[Freesurfer] Proposed addition for Freesurfer - automated control points

[Chris Adamson]

External Email - Use Caution

Freesurfer devs,

I presented an automated control point adding tool at HBM and a few freesurfer 
lab people came over and had a look. I was wondering if someone would like to 
review it for either inclusion or to perhaps reference from the wiki as a tool 
for people to use if they choose?

Thanks in advance,

Chris.

Dr Chris Adamson
Senior Research Officer
Developmental Imaging, Clinical Sciences

Murdoch Childrens Research Institute
The Royal Children's Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adam...@mcri.edu.au
www.mcri.edu.au


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[Freesurfer] Freeview not showing images

[Mark Wagshul]

External Email - Use Caution

Hi.

I'm a newbie to Freeview, hoping that this is a simple problem.  When I open it 
(specifying the lh.pial surface), I get this view:

[cid:image001.jpg@01D40F16.EC48FB10]

Anyone have an idea what's going on here, is it an issue with the screen 
resolution settings?

Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einstein.yu.edu

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[Freesurfer] mri_glmfit question

[Nillo, Ryan Michael R]

External Email - Use Caution

Hello FreeSurfer Users,


I want to run an ROI-based analysis on mri_glmfit as opposed to vertex-based. I 
know that if I run mri_glmfit with the --table flag and give it the output of 
asegstats2table or aparcstats2table, it will run the analysis on the ROIs and 
output tables showing significance. In each contrast directory that was created 
from mri_glmfit, I see there is a pcc.mgh. Is there any way to display this on 
the surface or put it into a table format?


Mahalo,


Ryan M Nillo

Staff Research Associate I

UCSF Department of Radiology and Biomedical Imaging
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[Freesurfer] recon.all strange run time

[Ottavio Morciano]

External Email - Use Caution

Hi!I have a macbook pro MY 2014 with a Intel Core i7(quad core,2.7 ghz) and
16 gb of ram with El Capitan.This Macbook to run recon-all it takes 47
hours with -openmp 8 flag.

A Dell with Intel Core i7 3632Q,8 GB RAM DDR3 1600mhz with Linux  takes 8
hours...The same Dell on windows with linux virtualizated takes 13 hours.

Why recon-all on mac is so slow? is the OS?the type of compilator used for
each platform?freesurfer not optimized for El Capitan? the architecture of
the cpu?

Some Advice?

Morciano Ottavio

MD Student
Università Di Foggia.Italy
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Re: [Freesurfer] Poor occipital signal and low contrast

[Bruce Fischl]

Hi Megha

looking at the scan you sent I can tell gray from white over most of the 
occipital lobe, so I think control points could recover reasonable 
surfaces. I would try leaving a "trail" of them going from the 
inferior-most, very dark places heading up.


cheers
Bruce


On Thu, 28 Jun 2018, 
Chawla, Megha wrote:




External Email - Use Caution

Hi, I'm just resending this email in case you missed it. 


Thanks!

Megha 



_
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on
behalf of Chawla, Megha 
Sent: Wednesday, June 20, 2018 11:11 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Poor occipital signal and low contrast  

External Email - Use Caution


Hi, 


I have scans for ~60 participants, and for some reason the scans are of visibly 
poor quality
when I convert them to .mgz (blurry, very low contrast). The white boundary 
also seems to
exclude considerable white matter in the occipital in about half of the scans 
(best seen in
sag view). Because of the extremely low contrast, I am unable to manually add 
control points
as I cannot visibly tell the difference between wm and gm. I am attaching 
orig.mgz for one
participant here.


Acquisition parameters for these scans were: High-resolution T1-weighted 
anatomical images (1
× 1 × 1 mm3) were acquired with an MPRAGE pulse sequence (TI=900 ms, sagittal 
slices, 256 ×
256 matrix) using a Siemens Allegra 3T head-only scanner.


I tried running more iterations of during the nu_correct (as suggested
here: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-November/008985.html)
 using
the following command:

mc2835% recon-all -autorecon1 -nuintensitycor -nuiterations 10 -subjid 30026_FS


but got the following error: 

ERROR: Flag -nuiterations unrecognized.

-autorecon1 -nuiterations 10 -subjid 30026_FS

Darwin Ifats-Mac-Pro.med.yale.internal 16.7.0 Darwin Kernel Version 16.7.0: Thu 
Jun 15
17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Tue Jun 19 14:56:04 EDT 2018


For more details, see the log file 

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


Is there any way to salvage this data for analysis? 


Any help will be really appreciated. 


Thank you!


Megha 



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Re: [Freesurfer] Poor occipital signal and low contrast

[Chawla, Megha]

External Email - Use Caution

Hi, I'm just resending this email in case you missed it.


Thanks!

Megha



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Chawla, Megha 

Sent: Wednesday, June 20, 2018 11:11 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Poor occipital signal and low contrast


External Email - Use Caution

Hi,


I have scans for ~60 participants, and for some reason the scans are of visibly 
poor quality when I convert them to .mgz (blurry, very low contrast). The white 
boundary also seems to exclude considerable white matter in the occipital in 
about half of the scans (best seen in sag view). Because of the extremely low 
contrast, I am unable to manually add control points as I cannot visibly tell 
the difference between wm and gm. I am attaching orig.mgz for one participant 
here.


Acquisition parameters for these scans were: High-resolution T1-weighted 
anatomical images (1 × 1 × 1 mm3) were acquired with an MPRAGE pulse sequence 
(TI=900 ms, sagittal slices, 256 × 256 matrix) using a Siemens Allegra 3T 
head-only scanner.


I tried running more iterations of during the nu_correct (as suggested here: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-November/008985.html)
 using the following command:

mc2835% recon-all -autorecon1 -nuintensitycor -nuiterations 10 -subjid 30026_FS


but got the following error:

ERROR: Flag -nuiterations unrecognized.

-autorecon1 -nuiterations 10 -subjid 30026_FS

Darwin Ifats-Mac-Pro.med.yale.internal 16.7.0 Darwin Kernel Version 16.7.0: Thu 
Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Tue Jun 19 14:56:04 EDT 2018


For more details, see the log file

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


Is there any way to salvage this data for analysis?


Any help will be really appreciated.


Thank you!


Megha

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Re: [Freesurfer] Errors in scans

[Nasiriavanaki, Zahra]

Hi Doug


Thanks for your reply.

I have not unpacked the error ones!

I will go for it and let you know if there was a problem.




Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Thursday, June 28, 2018 9:57:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Errors in scans

Are the output volumes being created? Do they look ok? Sometimes
unpacksdcmdir will print out an error when there is not actually an
error there (eg, if it does not see the expected number of files, but
some times its expectation is wrong). In dcmunpack (the replacement for
unpacksdcmdir), I don't print out the ok/err because it it not always
reliable.

On 06/28/2018 11:35 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesufer developers
>
>
> We are getting some errors in our resting state and ASL
> scans. Everything goes fine while we are scaning the subjects, but
> when we look at the data in BORGET, some of them come out with errors.
> I copied one of the scaninfo files, so you can see the errors.
> Is there anyway to not get errors? Or shall we just unpack the ok data
> and go on?
>
> Thanks
> 1   localizer_64ch  ok  512 512   3   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535
>   2 AAHead_Scout  ok  160 160 128   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717
>   3 AAHead_Scout  ok  162 162   5   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708
>   4 AAHead_Scout  ok  162 162   3   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712
>   5 AAHead_Scout  ok  162 162   3   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715
>   6 MEMPRAGE  ok  256 256 176   4
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274
>   7 MEMPRAGE  ok  256 256 176   4
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273
>   8 MEMPRAGE  ok  256 256 176   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299
>   9 fMRI_DistortionMap_PA  ok   92  92  57   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688
>  10 fMRI_DistortionMap_AP  ok   92  92  57   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923
>  11 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295
>  12 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419
>  13 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555
>  14 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697
>  15 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838
>  16 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987
>  17 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134
>  18 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274
>  19 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180
> MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422
>  20 tgse_pcasl_optBS_M0_PLD2000  ok   96  96   1  22
> MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829
> 21 tgse_pcasl_optBS_M0_PLD2000 err   96  96   1   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101
>  22 HCP_CMRR_SpinEchoFieldMap_AP  ok  104 104  72   3
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321
>  23 HCP_CMRR_SpinEchoFieldMap_PA  ok  104 104  72   3
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977
> 24 HCP_CMRR_fMRI_rest_AP err  104 104  72   1
> MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554
>  25 HCP_CMRR_fMRI_rest_AP err  104 104  72 216
> MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992
> 26 HCP_CMRR_fMRI_rest_PA err  104 104  72   1
> MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846
>  27 HCP_CMRR_fMRI_rest_PA  ok  104 104  72 488
> MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Errors in scans

[Douglas N. Greve]

Are the output volumes being created? Do they look ok? Sometimes 
unpacksdcmdir will print out an error when there is not actually an 
error there (eg, if it does not see the expected number of files, but 
some times its expectation is wrong). In dcmunpack (the replacement for 
unpacksdcmdir), I don't print out the ok/err because it it not always 
reliable.

On 06/28/2018 11:35 AM, Nasiriavanaki, Zahra wrote:
>
> Hi Freesufer developers
>
>
> We are getting some errors in our resting state and ASL 
> scans. Everything goes fine while we are scaning the subjects, but 
> when we look at the data in BORGET, some of them come out with errors.
> I copied one of the scaninfo files, so you can see the errors.
> Is there anyway to not get errors? Or shall we just unpack the ok data 
> and go on?
>
> Thanks
> 1       localizer_64ch  ok  512 512   3   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535
>   2         AAHead_Scout  ok  160 160 128   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717
>   3         AAHead_Scout  ok  162 162   5   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708
>   4         AAHead_Scout  ok  162 162   3   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712
>   5         AAHead_Scout  ok  162 162   3   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715
>   6             MEMPRAGE  ok  256 256 176   4 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274
>   7             MEMPRAGE  ok  256 256 176   4 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273
>   8             MEMPRAGE  ok  256 256 176   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299
>   9 fMRI_DistortionMap_PA  ok   92  92  57   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688
>  10 fMRI_DistortionMap_AP  ok   92  92  57   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923
>  11 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295
>  12 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419
>  13 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555
>  14 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697
>  15 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838
>  16 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987
>  17 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134
>  18 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274
>  19 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
> MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422
>  20 tgse_pcasl_optBS_M0_PLD2000  ok   96  96   1  22 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829
> 21 tgse_pcasl_optBS_M0_PLD2000 err   96  96   1   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101
>  22 HCP_CMRR_SpinEchoFieldMap_AP  ok  104 104  72   3 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321
>  23 HCP_CMRR_SpinEchoFieldMap_PA  ok  104 104  72   3 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977
> 24 HCP_CMRR_fMRI_rest_AP err  104 104  72   1 
> MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554
>  25 HCP_CMRR_fMRI_rest_AP err  104 104  72 216 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992
> 26 HCP_CMRR_fMRI_rest_PA err  104 104  72   1 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846
>  27 HCP_CMRR_fMRI_rest_PA  ok  104 104  72 488 
> MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Errors in scans

[Nasiriavanaki, Zahra]

Hi Freesufer developers

We are getting some errors in our resting state and ASL scans. Everything goes 
fine while we are scaning the subjects, but when we look at the data in BORGET, 
some of them come out with errors.
I copied one of the scaninfo files, so you can see the errors.
Is there anyway to not get errors? Or shall we just unpack the ok data and go 
on?

Thanks

1   localizer_64ch  ok  512 512   3   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535
  2 AAHead_Scout  ok  160 160 128   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717
  3 AAHead_Scout  ok  162 162   5   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708
  4 AAHead_Scout  ok  162 162   3   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712
  5 AAHead_Scout  ok  162 162   3   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715
  6 MEMPRAGE  ok  256 256 176   4 
MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274
  7 MEMPRAGE  ok  256 256 176   4 
MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273
  8 MEMPRAGE  ok  256 256 176   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299
  9 fMRI_DistortionMap_PA  ok   92  92  57   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688
 10 fMRI_DistortionMap_AP  ok   92  92  57   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923
 11 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295
 12 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419
 13 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555
 14 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697
 15 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838
 16 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987
 17 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134
 18 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274
 19 ep2d_bold_SMS3_PAT2_2p5iso  ok   92  92  57 180 
MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422
 20 tgse_pcasl_optBS_M0_PLD2000  ok   96  96   1  22 
MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829
 21 tgse_pcasl_optBS_M0_PLD2000 err   96  96   1   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101
 22 HCP_CMRR_SpinEchoFieldMap_AP  ok  104 104  72   3 
MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321
 23 HCP_CMRR_SpinEchoFieldMap_PA  ok  104 104  72   3 
MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977
 24 HCP_CMRR_fMRI_rest_AP err  104 104  72   1 
MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554
 25 HCP_CMRR_fMRI_rest_AP err  104 104  72 216 
MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992
 26 HCP_CMRR_fMRI_rest_PA err  104 104  72   1 
MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846
 27 HCP_CMRR_fMRI_rest_PA  ok  104 104  72 488 
MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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Re: [Freesurfer] Moderation analysis in Freesurfer

[Douglas N. Greve]

I don't think it is possible to do as a mixed effect. You can do this 
with the standard GLM by using a per vertex regressor (--pvr 
thickness.mgh to mri_glmfit)


On 06/27/2018 12:12 PM, Mark Wagshul wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> We are interested in looking at the moderating effect of grey matter 
> thickness on a non-imaging outcome measure.  Thus, the model would be:
>
> Outcome measure =  Condition + GM thickness + Condition * GM thickness 
> + covariates.
>
> where Condition is a categorical variable (1/2, for two conditions of 
> the non-imaging measures).  The Freesurfer GLM usually solves for the 
> thickness as a function of some contrast, but is really just 
> determining the voxel-wise statistical significant of a GLM, so should 
> be doable even with the imaging variable on the RHS.  Ideally, we 
> would like to run this as a linear mixed model with subject as a 
> random effect, and the condition as a repeated measure.
>
> Is this possible to do with the current Freesurfer software, and if 
> so, how would I implement it?
>
> Thanks for any advice you can provide.
>
> Mark
>
> 
> Mark Wagshul, PhD
> Associate Professor
> Gruss Magnetic Resonance Research Center
> Albert Einstein College of Medicine
> Bronx, NY 10461
>
> Ph: 718-430-4011
>
> FAX: 718-430-3399
>
> Email: mark.wags...@einstein.yu.edu 
>
> einstein-logo-rgb
>
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Re: [Freesurfer] error when running eddy_correct

[Douglas N. Greve]

Can you replicate the error outside of dt_recon? If so, then you should 
make a  posting to the FSL group.

On 06/28/2018 02:03 AM, Куликова Софья Петровна wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> I was trying to run dt_recon (on centos7 system) but have got an error at the 
> eddy_correct stage, saying there is no $FSLDIR/bin/imglob file.
> Indeed, it is not there. However, I gave installed FSL according to their 
> tutorial without any errors and have no problem with running dt_recon on 
> another machine.
> Could you kindly tell me how can I deal with this issue?
>
> Best regards,
> Sofya Kulikova
> PhD Neuroscience, HSE-Perm
>
>
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[Freesurfer] error when running eddy_correct

[Куликова Софья Петровна]

External Email - Use Caution

Hello FreeSurfer Developers,

I was trying to run dt_recon (on centos7 system) but have got an error at the 
eddy_correct stage, saying there is no $FSLDIR/bin/imglob file.
Indeed, it is not there. However, I gave installed FSL according to their 
tutorial without any errors and have no problem with running dt_recon on 
another machine.
Could you kindly tell me how can I deal with this issue?

Best regards,
Sofya Kulikova
PhD Neuroscience, HSE-Perm
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