[Freesurfer] trac-all using nifti

2018-09-16 Thread Heidi Emmanuel Foo 
External Email - Use Caution

Hi Anastasia,

I am currently trying to run trac-all with my DWI data. I do not have the
DICOM but only the Nifti files and I would like to use the same bval and
bvec template for every subject. I created a configiration file as
attached. However, I have the following error message:

: Command not found.
: Command not found.
set: Variable name must begin with a letter.
does not exist.DIR /data_int/heidi/forHeidi/Preprocessed

It would be great if you could advise me on what to do.

Thank you!

Best Regards,
Heidi Foo
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
setenv SUBJECTS_DIR /data_int/heidi/forHeidi/Preprocessed

# Output directory where trac-all results will be saved
set dtroot = /data_int/heidi/forHeidi/Preprocessed

# Subject IDs
set subjlist = (FS1 FS2 FS3)

# Input diffusion DICOMs
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
set dcmroot = /data_int/heidi/forHeidi/DWI/dwi
set dcmlist = (dwi_1.nii dwi_2.nii dwi_3.nii)

# Specify diffusion-encoding table 
set bvecfile = /data_int/heidi/forHeidi/DWI/bvecs.txt

# Specify b-value table 
set bvalfile = /data_int/heidi/forHeidi/DWI/bvals.txt

# Eddy-current
set doeddy = 1

# If gradients will be rotated to match eddy-current compensation
set dorotbvecs = 1

# If anatomical brain mask will be used 
set usemaskanat = 1

# Threshold for DWI-based brain mask extraction 
set thrbet = 0.3

# Intra-subject registration method 
set doregflt = 0
set doregbbr = 1

# Inter-subject registration method 
set doregmni = 1
set doregcsv = 0
set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
set doregcvs = 0

# Specify which white-matter pathways to reconstruct 
set pathlist = ( lh.cst_AS rh.cst_AS \
lh.ilf_AS rh.ilf_AS \
lh.unc_AS rh.unc_AS \
fmajor_PP fminor_PP \
lh.atr_PP rh.atr_PP \
lh.cab_PP rh.cab_PP \
lh.ccg_PP rh.ccg_PP \
lh.slfp_PP rh.slfp_PP \
lh.slft_PP rh.slft_PP )

# Specify the number of path control points 
set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5)

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[Freesurfer] mris_register problem

2018-09-16 Thread Chris Adamson 
External Email - Use Caution

Freesurfer experts,

I'm having an issue with projecting labels from an atlas to a subject. I have a 
static annot file on the atlas that I want to paint onto my subject. The 
pipeline I have performed is to mris_register my subject to the atlas and then 
mri_surf2surf on the annot file using the registered spherical surfaces.

The labels, when painted, are incorrectly oriented. How can I debug the output 
of the registration to check if the registration is working? I assume the 
registration works in the 2D parameterised space, can I extract parameterised 
versions of the curvature maps at each iteration of the registration.

The strange thing is that when I view the spherical surfaces in freeview with 
the overlaid curvature maps they look in alignment prior to registration, but 
using this unregistered sphere still puts the labels in an incorrect 
orientation. So it appears as if there is some rotation that is being done 
internally that isn't shown in freeview.

Please advise,

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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Re: [Freesurfer] Hippocampal-Amygdala subfields error

2018-09-16 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Hi Eugenio,

It was happened in only in 17 subjects (sample size is 295). I repeated the
process several times and I got always the same error.

Thank you very much for your help!.


Cheers,

El dom., 16 sept. 2018 a las 19:14, Iglesias Gonzalez, Eugenio (<
e.igles...@ucl.ac.uk>) escribió:

> External Email - Use Caution
>
> Wow sorry about this. I have to carefully check whether it’s a different /
> related bug, or if the fix only made it to the Linux version. Is it
> happening for all subjects, or only some?
>
> I’m traveling / on vacation these days but will take a look as soon as I
> can.
>
> Cheers,
>
> /E
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández 
> *Reply-To: *Freesurfer support list 
> *Date: *Sunday, 16 September 2018 at 15:52
> *To: *Freesurfer support list 
> *Subject: *Re: [Freesurfer] Hippocampal-Amygdala subfields error
>
>
>
> *External Email - Use Caution*
>
>
>
> Hi Eugenio,
>
>
>
> I have downloaded the most recent dev version (
> freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
> 
> ) from here  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and
> I get the same error.
>
>
>
> My version of Mac is Mac OS High Sierra Version 10.13.3
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Fitting mesh to image data mask took 683.6633 seconds Transforming points
> Transforming points Wrote image to file image.mgz INFO: dst volume info
> differs from the one stored in lta.  gets modified now. volume geometry:
> extent  : (691, 691, 473) voxel   : ( 0.,  0.,  0.) x_(ras) : (
> 0., -1.,  0.) y_(ras) : (-0.0047,  0.,  1.) z_(ras) : (
> 1.,  0.,  0.0047) c_(ras) : ( 4.2397, 13.6233, 12.2196) file:
> T2isotropic.mgz volume geometry: extent  : (640, 640, 225) voxel   : (
> 0.3594,  0.3594,  0.7000) x_(ras) : ( 0., -1.,  0.) y_(ras) :
> (-0.0047,  0.,  1.) z_(ras) : ( 1.,  0.,  0.0047) c_(ras) :
> ( 4.2397, 13.6234, 12.2196) file:
> /Applications/freesurfer/subjects/5095/mri/orig/T2.nii Constructing
> image-to-world transform from header information (asmr1.mgz) Constructing
> image-to-world transform from header information
> (/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
> Wrote image to file asmr2.mgz This file does not contain MRI parameters
> This file does not contain MRI parameters In an assignment  A(:) = B, the
> number of elements in A and B must be the same. Error in
> segmentSubjectT2_autoEstimateAlveusML (line 2147)
> MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es
>  17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17
> 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2
> hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de
> 2018, 15:35:35 CEST For more details, see the log file
> /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log*
>
>
>
>
>
>
>
>
>
>
>
>
>
> *What could be the problem?*
>
>
>
>
>
> *Thanks in advance, *
>
>
>
> *Best wishes, *
>
>
>
>
>
> El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (<
> e.igles...@ucl.ac.uk>) escribió:
>
> *External Email - Use Caution*
>
> Hi Miguel Angel,
>
> This bug was recently fixed in the dev version. If you download the most
> recent one, you won’t have this problem.
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández 
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 13 September 2018 at 21:12
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Hippocampal-Amygdala subfields error
>
>
>
> *External Email - Use Caution*
>
>
>
> Hello Freesurfer devs,
>
>
>
> I ran the hippocampal and amygdala subfields command in my sample and I
> get the following error in several subjects:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Constructing image-to-world transform from header information (asmr1.mgz)
> Constructing image-to-world transform from header information
> (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
> Wrote image to file asmr2.mgz This file does not contain MRI parameters
> This file does not contain MRI parameters In an assignment  A(:) = B, the
> number of elements in A and B must be the same. Error in
> segmentSubjectT2_autoEstimateAlveusML (line

Re: [Freesurfer] Hippocampal-Amygdala subfields error

2018-09-16 Thread Iglesias Gonzalez, Eugenio 
External Email - Use Caution

Wow sorry about this. I have to carefully check whether it’s a different / 
related bug, or if the fix only made it to the Linux version. Is it happening 
for all subjects, or only some?
I’m traveling / on vacation these days but will take a look as soon as I can.
Cheers,
/E

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Miguel Ángel Rivas 
Fernández 
Reply-To: Freesurfer support list 
Date: Sunday, 16 September 2018 at 15:52
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal-Amygdala subfields error


External Email - Use Caution

Hi Eugenio,

I have downloaded the most recent dev version ( 
freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
 ) from here  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and I 
get the same error.

My version of Mac is Mac OS High Sierra Version 10.13.3


Fitting mesh to image data mask took 683.6633 seconds
Transforming points
Transforming points
Wrote image to file image.mgz
INFO: dst volume info differs from the one stored in lta.  gets modified now.
volume geometry:
extent  : (691, 691, 473)
voxel   : ( 0.,  0.,  0.)
x_(ras) : ( 0., -1.,  0.)
y_(ras) : (-0.0047,  0.,  1.)
z_(ras) : ( 1.,  0.,  0.0047)
c_(ras) : ( 4.2397, 13.6233, 12.2196)
file: T2isotropic.mgz
volume geometry:
extent  : (640, 640, 225)
voxel   : ( 0.3594,  0.3594,  0.7000)
x_(ras) : ( 0., -1.,  0.)
y_(ras) : (-0.0047,  0.,  1.)
z_(ras) : ( 1.,  0.,  0.0047)
c_(ras) : ( 4.2397, 13.6234, 12.2196)
file: /Applications/freesurfer/subjects/5095/mri/orig/T2.nii
Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)



MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es 17.4.0 Darwin Kernel 
Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; 
root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at domingo, 16 de septiembre de 
2018, 15:35:35 CEST

For more details, see the log file 
/Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log






What could be the problem?


Thanks in advance,

Best wishes,


El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio 
(mailto:e.igles...@ucl.ac.uk>>) escribió:

External Email - Use Caution
Hi Miguel Angel,
This bug was recently fixed in the dev version. If you download the most recent 
one, you won’t have this problem.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Miguel Ángel Rivas Fernández 
mailto:miguelrivasf...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 13 September 2018 at 21:12
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Hippocampal-Amygdala subfields error


External Email - Use Caution

Hello Freesurfer devs,

I ran the hippocampal and amygdala subfields command in my sample and I get the 
following error in several subjects:

Constructing image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing 
image-to-world transform from header information (asmr1.mgz)
Constructing image-to-world transform from header information 
(/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
Wrote image to file asmr2.mgz
This file does not contain MRI parameters
This file does not contain MRI parameters
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)

MATLAB:subsassignnumelmismatch
Darwin rmnlab1.inv.usc.es 17.4.0 Darwin Kernel 
Version 17.4.0: Sun Dec 17 09:19:54 PST 2017;

[Freesurfer] is infant pipeline available in freesurfer?

2018-09-16 Thread yuanchao.zha...@gmail.com 
External Email - Use Caution

Hi experts,

I want to compare the morphological indice (such cortical thickness) between 
two groups of infants (age < 2), namely diseased group and a control group.

I see that freesurfer cannot process MRI image of children smaller than 4 
years. I am wondering if the infant pipeline available in freesurfer?
I noticed that some one in freesurfer are developing such a pipeline.

thanks a lot!
Best,

Yuanchao Zhang



yuanchao.zha...@gmail.com
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[Freesurfer] ?????? ?????? questions about trac-all -stat

2018-09-16 Thread ?????? 
External Email - Use Caution

Hi Yendiki, Anastasia,


Thank you very much for your reply! I have two more question. 
(1)Even in the MNI space, the path positions of each subject could not be 
exactly coincident. So,how to identify the common midpoint for all subjects? 
(2)how to identify step size of the equally sized step you mentioned above?


Thanks!
Qianwen


--  --
??: "Yendiki, Anastasia";
: 2018??9??13??(??) 11:44
??: "Freesurfer support list";

: Re: [Freesurfer]??  questions about trac-all -stat



 Hi Qianwen,
 
 
 (1) & (2): The native space coordinates along the path of all subjects (which 
are in their path stats files) are mapped to MNI space simply to identify a 
common midpoint for all subjects. This midpoint is mapped back to native space, 
and the FA/MD/etc.  values for each subject are sampled along the path by 
stepping out by equally sized steps from the midpoint towards both ends. At 
each step, you get one row of the group table.
 
 
 (3): Look for the paragraph "This text file contains various diffusion 
measures in the tutorial:
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
 And slide ??Path stats (values along the path)?? in the course slides:
 http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt
 
 
 Hope this helps,
 a.y
 
 
   From:  on behalf of ?? 
<627611...@qq.com>
 Reply-To: Freesurfer support list 
 Date: Wednesday, September 12, 2018 at 9:47 PM
 To: Freesurfer support list 
 Subject: [Freesurfer] ?? questions about trac-all -stat
 
 
 
   
External Email - Use Caution
 

 Hi Yendiki, Anastasia,
  I am very sorry that I did not make myself clear. I mean I want to know how 
trac-all ?Cstat does it.
 
 
  (1)how to determine the first position and last position of all subjects' 
pathways when converting all pathstats.byvoxel.txt files to a table for group 
analyses?
 In the tabel , The first position and last position of all subjects' pathways 
are determined by the longest pathway.
 
 
 (2)how to complete correspondence of  points between subjects?
 In the course slides, it said"Correspondence of points between subjects based 
on Euclidean distance in MNI space".This  sentence is so vague that I can't 
understand it.
 
 
 (3)what is values in table for group analyses,diffusion measure of center or 
something else?
 
 
 I am very sorry that my question is a bit more, but I still hope that you can 
answer my doubts. Thanks!
 
 
 Qianwen
 
 

 
  
 
 
 
 --  --
  ??: "Yendiki, Anastasia";
 : 2018??9??12??(??) 10:40
 ??: "Freesurfer support list";
 
 : Re: [Freesurfer] questions about trac-all -stat
 
 
 
  Hi Qianwen ?C You don??t have to do (1) and (2), trac-all ?Cstat does that 
for you. For a description of the measures, see the tutorial:
 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics
 and the course slides:
 http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt
 
 
 Best,
 
 
 a.y
  
 
  
 
  
 
   From:  on behalf of ?? 
<627611...@qq.com>
 Reply-To: Freesurfer support list 
 Date: Wednesday, September 12, 2018 at 1:13 AM
 To: freesurfer 
 Subject: [Freesurfer] questions about trac-all -stat
 
 
 
   
External Email - Use Caution
 

 Dear experts, I have some questions about along-path analysis:
 (1)how to determine the first position and last position of all subjects' 
pathway when converting all pathstats.byvoxel.txt files to a table for group 
analyses?
 
 
 (2)how to complete correspondence of  points between subjects?
 
 
 (3)what is values in table for group analyses,diffusion measure of center or 
something else?
 
 
 Thanks!
 Qianwen___
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Re: [Freesurfer] Hippocampal-Amygdala subfields error

2018-09-16 Thread Miguel Ángel Rivas Fernández 
External Email - Use Caution

Hi Eugenio,

I have downloaded the most recent dev version (
freesurfer-darwin-OSX-ElCapitan-dev.tar.gz

) from here  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev and I
get the same error.

My version of Mac is Mac OS High Sierra Version 10.13.3







































*Fitting mesh to image data mask took 683.6633 secondsTransforming
pointsTransforming pointsWrote image to file image.mgzINFO: dst volume info
differs from the one stored in lta.  gets modified now.volume
geometry:extent  : (691, 691, 473)voxel   : ( 0.,  0.,
0.)x_(ras) : ( 0., -1.,  0.)y_(ras) : (-0.0047,  0.,
1.)z_(ras) : ( 1.,  0.,  0.0047)c_(ras) : ( 4.2397, 13.6233,
12.2196)file: T2isotropic.mgzvolume geometry:extent  : (640, 640,
225)voxel   : ( 0.3594,  0.3594,  0.7000)x_(ras) : ( 0., -1.,
0.)y_(ras) : (-0.0047,  0.,  1.)z_(ras) : ( 1.,  0.,
0.0047)c_(ras) : ( 4.2397, 13.6234, 12.2196)file:
/Applications/freesurfer/subjects/5095/mri/orig/T2.niiConstructing
image-to-world transform from header information (asmr1.mgz)Constructing
image-to-world transform from header information
(/Applications/freesurfer/subjects/5095/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote
image to file asmr2.mgzThis file does not contain MRI parametersThis file
does not contain MRI parametersIn an assignment  A(:) = B, the number of
elements in A and B must be the same.Error in
segmentSubjectT2_autoEstimateAlveusML (line
2147)MATLAB:subsassignnumelmismatchDarwin rmnlab1.inv.usc.es
 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17
09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64T2 hippocampal
subfields exited with ERRORS at domingo, 16 de septiembre de 2018, 15:35:35
CESTFor more details, see the log file
/Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log*






*What could be the problem?*



*Thanks in advance, *


*Best wishes, *


El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (<
e.igles...@ucl.ac.uk>) escribió:

> External Email - Use Caution
>
> Hi Miguel Angel,
>
> This bug was recently fixed in the dev version. If you download the most
> recent one, you won’t have this problem.
>
> Cheers,
>
> /Eugenio
>
>
>
> --
>
> Juan Eugenio Iglesias
>
> ERC Senior Research Fellow
>
> Centre for Medical Image Computing (CMIC)
>
> University College London
>
> http://www.jeiglesias.com
>
> http://cmictig.cs.ucl.ac.uk/
>
>
>
>
>
> *From: * on behalf of Miguel
> Ángel Rivas Fernández 
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 13 September 2018 at 21:12
> *To: *Freesurfer support list 
> *Subject: *[Freesurfer] Hippocampal-Amygdala subfields error
>
>
>
> *External Email - Use Caution*
>
>
>
> Hello Freesurfer devs,
>
>
>
> I ran the hippocampal and amygdala subfields command in my sample and I
> get the following error in several subjects:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Constructing image-to-world transform from header information (asmr1.mgz)
> Constructing image-to-world transform from header information
> (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
> Wrote image to file asmr2.mgz This file does not contain MRI parameters
> This file does not contain MRI parameters In an assignment  A(:) = B, the
> number of elements in A and B must be the same. Error in
> segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing
> image-to-world transform from header information (asmr1.mgz) Constructing
> image-to-world transform from header information
> (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)
> Wrote image to file asmr2.mgz This file does not contain MRI parameters
> This file does not contain MRI parameters In an assignment  A(:) = B, the
> number of elements in A and B must be the same. Error in
> segmentSubjectT2_autoEstimateAlveusML (line 2147)*
>
>
>
>
>
>
> *MATLAB:subsassignnumelmismatch Darwin rmnlab1.inv.usc.es
>  17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17
> 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64 T2
> hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de
> 2018, 21:37:33 CEST*
>
>
>
>
>
>
>
> What would be the reason?
>
>
>
>
>
> Thanks in advance,
>
>
>
>
>
> Best wishes,
>
>
> --
>
> *Miguel Ángel Rivas Fernández*
> ___
> 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
>

Re: [Freesurfer] Download and Registration issue

2018-09-16 Thread Juliane Corlier 
External Email - Use Caution

Hi Andrew, 

Just to let you know that I was able to resolve the download issue - it was a 
matter of the university network. 
I’ve tried doing this off campus and I was able to download the dmg installer 
using the provided link, so it must be a firewall issue.
Just for your future reference. 

Thanks!

Juliana



> On Sep 12, 2018, at 2:16 PM, Hoopes, Andrew  wrote:
> 
> Hi Juliana, does the download fail when you paste this link directly in your 
> browser - 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg
>  
> 
>  ?
>  
> And what are you trying to register for? a wiki account?
>  
> best,
> Andrew
>  
>  
> From:  > on behalf of Juliane Corlier 
> mailto:juliane.corl...@gmail.com>>
> Reply-To: FS Help  >
> Date: Tuesday, September 11, 2018 at 2:36 PM
> To: FS Help  >
> Subject: [Freesurfer] Download and Registration issue
>  
> External Email - Use Caution
> 
> Dear list,  
>  
> I have to issues:
>  
> 1) I am trying to download a dmg installer file for Freesurfer from this 
> website: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall 
> 
> I get an error that the page is not working/can’t be opened. 
>  
>  
> 2) I am trying to set up an account via the new registration link, but I get 
> an error code saying “You are not allowed to do newaccount on this page. 
> Login and try again.”
>  
> Please let me know if those are only temporary problems or how could I 
> resolve them.
>  
>  
> Thank you, 
>  
> Juliana
>  
>  
>  
>  
>  
>  
>  
> ___
> 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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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] FS-FAST and thalami nuclei

2018-09-16 Thread stdp82 
External Email - Use Caution

Hi list,

I would like to use as seed the output of segmentation of the thalamic nuclei 
in FS-FAST. Probably some nuclei may be too small to be used as seed. Are you 
agree? I wonder if to merge the outputs in 5-10 subregions (e.g. AV, MD, MC 
etc...) could be the most appropriate way. What do you advise?


Thanks

Stefano___
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.