 AM

To: "Hoopes, Andrew" >
Cc: FS Help 
>
Subject: Re: [Freesurfer] unable to open freeview

An update,
in the .bash_profile file, there is a line about linuxbrew. Do you recommend 
that I remove it? Sending the file attached.
Best,
Darko

On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
> wrote:
Hi Andrew,
sorry for the delay. Attached is the hidden bashrc file from my Home folder. It 
doesn't seem to specify anything about linuxbrew, so I don't know why this 
error is showing up. Thanks a lot for any suggestions!
Best,
Darko

On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
Are you using a bash shell? If you are, there should be a file located at 
~/.bashrc (it’s a hidden file in your home folder)
Andrew


From: Darko Komnenić >
Date: Tuesday, April 17, 2018 at 2:24 PM

To: "Hoopes, Andrew" >
Cc: FS Help 
>
Subject: Re: [Freesurfer] unable to open freeview

Hi Andrew,
thanks a lot for your feedback!
I renamed the original fine, so it is now called just tcl_setup, and here is 
the output I got after typing "freeview"

/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
 Linuxbrew directory detected, but it seems to be broken.  Try to remove 
'/home/lisak/.linuxbrew' and try 
again./bin:/home/lisak/Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Unmatched ".
So this looks pretty much like the error I got when using Human Connectome 
Project pipelines (to answer your earlier question, the only time I got this 
error before was while running FreeSurferPipelineBatch.sh in HCP pipelines, 
specifically after the start of FreeSurferHighResWhite script). I don't use 
FreeSurfer for anything else on this computer, since this is the special 
5.3-HCP version, and I use FS6 on a different computer. Also, the Unmatched 
quote error does not appear when running FSL or other programs.
(Not sure if you're familiar with HCP pipelines, but they are used (among other 
things) to estimate cortical myelin content, and have 3 main preprocessing 
pipelines, PreeFS one, FS one, and PostFS one - I got the Unmatched ". error in 
the FS one. When writing to their mailing list, I was told that it seems like 
an error unique to my computer, and they have not encountered it before.)

Anyway, the Linuxbrew error appears again now after trying to start freeview.
I searched for bashrc on my computer and I got two locations, one in perl 
subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so 
it's probably not the one you meant. The former is quite a long file, but does 
not mention linuxbrew at any point. I am sending the file attached.
I would be really very grateful if you would try helping out with this. I have 
been googling this error, but was not able to find anything.
Thanks a bunch!
Darko


On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
> wrote:
Hi Darko, there’s a big difference between using single vs double quotes in 
shell scripting – single quotes prevent variable expansion. Your modification 
to tcl_setup actually renders your PATH completely unusable. The quote syntax 
in the setup scripts shouldn’t cause any problems, and your unmatched errors 

Re: [Freesurfer] unable to open freeview

[Darko Komnenić]

External Email - Use Caution

Hi Andrew,
I commented out the last two lines, and the same error message still
appears. Please let me know if you have any other suggestions. Thanks!
Best,
Darko

On Thu, Apr 19, 2018 at 6:08 PM, Hoopes, Andrew 
wrote:

> Hi Darko, try commenting out the last two lines and rerunning freeview
> (it’s possible that the error message getting inserted into your PATH is
> the source of these issues):
>
> # export PATH="$HOME/.linuxbrew/bin:$PATH"
>
> # export PATH="$(brew --prefix)/bin:$PATH"
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Thursday, April 19, 2018 at 6:54 AM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> An update,
>
> in the .bash_profile file, there is a line about linuxbrew. Do you
> recommend that I remove it? Sending the file attached.
>
> Best,
>
> Darko
>
>
>
> On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
> wrote:
>
> Hi Andrew,
>
> sorry for the delay. Attached is the hidden bashrc file from my Home
> folder. It doesn't seem to specify anything about linuxbrew, so I don't
> know why this error is showing up. Thanks a lot for any suggestions!
>
> Best,
>
> Darko
>
>
>
> On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
>
> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks a lot for your feedback!
>
> I renamed the original fine, so it is now called just tcl_setup, and here
> is the output I got after typing "freeview"
>
> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> Unmatched ".
>
> So this looks pretty much like the error I got when using Human Connectome
> Project pipelines (to answer your earlier question, the only time I got
> this error before was while running FreeSurferPipelineBatch.sh in HCP
> pipelines, specifically after the start of FreeSurferHighResWhite script).
> I don't use FreeSurfer for anything else on this computer, since this is
> the special 5.3-HCP version, and I use FS6 on a different computer. Also,
> the Unmatched quote error does not appear when running FSL or other
> programs.
>
> (Not sure if you're familiar with HCP pipelines, but they are used (among
> other things) to estimate cortical myelin content, and have 3 main
> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
> Unmatched ". error in the FS one. When writing to their mailing list, I was
> told that it seems like an error unique to my computer, and they have not
> encountered it before.)
>
>
>
> Anyway, the Linuxbrew error appears again now after trying to start
> freeview.
>
> I searched for bashrc on my computer and I got two locations, one in perl
> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
> it's probably not the one you meant. The former is quite a long file, but
> does not mention linuxbrew at any point. I am sending the file attached.
>
> I would be really very grateful if you would try helping out with this. I
> have been googling this error, but was not able to find anything.
>
> Thanks a bunch!
>
> Darko
>
>
>
>
>
> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, there’s a big difference between using single vs double quotes
> in shell scripting – single quotes prevent variable expansion. Your
> modification to tcl_setup actually renders your PATH completely unusable.
> The quote syntax in the setup scripts shouldn’t cause any problems, and
> your unmatched errors indicate a more low-level issue that should probably
> get fixed directly. Are you only getting these unmatched errors with
> freesurfer tools? I can try to help you solve this, but I’m not quite sure
> I understand the initial problem.
>
>
>
> PS: At some point in your .bashrc is linuxbrew called? You don’t want that
> “Linuxbrew directory detected…” error in your PATH variable
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 1:21 PM
>
>
> *To: *"Hoopes, 

Re: [Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Douglas,

Thank you so much for your response. My atlas is nii.gz format. What should I 
do to get the cortical thickness, surface area and volume for various cortical 
regions? Thanks in advance. 

Best,
Ting


> On Apr 19, 2018, at 11:28 AM, Douglas N. Greve  wrote:
> 
> Is the atlas in GCA format? If so, then you can use gca-apply
> 
> 
> On 04/19/2018 10:09 AM, Ting Li wrote:
>> Hi Freesurfer Experts,
>> 
>> We want to run recon-all with a custom atlas which is generated from 
>> ANTs multivariate template construction. What is the right procedure 
>> to run recon-all? Run recon-all to my atlas itself first and them use 
>> this output as a template or I use the custom template directly. I 
>> looked up your email database to search related topic and got lost. I 
>> have sent another email to your group and no response received. Please 
>> help me.
>> 
>> Thanks for you time. I look forward to hearing from you.
>> 
>> Best,
>> Ting
>> 
>> 
>> ___
>> 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

Re: [Freesurfer] Recon-all with custom atlas

[Douglas N. Greve]

Is the atlas in GCA format? If so, then you can use gca-apply


On 04/19/2018 10:09 AM, Ting Li wrote:
> Hi Freesurfer Experts,
>
> We want to run recon-all with a custom atlas which is generated from 
> ANTs multivariate template construction. What is the right procedure 
> to run recon-all? Run recon-all to my atlas itself first and them use 
> this output as a template or I use the custom template directly. I 
> looked up your email database to search related topic and got lost. I 
> have sent another email to your group and no response received. Please 
> help me.
>
> Thanks for you time. I look forward to hearing from you.
>
> Best,
> Ting
>
>
> ___
> 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


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] Non-parametric correlation between FC and neuropsychological/volumetric outcomes

[Douglas N. Greve]

I'm not sure what you mean. Can you elaborate? Is this an individual 
analysis or a group analysis?


On 04/18/2018 10:10 AM, std...@virgilio.it wrote:
>
> Hi list,
>
> which the best way to perform a whole-brain correlation of the FC 
> assessed by FS-FAST with the volumetic or neuropsychological outcomes?
> Please note that my question is specifically addressed to those 
> factors (neuropsycholgical scores or volume of seed) did not show a 
> normal distribution and that cannot be trasformed.
>
> Thanks
>
> Kind regards
>
>
> Stefano
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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] mni152reg yields bad registration

[Douglas N. Greve]

I don't know what might have happened (under the hood, mni152reg uses 
the FSL flirt program). If you want a non-linear registration, then 
you'll need to use CVS (mri_cvs_register) and choose the mni target. If 
you just want the aparc of the aparc+aseg, then don't go into the volume 
at all.


On 04/17/2018 01:57 PM, Zimmerman, Jared wrote:
>
> Hi All,
>
> I’m trying to register the aparc+aseg volumes from subject T1 space to 
> MNI152 space and running into problems.  I’ve taken the following steps
>
> 1.mri152reg –s Subj241
>
> 2.mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz 
> --mov $SUBJECTS_DIR/Subj241/mri/aparc+aseg.mgz --o 
> Subj241_aparc+aseg_mni2mm.nii.gz --reg 
> $SUBJECTS_DIR/Subj241/mri/transforms/reg.mni152.2mm.dat
>
> This yields an image that is rotated and shrunken relative to the 
> MNI152_T1_2mm template as shown in the attached image.
>
> I’m wondering if this is the right way to do what I’d like to do.  The 
> reg.mni152.2mm.dat file is only a linear transform, but I’d like to 
> apply a non-linear transformation to the subject aparc+aseg to get it 
> well matched to the MNI152 template space.  Some of my subjects have 
> atypical head shapes and I really think a non-linear warp will be 
> necessary to achieve a good fit.
>
> I’ve run the MNI152 1mm template through recon-all so I have that as a 
> reference.  Is there a way to map volumes from one subject space to 
> another via fsaverage or sphere sort of like mri_label2label does for 
> labels?
>
> Alternatively, I could just calculate the appropriate T1 to MNI warps 
> with FNIRT or ANTs and apply those to the aparc+aseg, but I figured it 
> would be possible to do with FreeSurfer without calculating any new 
> transforms.
>
> Thanks,
>
> Jared
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Re: [Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

[Douglas N. Greve]

The group analysis for more complicated designs is the same as for 
thickness analysis and can be found, eg, here

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

It will only analyze the dat you give it (ie, bold amplitude, cvr, 
thickness)

On 04/17/2018 02:23 PM, Arsenije Subotic wrote:
> Hi Doug,
>
> I am able to get up to the mrs_glmfit step of the Surface Based Group fMRI 
> Analysis, but it does not indicate how a comparison should be made between 
> the two groups that I have. It only gives information on how to perform a one 
> sample group mean test (osgm). In addition, when you mention using a 
> mrs_glmfit-sim command, does this also generate cerebrovascular reactivity 
> values, or does it only provide cortical thickness values? I was also hoping 
> that I could potentially visualize an average area of low BOLD CVR for both 
> groups. Is that possible?
>
> Thanks,
> Arsenije
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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] unable to open freeview

[Hoopes, Andrew]

Hi Darko, try commenting out the last two lines and rerunning freeview (it’s 
possible that the error message getting inserted into your PATH is the source 
of these issues):
# export PATH="$HOME/.linuxbrew/bin:$PATH"
# export PATH="$(brew --prefix)/bin:$PATH"


From: Darko Komnenić 
Date: Thursday, April 19, 2018 at 6:54 AM
To: "Hoopes, Andrew" 
Cc: FS Help 
Subject: Re: [Freesurfer] unable to open freeview

An update,
in the .bash_profile file, there is a line about linuxbrew. Do you recommend 
that I remove it? Sending the file attached.
Best,
Darko

On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
> wrote:
Hi Andrew,
sorry for the delay. Attached is the hidden bashrc file from my Home folder. It 
doesn't seem to specify anything about linuxbrew, so I don't know why this 
error is showing up. Thanks a lot for any suggestions!
Best,
Darko

On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
Are you using a bash shell? If you are, there should be a file located at 
~/.bashrc (it’s a hidden file in your home folder)
Andrew


From: Darko Komnenić >
Date: Tuesday, April 17, 2018 at 2:24 PM

To: "Hoopes, Andrew" >
Cc: FS Help 
>
Subject: Re: [Freesurfer] unable to open freeview

Hi Andrew,
thanks a lot for your feedback!
I renamed the original fine, so it is now called just tcl_setup, and here is 
the output I got after typing "freeview"

/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
 Linuxbrew directory detected, but it seems to be broken.  Try to remove 
'/home/lisak/.linuxbrew' and try 
again./bin:/home/lisak/Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Unmatched ".
So this looks pretty much like the error I got when using Human Connectome 
Project pipelines (to answer your earlier question, the only time I got this 
error before was while running FreeSurferPipelineBatch.sh in HCP pipelines, 
specifically after the start of FreeSurferHighResWhite script). I don't use 
FreeSurfer for anything else on this computer, since this is the special 
5.3-HCP version, and I use FS6 on a different computer. Also, the Unmatched 
quote error does not appear when running FSL or other programs.
(Not sure if you're familiar with HCP pipelines, but they are used (among other 
things) to estimate cortical myelin content, and have 3 main preprocessing 
pipelines, PreeFS one, FS one, and PostFS one - I got the Unmatched ". error in 
the FS one. When writing to their mailing list, I was told that it seems like 
an error unique to my computer, and they have not encountered it before.)

Anyway, the Linuxbrew error appears again now after trying to start freeview.
I searched for bashrc on my computer and I got two locations, one in perl 
subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so 
it's probably not the one you meant. The former is quite a long file, but does 
not mention linuxbrew at any point. I am sending the file attached.
I would be really very grateful if you would try helping out with this. I have 
been googling this error, but was not able to find anything.
Thanks a bunch!
Darko


On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
> wrote:
Hi Darko, there’s a big difference between using single vs double quotes in 
shell scripting – single quotes prevent variable expansion. Your modification 
to tcl_setup actually renders your PATH completely unusable. The quote syntax 
in the setup scripts shouldn’t cause any problems, and your unmatched errors 
indicate a more low-level issue that should probably get fixed directly. Are 
you only getting these unmatched errors with freesurfer tools? I can try to 
help you solve this, but I’m not quite sure I understand the initial problem.

PS: At some point in your .bashrc is linuxbrew called? You don’t want that 
“Linuxbrew directory detected…” error in your PATH variable

From: Darko Komnenić >
Date: Tuesday, April 17, 2018 at 1:21 PM

To: "Hoopes, Andrew" >
Cc: FS Help 
>
Subject: Re: [Freesurfer] unable to open freeview

Hi Andrew,
OK, so here is what happened:

After adding the echo $PATH under the first line, my output is now this:

Re: [Freesurfer] How FDR was used to correct for multiple comparisons

[Douglas N. Greve]

Yes, that looks right. It is the basic FDR computation


On 04/18/2018 12:53 PM, Livia Liu wrote:
>
> Dear Douglas,
>
> Thank you for your reply. I read the related FDR paper given in the 
> “mri_fdr –help”.
>
> Please tell me if the FDR correction in FreeSurfer do like the below.
>
> For the V vertices being tested, the general procedure is as follows:
>
> (1) Select a desired FDR bound q between 0 and 1. This is the maximum 
> FDR that the researcher is willing to tolerate on average and we 
> select q=0.05.
>
> (2) Order the P values from smallest to largest: P(1) ≤P(2) ≤••≤P(v). 
> Let v(i) be the vertex corresponding to P value P(i).
>
> (3) Let r be the largest i for which: P(i) ≤i/V*q/c(V), where c(V) is 
> a predetermined constant.
>
> (4) Declare the voxels v(1), . . . ,v(r) active, or in other words, 
> threshold the image of test statistics at the value corresponding to 
> the P value P(r).
>
> If I response like this, is it right?
>
> Thank you very much, and looking forward to reply.
>
> Kind regards,
>
> Livia
>
>
> 2018-04-18 0:41 GMT+08:00 Douglas Greve  >:
>
> You should read the FDR paper for more detail. But the FDR is the
> number of false positives relative to the total number of
> positives. The way it is interpreted is that when you look at an
> image, 5% of the voxels above threshold are false. You don't know
> which 5%. If the 5% came out of a big blob, probably you would not
> change your conclusion about that blob. If there were a few single
> voxels that were above threshold, you probably don't want to write
> your paper around it.
>
>
> On 4/16/18 11:42 PM, Livia Liu wrote:
>>
>> Dear Douglas,
>>
>>
>> Thank you for your reply. I run “mri_fdr –help” to get docs that
>> include some information for how to use this command. However, I
>> still don’t know how FDR was used to correct for multiple
>> comparisons.
>>
>>
>> This question is an opinion given by one reviewer, and I really
>> don’t know how to reply.
>>
>> For the description "To correct for multiple comparisons, the
>> thresholds of the P maps were set to yield an expected false
>> discovery rate (FDR) of 0.05." The reviewer said “Would help to
>> provide more details as to how FDR was used to correct for multiple?”
>>
>>
>> Would you please give me some help to response the question?
>> Thank you very much.
>>
>>
>> Kind regards,
>>
>> Livia
>>
>>
>> 2018-04-17 0:40 GMT+08:00 Douglas N. Greve
>> >:
>>
>> You can also use mri_fdr Run  it with --help to get docs
>>
>>
>> On 04/16/2018 10:23 AM, Livia Liu wrote:
>> >
>> > Dear FS experts,
>> >
>> > I'd like to know that how FDR was used to correct for multiple
>> > comparisons. I do FDR correction in two way in FreeSurfer.
>> >
>> > 1, Do the FDR correction in the qdec tool. And the page of
>> “False
>> > Discovery Rate” in the page “Multiple-Comparisons
>> Correction in Qdec”
>> > was lost.
>> >
>> > 2, Use “lme_mass_FDR.m” to do the FDR correction in LME
>> model, which
>> > was based on Tom's FDR.m in the github, however the page
>> was also lost.
>> >
>> > Would help to provide more details as to how FDR in the two
>> way was
>> > used to correct for multiple comparisons?
>> >
>> >
>> > Thank you very much, and looking forward to reply.
>> >
>> > Kind regards,
>> >
>> > Livia
>> >
>> >
>> >
>> >
>> > ___
>> > 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
>> 

Re: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

[Douglas N. Greve]

How does the input image look, ie, orig.mgz?


On 04/19/2018 09:49 AM, Jones, Richard wrote:
>
> I ran the command shown below to do recon-all on DICOM images from a 
> Philips Ingenia scanner using the development version of freesurfer on 
> a Mac running high Sierra.
>
> recon-all -i 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm -subject 
> HOPE_SS020 –all
>
> The program crashed with the error “ERROR: mpr2mni305 failed, see 
> transforms/talairach_avi.log”
>
> The talairach_avi.log file is shown below, followed by the log file. 
> As a test I ran the same command, on the same data, using Freesurfer 6 
> and that ran without problems (except that it didn’t handle the 
> diffusion tags in the Philips DICOM header correctly so I had to set 
> FS_LOAD_DWI=0, this was not a problem in the development version). Any 
> suggestions as to what may be causing the problems with the library in 
> the development version?
>
> Thanks,
>
> Richard
>
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri
>
> /Applications/freesurfer_dev/bin/talairach_avi
>
> --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
>
> $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
>
> Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
> 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> Thu Apr 19 08:45:01 EDT 2018
>
> mri_convert.bin orig_nu.mgz talsrcimg.img
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from orig_nu.mgz...
>
> TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
>
> i_ras = (-1, 7.45058e-09, 0)
>
> j_ras = (3.72529e-09, -4.88944e-09, -1)
>
> k_ras = (0, 1, 4.88944e-09)
>
> writing to talsrcimg.img...
>
> Analyze Output Matrix
>
> -1.0   0.0   0.0   128.15305;
>
> 0.0  -0.0   1.0  -116.15433;
>
> 0.0  -1.0   0.0   128.60870;
>
> 0.0   0.0   0.0   1.0;
>
> 
>
> INFO: set hdr.hist.orient to -1
>
> mpr2mni305 talsrcimg
>
> Thu Apr 19 08:45:02 EDT 2018
>
> /Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
>
> $Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
>
> target=711-2C_as_mni_average_305
>
> -
>
> analyzeto4dfp talsrcimg -O0 -y
>
> -
>
> $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
>
> Thu Apr 19 08:45:02 2018
>
> Writing: talsrcimg.4dfp.hdr
>
> $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
>
> Reading: talsrcimg.hdr
>
> header size 348 bytes
>
> hdr.dime.datatype offset=70    value=2
>
> hdr.dime.bitpix offset=72    value=8
>
> hdr.hist.orient offset=252  value=-1
>
> dimensionality 4
>
> dimensions   256   256 256 1
>
> Reading: talsrcimg.img
>
> Writing: talsrcimg.4dfp.img
>
> Writing: talsrcimg.4dfp.ifh
>
> ifh2hdr talsrcimg -r0to255
>
> ori=2
>
> -
>
> gauss_4dfp talsrcimg 1.1
>
> -
>
> dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
>
>   Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
>
>   Reason: image not found
>
> Abort
>
> ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
>
> ERROR: mpr2mni305 execution aborted
>
> Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
>
> Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
>
> INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
>
> Actual FREESURFER_HOME /Applications/freesurfer_dev
>
> Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  
> 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> /Applications/freesurfer_dev/subjects/HOPE_SS020
>
> \n mri_convert 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
>
> mri_convert.bin 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
> /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
>
> $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
>
> reading from 
> /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
>
> Starting DICOMRead2()
>
> dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
>
> dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
>
> Ref Series No = 301
>
> Found 202 files, checking for dicoms
>
> Found 200 dicom files in series.
>
> First Sorting
>
> Computing Slice Direction
>
> Vs: -0.897217 -0.0611658 0.0354633
>
> Vs: -0.996909 -0.0679621 0.0394038
>
> Second Sorting
>
> IsDWI = 0, IsPhilipsDWI = 0
>
> Counting frames
>
> nframes = 1
>
> nslices = 200
>
> ndcmfiles = 200
>
> PE Dir = ROW (dicom read)
>
> Loading pixel data
>
> TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
>
> i_ras = (0.0644896, -0.994415, 0.0835493)
>
> j_ras = 

Re: [Freesurfer] LGI for the lobar annotation

[Douglas N. Greve]

yes


On 04/19/2018 07:17 AM, Fernanda Hansen P. de Moraes wrote:
> Douglas, thank you very much again.
> So I can assume it is the lGI for the area (in this case the lobe)?
>
> Thank you again!
>
> On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve  > wrote:
>
> The "intensity" is the mean value of the input (lh.pial_lgi in
> this case) averaged over vertices. If  you wan the total number,
> multiply it by the number of vertices or re-run with --accumulate.
> The area is the surface area of the entire lobe.
>
>
> On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes wrote:
>> Sorry, my mistake.
>>
>> mri_segstats --annot DA011 lh lobesStrict --i
>> DA011/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats
>>
>> On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve
>> > wrote:
>>
>> What is your command line? Also, please remember to post to
>> the list
>>
>>
>> On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote:
>> > Dear Douglas,
>> >
>> > thank you.
>> >
>> >  The code worked, but I didn't understand the result very
>> well. What
>> > means intensity? The area, is the ara from the piall_lgi
>> surface
>> > (outer surface)?
>> >
>> > Thank you again
>> >
>> > On Tue, Apr 17, 2018 at 1:07 PM Douglas Greve
>> 
>> > > >> wrote:
>> >
>> >     If you run it with --help you will see an example
>> >
>> >
>> >     On 4/16/18 7:16 AM, Fernanda Hansen P. de Moraes wrote:
>> >>     Thank you, Douglas,
>> >>
>> >>     do you have any suggestions on how to make you work?
>> >>
>> >>     Fernanda
>> >>
>> >>
>> >>
>> >>     On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve
>> >>     > 
>> > >> wrote:
>> >>
>> >>         that should work, except the command line is not
>> quite right
>> >>
>> >>
>> >>         On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes
>> wrote:
>> >>>         Good night,
>> >>>
>> >>>         does anyone know if it is possible to calculate
>> the lGI for
>> >>>         the ?h.lobesStrict.annot? And if it yes, how can
>> I do it?
>> >>>
>> >>>         I've already tried to use:
>> >>>
>> >>>         /mri_segstats --annot
>> subjxx/label/lh.lobesStrict.annot --i
>> >>>  $SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum
>> >>>  lh.lobesStrict.annot.pial_lgi.stats/
>> >>>
>> >>>         Thank you!
>> >>>         --
>> >>>         Fernanda Hansen P. de Moraes
>> >>>         Física Médica | Instituto D'Or de Pesquisa e
>> Ensino | Rede
>> >>>         D'Or São Luiz
>> >>>
>> >>>
>> >>>  ___
>> >>>         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.
>> >>
>> >>     --
>> >>     Fernanda Hansen P. de Moraes
>> >>     Física Médica | Instituto D'Or de 

[Freesurfer] SLURM - speed processing

[Alexandre Obert]

External Email - Use Caution

Hi all,

I'm definitively a noob with both freesurfer and SLURM processes and I
wonder if anyone could give me some advice.
I tried processing a subject (including hippocampal segmentation) using the
following command (freesurfer 6.0.0):

recon-all -all -s s03 -hippocampal-subfields-T1

It took nearly 12h to process.
I then submit this job to a supercomputer (using slurm) and I asked for
nearly 30Go RAM
It took nearly 7h to process. That seems good but I wonder if it's possible
to speed it up a little more?

Regards,

Alex
___
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] Freesurfer dev version : recon all error mpr2mni305

[Hoopes, Andrew]

Hi Richard, thanks for pointing this out – I’ll take a look into it.

best
Andrew

From:  on behalf of "Jones, Richard" 

Reply-To: FS Help 
Date: Thursday, April 19, 2018 at 9:49 AM
To: FS Help 
Subject: [Freesurfer] Freesurfer dev version : recon all error mpr2mni305

I ran the command shown below to do recon-all on DICOM images from a Philips 
Ingenia scanner using the development version of freesurfer on a Mac running 
high Sierra.

recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
-subject HOPE_SS020 –all

The program crashed with the error “ERROR: mpr2mni305 failed, see 
transforms/talairach_avi.log”

The talairach_avi.log file is shown below, followed by the log file. As a test 
I ran the same command, on the same data, using Freesurfer 6 and that ran 
without problems (except that it didn’t handle the diffusion tags in the 
Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a 
problem in the development version). Any suggestions as to what may be causing 
the problems with the library in the development version?

Thanks,

Richard

/Applications/freesurfer_dev/subjects/HOPE_SS020/mri
/Applications/freesurfer_dev/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Thu Apr 19 08:45:01 EDT 2018
mri_convert.bin orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (-1, 7.45058e-09, 0)
j_ras = (3.72529e-09, -4.88944e-09, -1)
k_ras = (0, 1, 4.88944e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.0   0.0   0.0   128.15305;
0.0  -0.0   1.0  -116.15433;
0.0  -1.0   0.0   128.60870;
0.0   0.0   0.0   1.0;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Apr 19 08:45:02 EDT 2018
/Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Thu Apr 19 08:45:02 2018
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype  offset=70value=2
hdr.dime.bitpix offset=72value=8
hdr.hist.orient   offset=252  value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
  Reason: image not found
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted


Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
Actual FREESURFER_HOME /Applications/freesurfer_dev
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Applications/freesurfer_dev/subjects/HOPE_SS020
\n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
Ref Series No = 301
Found 202 files, checking for dicoms
Found 200 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.897217 -0.0611658 0.0354633
Vs: -0.996909 -0.0679621 0.0394038
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 200
ndcmfiles = 200
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (0.0644896, -0.994415, 0.0835493)
j_ras = (0.0448617, -0.08075, -0.995724)
k_ras = 

Re: [Freesurfer] Freesurfer and crypt

[Bennet Fauber]

External Email - Use Caution

Hi, Rob,

The call to crypt() appears to be in FreeSurfer's license validation
routine, since it is immediately after reading the license file.  In the
sense that FreeSurfer cannot run without some sort of license, and that
license validation is using the native Unix crypt() function to validate,
it's not quite OpenSource.  I think someone at FreeSurfer would need to
replace the single call to the crypt() function with some other function
that isn't marked as 'insecure' to bypass this.

I thought I saw something earlier on the mailing list about this, and that
there was a workaround, but I am unable to locate it again.  Any chance
this could get passed to the developer who maintains the license validation
code?  Depending on the code and their willingness to share, we might be
able to contribute an alternative for systems with the elevated security.

This currently may not be a bit issue, but we are seeing increasing
strictness on our end to comply with federal security guidelines, and it
may not just be our Medical Center and local VA that are pushing these
security measures.

This is what it looks like when it succeeds.

11527 open("/sw/arcts/centos7/freesurfer/6.0.0/license.txt", O_RDONLY) = 3
11527 fstat(3, {st_mode=S_IFREG|0644, st_size=52, ...}) = 0
11527 mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1,
0) = 0x2b4bcc176000
11527 read(3, "ben...@umich.edu\n6925\n *CpU.rbF6"..., 8192) = 52
11527 read(3, "", 8192) = 0
11527 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
11527 read(4, "0\n", 31)= 2
11527 close(4)  = 0
11527 close(3)  = 0
11527 munmap(0x2b4bcc176000, 8192)  = 0
11527 getcwd("/home/bennet/tmp/freesurfer", 4096) = 28
11527 open("/home/bennet/tmp/freesurfer/sample-001.mgz", O_RDONLY) = 3

I do not believe that this is something that can be 'whitelisted', as this
is set in the Linux kernel at boot time.

Thanks,-- bennet


On Thu, Apr 12, 2018 at 11:29 AM, Dicamillo, Robert <
rdicami...@mgh.harvard.edu> wrote:

> Hello Bennet,
>
> Maybe someone else can chime in on this, as I have not worked on a system
> with FIPS, but perhaps there is a way for the FIPS administrator to white
> list
> all the Freesurfer binaries (and the license file), as security exempt.
>
> I know some Enterprise/business applications like Adobe’s Acrobat, etc.,
> (closed source) are built with code to work on FIPS compliant systems, but
> I don’t see there is currently anything in Freesurfer (essentially open
> source),
> code that knows about cryptographic modules, digital signatures, etc. to
> work on
> a secure system.  Even turning on SElinux for linux OS can be an
> issue for some programs.
>
> Another thing to inquire about is if the IT folks maintain any non-secure
> servers,
> , i.e., I would not assume that any application will just work in a secure
> environment.
>
> - rob
>
> > On Apr 12, 2018, at 10:51 AM, Bennet Fauber  wrote:
> >
> > It appears that FreeSurfer is not compatible with systems for which
> > FIPS level security is mandated.  In our case, I am told this is part
> > of our data use agreement with the VA.
> >
> > We tried to run it, and I get the following stack trace showing what
> > appears to be license validation using the crypt() function, which is
> > blacklisted by the Linux kernel by the FIPS configuration.
> >
> > 28063 open("/opt/apps/freesurfer-6.0/freesurfer/license.txt", O_RDONLY)
> = 3
> > 28063 fstat(3, {st_mode=S_IFREG|0644, st_size=59, ...}) = 0
> > 28063 mmap(NULL, 4096, PROT_READ|PROT_WRITE,
> > MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fa319883000
> > 28063 read(3, "issc-sysad...@umich.edu\n23098\n*C"..., 4096) = 59
> > 28063 read(3, "", 4096) = 0
> > 28063 open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4
> > 28063 read(4, "1\n", 31)= 2
> > 28063 close(4)  = 0
> > 28063 write(1, "ERROR: crypt() returned null wit"..., 46) = 46
> > 28063 exit_group(1)
> >
> > Is there a workaround so we can run FreeSurfer FIPS-enabled systems?
> >
> > Appreciate your consideration of this question,
> >
> > -- bennet
> >
> >
> >
> > On Thu, Mar 29, 2018 at 5:05 PM, Bennet Fauber  wrote:
> >> I have a couple of users here who are reporting that on machines with
> >> FIPS enabled, which in turn disables certain cryptographic functions,
> >> FreeSurfer core dumps with a call to the crypt() function, which FIPS
> >> disables.
> >>
> >> Someone speculated based on output from strace that this is FreeSurfer
> >> possibly attempting to validate its license.
> >>
> >> Is this a known problem?  Is there a solution?
> >>
> >> We have a university compliance office and possibly similar people
> >> from our local VA who are insisting that FIPS be enabled.
> >>
> >> If you need more information, please let me know and I will try to
> >> obtain it for you.
> >>
> 

[Freesurfer] Recon-all with custom atlas

[Ting Li]

External Email - Use Caution

Hi Freesurfer Experts,

We want to run recon-all with a custom atlas which is generated from ANTs 
multivariate template construction. What is the right procedure to run 
recon-all? Run recon-all to my atlas itself first and them use this output as a 
template or I use the custom template directly. I looked up your email database 
to search related topic and got lost. I have sent another email to your group 
and no response received. Please help me. 

Thanks for you time. I look forward to hearing from you. 

Best,
Ting___
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[Freesurfer] hippocampal segmentation development version question

[Maureen McHugo]

Hi,

I am interested in using the head/body/tail output from the hippocampal
subfield segmentation module. Is there a reference or description of what
landmarks were used to separate head/body and body/tail? Thanks!

Maureen
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Freesurfer dev version : recon all error mpr2mni305

[Jones, Richard]

I ran the command shown below to do recon-all on DICOM images from a Philips 
Ingenia scanner using the development version of freesurfer on a Mac running 
high Sierra.

recon-all -i /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
-subject HOPE_SS020 -all

The program crashed with the error "ERROR: mpr2mni305 failed, see 
transforms/talairach_avi.log"

The talairach_avi.log file is shown below, followed by the log file. As a test 
I ran the same command, on the same data, using Freesurfer 6 and that ran 
without problems (except that it didn't handle the diffusion tags in the 
Philips DICOM header correctly so I had to set FS_LOAD_DWI=0, this was not a 
problem in the development version). Any suggestions as to what may be causing 
the problems with the library in the development version?

Thanks,

Richard

/Applications/freesurfer_dev/subjects/HOPE_SS020/mri
/Applications/freesurfer_dev/bin/talairach_avi
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
Thu Apr 19 08:45:01 EDT 2018
mri_convert.bin orig_nu.mgz talsrcimg.img
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from orig_nu.mgz...
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (-1, 7.45058e-09, 0)
j_ras = (3.72529e-09, -4.88944e-09, -1)
k_ras = (0, 1, 4.88944e-09)
writing to talsrcimg.img...
Analyze Output Matrix
-1.0   0.0   0.0   128.15305;
0.0  -0.0   1.0  -116.15433;
0.0  -1.0   0.0   128.60870;
0.0   0.0   0.0   1.0;

INFO: set hdr.hist.orient to -1
mpr2mni305 talsrcimg
Thu Apr 19 08:45:02 EDT 2018
/Applications/freesurfer_dev/bin/mpr2mni305 talsrcimg
$Id: mpr2mni305,v 1.5 2015/12/18 23:56:21 zkaufman Exp $
target=711-2C_as_mni_average_305

-
analyzeto4dfp talsrcimg -O0 -y
-

$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $
Thu Apr 19 08:45:02 2018
Writing: talsrcimg.4dfp.hdr
$Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $
Reading: talsrcimg.hdr
header size 348 bytes
hdr.dime.datatype  offset=70value=2
hdr.dime.bitpix offset=72value=8
hdr.hist.orient   offset=252  value=-1
dimensionality 4
dimensions   256   256   256 1
Reading: talsrcimg.img
Writing: talsrcimg.4dfp.img
Writing: talsrcimg.4dfp.ifh
ifh2hdr talsrcimg -r0to255
ori=2

-
gauss_4dfp talsrcimg 1.1
-

dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/7/libgfortran.4.dylib
  Referenced from: /Applications/freesurfer_dev/bin/gauss_4dfp
  Reason: image not found
Abort
ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134
ERROR: mpr2mni305 execution aborted


Subject Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
Current Stamp: freesurfer-darwin-OSX-ElCapitan-dev-20180415-0d56499
INFO: SUBJECTS_DIR is /Applications/freesurfer_dev/subjects
Actual FREESURFER_HOME /Applications/freesurfer_dev
Darwin meshuga.choa.org 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar  5 
22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
/Applications/freesurfer_dev/subjects/HOPE_SS020
\n mri_convert /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz \n
mri_convert.bin /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm 
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
$Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $
reading from /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm...
Starting DICOMRead2()
dcmfile = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat/IM-0001-0001.dcm
dcmdir = /Users/Shared/HOPE_SS_Data/HOPE_SS020_Anat
Ref Series No = 301
Found 202 files, checking for dicoms
Found 200 dicom files in series.
First Sorting
Computing Slice Direction
Vs: -0.897217 -0.0611658 0.0354633
Vs: -0.996909 -0.0679621 0.0394038
Second Sorting
IsDWI = 0, IsPhilipsDWI = 0
Counting frames
nframes = 1
nslices = 200
ndcmfiles = 200
PE Dir = ROW (dicom read)
Loading pixel data
TR=6.98, TE=3.14, TI=0.00, flip angle=8.00
i_ras = (0.0644896, -0.994415, 0.0835493)
j_ras = (0.0448617, -0.08075, -0.995724)
k_ras = (0.996909, 0.0679621, 0.0394038)
writing to /Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz...
#
#@# MotionCor Thu Apr 19 08:44:06 EDT 2018
Found 1 runs
/Applications/freesurfer_dev/subjects/HOPE_SS020/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
Only one run found so motion
correction will not be performed. I'll
copy the 

Re: [Freesurfer] LGI for the lobar annotation

[Fernanda Hansen P. de Moraes]

Douglas, thank you very much again.
So I can assume it is the lGI for the area (in this case the lobe)?

Thank you again!

On Wed, Apr 18, 2018 at 11:48 PM Douglas Greve 
wrote:

> The "intensity" is the mean value of the input (lh.pial_lgi in this case)
> averaged over vertices. If  you wan the total number, multiply it by the
> number of vertices or re-run with --accumulate. The area is the surface
> area of the entire lobe.
>
> On 4/18/18 3:23 PM, Fernanda Hansen P. de Moraes wrote:
>
> Sorry, my mistake.
>
> mri_segstats --annot DA011 lh lobesStrict --i DA011/surf/lh.pial_lgi --sum
> lh.lobesStrict.annot.pial_lgi.stats
>
> On Wed, Apr 18, 2018 at 4:13 PM Douglas N. Greve 
> wrote:
>
>> What is your command line? Also, please remember to post to the list
>>
>>
>> On 04/18/2018 02:10 PM, Fernanda Hansen P. de Moraes wrote:
>> > Dear Douglas,
>> >
>> > thank you.
>> >
>> >  The code worked, but I didn't understand the result very well. What
>> > means intensity? The area, is the ara from the piall_lgi surface
>> > (outer surface)?
>> >
>> > Thank you again
>> >
>> > On Tue, Apr 17, 2018 at 1:07 PM Douglas Greve > > > wrote:
>> >
>> > If you run it with --help you will see an example
>> >
>> >
>> > On 4/16/18 7:16 AM, Fernanda Hansen P. de Moraes wrote:
>> >> Thank you, Douglas,
>> >>
>> >> do you have any suggestions on how to make you work?
>> >>
>> >> Fernanda
>> >>
>> >>
>> >>
>> >> On Fri, Apr 13, 2018 at 5:56 PM Douglas Greve
>> >> > wrote:
>> >>
>> >> that should work, except the command line is not quite right
>> >>
>> >>
>> >> On 4/13/18 4:22 PM, Fernanda Hansen P. de Moraes wrote:
>> >>> Good night,
>> >>>
>> >>> does anyone know if it is possible to calculate the lGI for
>> >>> the ?h.lobesStrict.annot? And if it yes, how can I do it?
>> >>>
>> >>> I've already tried to use:
>> >>>
>> >>> /mri_segstats --annot subjxx/label/lh.lobesStrict.annot --i
>> >>> $SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum
>> >>> lh.lobesStrict.annot.pial_lgi.stats/
>> >>>
>> >>> Thank you!
>> >>> --
>> >>> Fernanda Hansen P. de Moraes
>> >>> Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede
>> >>> D'Or São Luiz
>> >>>
>> >>>
>> >>> ___
>> >>> 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.
>> >>
>> >> --
>> >> Fernanda Hansen P. de Moraes
>> >> Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or
>> >> São Luiz
>> >>
>> >>
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> 
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Fernanda Hansen P. de Moraes
>> > Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz
>>
>> --
> Fernanda Hansen P. de Moraes
> Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz
>
>
> --
Fernanda Hansen P. de Moraes
Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] unable to open freeview

[Darko Komnenić]

An update,
in the .bash_profile file, there is a line about linuxbrew. Do you
recommend that I remove it? Sending the file attached.
Best,
Darko

On Thu, Apr 19, 2018 at 11:59 AM, Darko Komnenić 
wrote:

> Hi Andrew,
> sorry for the delay. Attached is the hidden bashrc file from my Home
> folder. It doesn't seem to specify anything about linuxbrew, so I don't
> know why this error is showing up. Thanks a lot for any suggestions!
> Best,
> Darko
>
> On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
> wrote:
>
>> Are you using a bash shell? If you are, there should be a file located at
>> ~/.bashrc (it’s a hidden file in your home folder)
>>
>> Andrew
>>
>>
>>
>>
>>
>> *From: *Darko Komnenić 
>> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>>
>> *To: *"Hoopes, Andrew" 
>> *Cc: *FS Help 
>> *Subject: *Re: [Freesurfer] unable to open freeview
>>
>>
>>
>> Hi Andrew,
>>
>> thanks a lot for your feedback!
>>
>> I renamed the original fine, so it is now called just tcl_setup, and here
>> is the output I got after typing "freeview"
>>
>> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/bi
>> n:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
>> Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/
>> home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
>> Linuxbrew directory detected, but it seems to be broken.  Try to remove
>> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/Desktop
>> /fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/
>> local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/
>> usr/games:/usr/local/games:/snap/bin
>> Unmatched ".
>>
>> So this looks pretty much like the error I got when using Human
>> Connectome Project pipelines (to answer your earlier question, the only
>> time I got this error before was while running FreeSurferPipelineBatch.sh
>> in HCP pipelines, specifically after the start of FreeSurferHighResWhite
>> script). I don't use FreeSurfer for anything else on this computer, since
>> this is the special 5.3-HCP version, and I use FS6 on a different computer.
>> Also, the Unmatched quote error does not appear when running FSL or other
>> programs.
>>
>> (Not sure if you're familiar with HCP pipelines, but they are used (among
>> other things) to estimate cortical myelin content, and have 3 main
>> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
>> Unmatched ". error in the FS one. When writing to their mailing list, I was
>> told that it seems like an error unique to my computer, and they have not
>> encountered it before.)
>>
>>
>>
>> Anyway, the Linuxbrew error appears again now after trying to start
>> freeview.
>>
>> I searched for bashrc on my computer and I got two locations, one in perl
>> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
>> it's probably not the one you meant. The former is quite a long file, but
>> does not mention linuxbrew at any point. I am sending the file attached.
>>
>> I would be really very grateful if you would try helping out with this. I
>> have been googling this error, but was not able to find anything.
>>
>> Thanks a bunch!
>>
>> Darko
>>
>>
>>
>>
>>
>> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
>> wrote:
>>
>> Hi Darko, there’s a big difference between using single vs double quotes
>> in shell scripting – single quotes prevent variable expansion. Your
>> modification to tcl_setup actually renders your PATH completely unusable.
>> The quote syntax in the setup scripts shouldn’t cause any problems, and
>> your unmatched errors indicate a more low-level issue that should probably
>> get fixed directly. Are you only getting these unmatched errors with
>> freesurfer tools? I can try to help you solve this, but I’m not quite sure
>> I understand the initial problem.
>>
>>
>>
>> PS: At some point in your .bashrc is linuxbrew called? You don’t want
>> that “Linuxbrew directory detected…” error in your PATH variable
>>
>>
>>
>> *From: *Darko Komnenić 
>> *Date: *Tuesday, April 17, 2018 at 1:21 PM
>>
>>
>> *To: *"Hoopes, Andrew" 
>> *Cc: *FS Help 
>> *Subject: *Re: [Freesurfer] unable to open freeview
>>
>>
>>
>> Hi Andrew,
>>
>> OK, so here is what happened:
>>
>>
>>
>> After adding the echo $PATH under the first line, my output is now this:
>> "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/b
>> in:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/lisak/
>> Desktop/freesurfer/tktools:/home/lisak/Desktop/fsl/bin:/
>> home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
>> Linuxbrew directory detected, but it seems to be broken.  Try to remove
>> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/Desktop
>> /fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/usr/
>> 

Re: [Freesurfer] unable to open freeview

[Darko Komnenić]

Hi Andrew,
sorry for the delay. Attached is the hidden bashrc file from my Home
folder. It doesn't seem to specify anything about linuxbrew, so I don't
know why this error is showing up. Thanks a lot for any suggestions!
Best,
Darko

On Tue, Apr 17, 2018 at 11:07 PM, Hoopes, Andrew 
wrote:

> Are you using a bash shell? If you are, there should be a file located at
> ~/.bashrc (it’s a hidden file in your home folder)
>
> Andrew
>
>
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 2:24 PM
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> thanks a lot for your feedback!
>
> I renamed the original fine, so it is now called just tcl_setup, and here
> is the output I got after typing "freeview"
>
> /home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> Unmatched ".
>
> So this looks pretty much like the error I got when using Human Connectome
> Project pipelines (to answer your earlier question, the only time I got
> this error before was while running FreeSurferPipelineBatch.sh in HCP
> pipelines, specifically after the start of FreeSurferHighResWhite script).
> I don't use FreeSurfer for anything else on this computer, since this is
> the special 5.3-HCP version, and I use FS6 on a different computer. Also,
> the Unmatched quote error does not appear when running FSL or other
> programs.
>
> (Not sure if you're familiar with HCP pipelines, but they are used (among
> other things) to estimate cortical myelin content, and have 3 main
> preprocessing pipelines, PreeFS one, FS one, and PostFS one - I got the
> Unmatched ". error in the FS one. When writing to their mailing list, I was
> told that it seems like an error unique to my computer, and they have not
> encountered it before.)
>
>
>
> Anyway, the Linuxbrew error appears again now after trying to start
> freeview.
>
> I searched for bashrc on my computer and I got two locations, one in perl
> subfolder, and one in miniconda3 subfolder. The latter just has 2 lines, so
> it's probably not the one you meant. The former is quite a long file, but
> does not mention linuxbrew at any point. I am sending the file attached.
>
> I would be really very grateful if you would try helping out with this. I
> have been googling this error, but was not able to find anything.
>
> Thanks a bunch!
>
> Darko
>
>
>
>
>
> On Tue, Apr 17, 2018 at 7:52 PM, Hoopes, Andrew 
> wrote:
>
> Hi Darko, there’s a big difference between using single vs double quotes
> in shell scripting – single quotes prevent variable expansion. Your
> modification to tcl_setup actually renders your PATH completely unusable.
> The quote syntax in the setup scripts shouldn’t cause any problems, and
> your unmatched errors indicate a more low-level issue that should probably
> get fixed directly. Are you only getting these unmatched errors with
> freesurfer tools? I can try to help you solve this, but I’m not quite sure
> I understand the initial problem.
>
>
>
> PS: At some point in your .bashrc is linuxbrew called? You don’t want that
> “Linuxbrew directory detected…” error in your PATH variable
>
>
>
> *From: *Darko Komnenić 
> *Date: *Tuesday, April 17, 2018 at 1:21 PM
>
>
> *To: *"Hoopes, Andrew" 
> *Cc: *FS Help 
> *Subject: *Re: [Freesurfer] unable to open freeview
>
>
>
> Hi Andrew,
>
> OK, so here is what happened:
>
>
>
> After adding the echo $PATH under the first line, my output is now this:
> "/home/lisak/miniconda3/bin:/home/lisak/Desktop/freesurfer/
> bin:/home/lisak/Desktop/freesurfer/fsfast/bin:/home/
> lisak/Desktop/freesurfer/tktools:/home/lisak/Desktop/
> fsl/bin:/home/lisak/Desktop/freesurfer/mni/bin:/home/lisak/Desktop/fsl/bin:E:
> Linuxbrew directory detected, but it seems to be broken.  Try to remove
> '/home/lisak/.linuxbrew' and try again./bin:/home/lisak/
> Desktop/fsl/bin:/home/lisak/bin:/home/lisak/.local/bin:/
> usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:
> /usr/games:/usr/local/games:/snap/bin
> /home/lisak/Desktop/freesurfer/lib/qt/bin:/home/
> lisak/Desktop/freesurfer/lib/vtk/bin:$FS_TCL_HOME/bin:$PATH
> freeview.bin: Command not found."
>
> Also sending attached the tcf_setup files.
>
> I guess now I know a  bit more about what happened. I was running the
> Human Connectome Project