Re: [Freesurfer] hippocampal subfields downsampling question

[Joost Janssen]

Great question!

El 26/10/2017 17:09, "NIELS JANSSEN ."  escribió:

> In the mri output folder, I noticed that both the 0.33 mm and 1 mm
> (voxelspace) maps have subfields that do not overlap in space, meaning that
> each subfield occupies a unique location in space that does not overlap
> with other subfields (i.e., 12 subfields and 12 unique voxel intensities).
> I am wondering how this is achieved for both resolutions simultaneously. Do
> you 'fit' the subfields first to the 0.33 mm data and then transform the
> data to the 1mm space, or do you fit to both spaces separately? I would
> like to transform the subfields to 1.5 mm data and are able to do so
> accurately, but I run into problems with subfield overlap because of the
> down sampling. I am wondering how to best deal with this issue, and from
> seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there
> must be someway to deal with this issue.
>
>
> --
> Niels Janssen
> Brain Imaging Laboratory
> Institute of Biomedical Technologies
> Center for Biomedical Research of the Canary Islands
> University of La Laguna
> Tenerife, Spain
> https://sites.google.com/view/nielsjanssen/
>
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>
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> dispose of the e-mail.
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Re: [Freesurfer] Preproc-sess Error

[Douglas N Greve]

You can put it somewhere in your path


On 10/26/2017 10:35 AM, Hsu, Eugene wrote:
>
> Dear Dr. Greve,
>
>
> I checked $FREESURFER_HOME/bin in Stable 6 and 3dvolreg.afni is indeed 
> missing but I found it in 5.3.
>
>
> However, I don't have permission to copy the file from 5.3 over to 
> Stable 6:
>
>
>     cannot create regular file 
> `/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/3dvolreg.afni': 
> Permission denied
>
>
> Is there a way to get this done? Thanks so much for the help!
>
> --Eugene
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas Greve 
> 
> *Sent:* Wednesday, October 25, 2017 5:39:27 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Preproc-sess Error
>
> it is not in $FREESURFER_HOME/bin ? If not, you can copy it from 5.3
>
>
> On 10/25/17 4:59 PM, Hsu, Eugene wrote:
>>
>> Hi FreeSurfer Experts,
>>
>>
>> We're trying to run preproc-sess on FreeSurfer 6, but we're 
>> encountering an error when motion correcting:
>>
>>
>>     ERROR: cannot find AFNI command 3dvolreg.afni
>>
>>
>> When we tried Freesurfer 5.3 the preproc-sess ran to completion.
>>
>>
>> Thanks for your help!
>>
>> --Eugene
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] freesurfer errors-windows bash

[Iglesias Gonzalez, Eugenio]

Dear Alexandre,
It seems that problem is that you need the latest dev version to use this 
feature.
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/


From: Alexandre Obert 
Date: Thursday, 26 October 2017 at 16:31
To: "freesurfer@nmr.mgh.harvard.edu" , 
"Iglesias Gonzalez, Eugenio" 
Subject: Re: freesurfer errors-windows bash

Dear Eugenio,

The freesurfer version commands tells me that I run the 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version.
Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one and 
it worked.
Of course, recon-all also worked, telling be how to use it properly.

Regards,

Alexandre

2017-10-26 17:08 GMT+02:00 Alexandre Obert 
>:
Dear all,

I'm would like to run a hippocampal segmentation on my data.
However, I'm a beginner with freesurfer thus, I juste try to run the commands 
with subject training data.
I first try to run commands following the recent development 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 However, terminal says that the command segmentHA.sh doesn't exist.

I guess that it could be linked to the fact that I used bash in Windows but I 
can't find a way to check this..;

Any idea ?

Regards,

Alexandre

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Re: [Freesurfer] freesurfer errors-windows bash

[Alexandre Obert]

Dear Eugenio,

The freesurfer version commands tells me that I run
the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version.
Before using segmentHA_T1.sh command, I run the recon-all -all -s bert one
and it worked.
Of course, recon-all also worked, telling be how to use it properly.

Regards,

Alexandre

2017-10-26 17:08 GMT+02:00 Alexandre Obert :

> Dear all,
>
> I'm would like to run a hippocampal segmentation on my data.
> However, I'm a beginner with freesurfer thus, I juste try to run the
> commands with subject training data.
> I first try to run commands following the recent development (
> https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiO
> fAmygdala). However, terminal says that the command segmentHA.sh doesn't
> exist.
>
> I guess that it could be linked to the fact that I used bash in Windows
> but I can't find a way to check this..;
>
> Any idea ?
>
> Regards,
>
> Alexandre
>
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Re: [Freesurfer] freesurfer errors-windows bash

[Iglesias Gonzalez, Eugenio]

Dear Alexandre,
You need to download the latest dev version to have access to the new 
hippocampus/amygdala segmentation.
The other potential problem is that FreeSurfer is not sourced properly. Do 
other FreeSurfer commands work? E.g. do you get an output when you type:  
recon-all
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/


From:  on behalf of Alexandre Obert 

Reply-To: Freesurfer support list 
Date: Thursday, 26 October 2017 at 16:10
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] freesurfer errors-windows bash

Dear all,

I'm would like to run a hippocampal segmentation on my data.
However, I'm a beginner with freesurfer thus, I juste try to run the commands 
with subject training data.
I first try to run commands following the recent development 
(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
 However, terminal says that the command segmentHA.sh doesn't exist.

I guess that it could be linked to the fact that I used bash in Windows but I 
can't find a way to check this..;

Any idea ?

Regards,

Alexandre
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] hippocampal subfields downsampling question

[Iglesias Gonzalez, Eugenio]

Hi Niels,

The code works at .33 mm and ends up with a soft segmentation for each voxel, 
i.e., each voxel has a vector of probabilities corresponding to the different 
structures. So, they DO overlap. However, we don’t write those probabilities by 
default. Instead, we take the most likely label at each location (the one with 
the maximal probability), to create the discrete segmentation you’ve seen. 
Then, I do a simple nearest neighbor resampling to 1mm space, which I admit is 
a bit ugly (but fast).

My recommendation would be the following:

1. For each label of the discrete segmentation, including the background (treat 
is as any other subfield):
   1a. First extract it from the segmentation, to create a binary mask (e.g., 
CA1 vs everything else).
   1b. Resample this mask to your new space with linear interpolation. This 
will create a deformed mask that is not binary anymore, but will have values 
between 0 and 1 (or 0 and 255, depending on how you binarize in step 1a).

2. Go over all voxels in the target space. For each voxel, look at the values 
of the deformed masks. Assign the label of the mask with the highest value.

This procedure will create a smooth segmentation.

If you’re feeling really inspired, you’ve got another (prettier) option. Run 
the code with WRITE_POSTERIORS (see the wiki). Then, you can do the same thing, 
but skipping step 1a, and using the posteriors in step 1b directly instead. 
Note that the code does not write the posterior for the background, but you can 
easily calculate this as one minus the sum of all other posteriors (at each 
voxel).

I hope this helps!

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/


From:  on behalf of "NIELS JANSSEN ." 

Reply-To: Freesurfer support list 
Date: Thursday, 26 October 2017 at 16:08
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] hippocampal subfields downsampling question

In the mri output folder, I noticed that both the 0.33 mm and 1 mm (voxelspace) 
maps have subfields that do not overlap in space, meaning that each subfield 
occupies a unique location in space that does not overlap with other subfields 
(i.e., 12 subfields and 12 unique voxel intensities). I am wondering how this 
is achieved for both resolutions simultaneously. Do you 'fit' the subfields 
first to the 0.33 mm data and then transform the data to the 1mm space, or do 
you fit to both spaces separately? I would like to transform the subfields to 
1.5 mm data and are able to do so accurately, but I run into problems with 
subfield overlap because of the down sampling. I am wondering how to best deal 
with this issue, and from seeing non-overlapping subfields at both 0.33 and 1 
mm I am thinking there must be someway to deal with this issue.


--
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Center for Biomedical Research of the Canary Islands
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/
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[Freesurfer] freesurfer errors-windows bash

[Alexandre Obert]

Dear all,

I'm would like to run a hippocampal segmentation on my data.
However, I'm a beginner with freesurfer thus, I juste try to run the
commands with subject training data.
I first try to run commands following the recent development (
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala).
However, terminal says that the command segmentHA.sh doesn't exist.

I guess that it could be linked to the fact that I used bash in Windows but
I can't find a way to check this..;

Any idea ?

Regards,

Alexandre
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[Freesurfer] hippocampal subfields downsampling question

[NIELS JANSSEN .]

In the mri output folder, I noticed that both the 0.33 mm and 1 mm
(voxelspace) maps have subfields that do not overlap in space, meaning that
each subfield occupies a unique location in space that does not overlap
with other subfields (i.e., 12 subfields and 12 unique voxel intensities).
I am wondering how this is achieved for both resolutions simultaneously. Do
you 'fit' the subfields first to the 0.33 mm data and then transform the
data to the 1mm space, or do you fit to both spaces separately? I would
like to transform the subfields to 1.5 mm data and are able to do so
accurately, but I run into problems with subfield overlap because of the
down sampling. I am wondering how to best deal with this issue, and from
seeing non-overlapping subfields at both 0.33 and 1 mm I am thinking there
must be someway to deal with this issue.


-- 
Niels Janssen
Brain Imaging Laboratory
Institute of Biomedical Technologies
Center for Biomedical Research of the Canary Islands
University of La Laguna
Tenerife, Spain
https://sites.google.com/view/nielsjanssen/
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Re: [Freesurfer] Preproc-sess Error

[Hsu, Eugene]

Dear Dr. Greve,


I checked $FREESURFER_HOME/bin in Stable 6 and 3dvolreg.afni is indeed missing 
but I found it in 5.3.


However, I don't have permission to copy the file from 5.3 over to Stable 6:


cannot create regular file 
`/autofs/cluster/freesurfer/centos6_x86_64/stable6/bin/3dvolreg.afni': 
Permission denied


Is there a way to get this done? Thanks so much for the help!

--Eugene


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

Sent: Wednesday, October 25, 2017 5:39:27 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Preproc-sess Error


it is not in $FREESURFER_HOME/bin ? If not, you can copy it from 5.3

On 10/25/17 4:59 PM, Hsu, Eugene wrote:

Hi FreeSurfer Experts,


We're trying to run preproc-sess on FreeSurfer 6, but we're encountering an 
error when motion correcting:


ERROR: cannot find AFNI command 3dvolreg.afni


When we tried Freesurfer 5.3 the preproc-sess ran to completion.


Thanks for your help!

--Eugene





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[Freesurfer] Postdoctoral Fellow Positions in a longitudinal birth cohort imaging study

[Anqi Qiu]

Postdoctoral Fellow Positions

Job description:

Growing Up in Singapore Towards Healthy Outcomes (GUSTO) is the most
comprehensive birth cohort study over the world. The GUSTO mothers were
recruited during pregnancy between 2009 and 2010. We have followed the
GUSTO family since then. The GUSTO study collects the unique data on
cognitive functions, children behaviors, psychopathology, and brain
imaging at multiple points from birth to 7 years of age. We aim to study
whether mother’s mood, diet, and family lifestyle since pregnancy affect
1) their babies’ cognitive and brain development; 2) psychopathology later
in life. We also aim to examine the role of genetics in such maternal
influences.

We are looking for postdoctoral fellows who are interested in the GUSTO
study.
Requirements:
1.  PHD in Cognitive Neuroscience, or Psychology, or Imaging Genetics;
2.  Experience with MRI-based neuroimage techniques;
3.  Knowledge in statistical analysis is necessary;
4.  Good communication and writing skills in English language;
5.  Knowledge in longitudinal analysis will be plus plus.

If you are interested in the jobs listed above, please send your CV to
Dean’s Chair, Associate Prof. Anqi QIU
Department of Biomedical Engineering
National University of Singapore
Email: bi...@nus.edu.sg
Phone: +(65) 6516 7002




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[Freesurfer] Errors in LGI computation

[k . ohmstedt]

Dear Freesurfers,

I try computing the local gyrification index following the method  
developed by Marie Schaer and her colleagues. The process itself  
finishes without errors, yet there remain large grey areas of variable  
size on the cortex, indicating errors in the computation of the  
gyrification index.  They are mainly situated in the regions next to  
the ventricles.
I checked the reconstructed surfaces after running the recon-all  
command and there do not seem to be any errors or lesions.

My system is a Mac with macOS Sierra (Version 10.12.6) and freesurfer  
Version 6.0.0 is running.

Do you have any ideas what could cause these problems? Any help is  
appreciated!

Thank you in advance and best regards,

Kai Ohmstedt


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