Re: [Freesurfer] AAL and freesurfer atlas concordance

[Venkateswaran Rajagopalan]

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 Dear All

I have seen posts discussing about bringing AAL to freesurfer etc.

I am wondering whether anyone has created a table of concordance between
the regions in AAL to the freesurfer or the vice versa. If so can you
please share with me.
For my work I just want to know the mapping between the two atlases.

 Or is there any software or website (like the brain atlas concordance one)
from where I can find the concordance between the two atlas regions

Any help is greatly appreciated

Thanks
Venkat
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Re: [Freesurfer] Flipped left to right hemisphere subjects

[Greve, Douglas N.,Ph.D.]

Is the  volume actually left-right reversed?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lutz,Olivia (BIDMC - 
Psychiatry) 
Sent: Monday, August 20, 2018 4:55:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Flipped left to right hemisphere subjects


Hi Doug and Bruce,


thank you for the quick reply. As a follow-up question, we've edited our 
brainmasks for a dataset and want to flip some subjects left to right. I found 
instructions to flip the scans, however they are for the nu.mgz file 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal). Is is possible 
to apply this

mri_convert --in_orientation​ command to change the left and right labels of 
the brainmask so we don't have to re-edit as opposed to applying it to the 
nu.mgz file and regenerating the brainmask?

Thanks!
Olivia




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[Freesurfer] Fw: Parcellation label error

[Ali,Mohamed Tarek Mohamed]

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From: Ali,Mohamed Tarek Mohamed
Sent: Saturday, August 18, 2018 10:59 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Parcellation label error


Hello FreeSurfer Developers,


While I am using [vec,labels,cnames] = read_annotation('lh.aparc.annot'), I am 
getting values in labels which are not found in cnames.table(:,5). These values 
are 0. I assigned the values to the unknown area. However, when I looked at the 
number of vertices per brain regions I found that corpuscallosum has no 
vertices in the DK atlas.


This is my first week using a neuroimaging software and Freesurfer is my first 
software to work on, so I just don't know if that's ok or if there is something 
wrong.


I am attaching the output of a python code I wrote to count the number of 
vertices per brain region in the left hemisphere of a structural MRI image from 
our dataset.


Thanks in advance,

Mohamed T. Ali

Ph.D. student,
Bioengineering,

University of Louisville.
b'unknown' contains: 6695
b'insula' contains: 3551
b'temporalpole' contains: 552
b'precuneus' contains: 5189
b'frontalpole' contains: 351
b'transversetemporal' contains: 695
b'supramarginal' contains: 5915
b'superiorfrontal' contains: 9823
b'superiortemporal' contains: 5738
b'parstriangularis' contains: 2286
b'rostralmiddlefrontal' contains: 7656
b'medialorbitofrontal' contains: 2167
b'isthmuscingulate' contains: 1359
b'superiorparietal' contains: 7060
b'lateraloccipital' contains: 7440
b'lateralorbitofrontal' contains: 3510
b'fusiform' contains: 4661
b'posteriorcingulate' contains: 1783
b'inferiorparietal' contains: 6607
b'parahippocampal' contains: 965
b'caudalanteriorcingulate' contains: 779
b'parsopercularis' contains: 2422
b'rostralanteriorcingulate' contains: 853
b'precentral' contains: 6554
b'lingual' contains: 3628
b'postcentral' contains: 6424
b'bankssts' contains: 1613
b'corpuscallosum' contains: 0
b'paracentral' contains: 2045
b'parsorbitalis' contains: 936
b'entorhinal' contains: 458
b'caudalmiddlefrontal' contains: 2994
b'pericalcarine' contains: 1564
b'inferiortemporal' contains: 5501
b'middletemporal' contains: 5220
b'cuneus' contains: 2000
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Re: [Freesurfer] Flipped left to right hemisphere subjects

[Lutz,Olivia (BIDMC - Psychiatry)]

Hi Doug and Bruce,


thank you for the quick reply. As a follow-up question, we've edited our 
brainmasks for a dataset and want to flip some subjects left to right. I found 
instructions to flip the scans, however they are for the nu.mgz file 
(https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal). Is is possible 
to apply this

mri_convert --in_orientation? command to change the left and right labels of 
the brainmask so we don't have to re-edit as opposed to applying it to the 
nu.mgz file and regenerating the brainmask?

Thanks!
Olivia




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intended recipient, any dissemination, distribution, copying, or use of this 
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permanently delete it and immediately notify the sender. Thank you.
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[Freesurfer] correlation between blood biomarkers and longitudinal decrease in cortical thickness

[Foad Taghdiri]

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Hello,

I have done freesurfer (v6) longitudinal preprocessing for 20 subjects 
(baseline and 2-year follow-up). We also have levels of some blood biomarkers 
(e.g. tau, neurofilament light) for these subjects at the baseline. I am 
interested to figure out if the level of blood biomarkers at the baseline is 
related to the amount of cortical thinning over time, and if so, which brain 
regions’ cortical thinning are significantly correlated with the blood 
biomarker. I was wondering if you could please guide me through this analysis 
and let me know how I can do it.

Thanks
Best,
Foad


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Re: [Freesurfer] segmentHA_T1.sh exits with error

[Iglesias Gonzalez, Eugenio]

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Dear Antonin,
Thanks again for letting us know you had this problem; it turned out to be a 
small, silly bug in the code. I will fix it ASAP, and the updated code should 
be on the dev version in the next few days.
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 Antonin Skoch 

Reply-To: Freesurfer support list 
Date: Friday, 17 August 2018 at 18:16
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T1.sh exits with error


External Email - Use Caution
Dear experts,

I am running segmentHA_T1.sh. In about 3 subjects from 200, the script exits 
with following error:

In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1856)

MATLAB:subsassignnumelmismatch
Command exited with non-zero status 255

Full log file is attached. I have also uploaded whole subject (named 
segmentHA_T1_error.tar.gz ), including content of temporary directory  
hippoSF_T1_v21_right, to your server.

I am using dev version, build 2018-07-28. I am using customized recon-all, but 
it should not relate to this error. Could you please look at this issue?

Regards,

Antonin Skoch
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[Freesurfer] How to register fMRI data without upsampling voxel size?

[Maria Hakonen]

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Dear Freesurfer experts,

Could you please let me know how to normalize fMRI data without upsampling
the original voxel size from 5 x 5 x 7 mm to 2 x 2 x 2 mm? I have tried
this as follows:

1. Register functional (data.nii) to anatomical matrix



bbregister --s $subject --bold --init-fsl --mov data.nii --reg
register.dof6.dat



2. Register anatomical to mni152:

  mni152reg --s $subject



3. Create registration between functional and mni152

  mri_matrix_multiply -im register.dof6.dat -iim reg.mni152.2mm.dat -om
reg.mni152.dat



4. Resample func to mni152 space

 mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --mov
data.nii --reg reg.mni152.dat --o data.mni152.nii --no-resample



I checked the registrations after each step. After step 4, the functional
data and the template are not fully aligned if I use “no-resample”.
Without no-resample, the registration seems successful, but the fMRI data
has a voxel size of 2mm.

Best,

Maria
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[Freesurfer] How to install Biomedical Toolkit examples in Labview 2015?

[Bellamy Baron]

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Hi freesurfers,

Does anyone know how to install Biomedical Toolkit examples in Labview 2015?

I installed an evaluation version of Labview 2015, 2015DFDT, and 2015ASPT
under Windows 7.  Then, I installed the 2014BMTK but only one, I get the
Biomedical Workbench, but examples (source codes) are not installed.

In a second time, I marked the option of 2014_Support in the installation
of 2014BMTK, then examples are installed but in another file (Labview 2014)
and there are missing modules when I try to test these examples.

Thanks,


Bellamy
Specialist  - iWYZE
https://www.iwyze.co.za 
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Re: [Freesurfer] Lesion segmentation

[Mo Izady]

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Hi everyone,

I apologize for reposting this but I haven't received any response since
last week. Could someone pls help?

Here are my questions:

1) What is considered a lesion in subcortical segmentation? (tumor, MS,
stroke, etc)

2) Would you pls share the reference to the algorithm that FreeSurfer uses
for segmenting lesions?

Thanks in advance!

Mo


On Wed, Aug 15, 2018 at 4:35 PM, Mo Izady  wrote:

> Hi FreeSurfer experts,
>
> I have two questions; any hints are greatly appreciated:
>
> 1) What is considered lesion in subcortical segmentation? (tumor, MS,
> stroke, etc)
>
> 2) Would you pls share the reference to the algorithm that FreeSurfer
> uses for segmenting lesions?
>
> Thanks in advance!
>
> Mo Izady
>
> PhD Candidate in Neuroscience
> Arizona State University
>
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[Freesurfer] 3 positions to post

[Florence M]

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Hi,

I want to post a positions bellow, thanks to reply where I should go to
post it on free surfer please.

Best,
Florence


Postdoctoral Position on Imaging Genetics.docx
Description: MS-Word 2007 document


Research Engineer.docx
Description: MS-Word 2007 document


biostatistican.docx
Description: MS-Word 2007 document
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Re: [Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields

[Iglesias Gonzalez, Eugenio]

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Without having seen your FLAIR scans, I’d say probably not, but it’s an 
empirical question; give them a go! ;-)

--
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 Ole Johan Evjenth 
Sørhaug 
Reply-To: Freesurfer support list 
Date: Monday, 20 August 2018 at 13:17
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields


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Dear freesurfer experts,

I'm interested in doing subfield segmentations of the hippocampus in version 
6.0. What I am specifically interested in, is that if I can expect better 
segmentations if I use a 1mm isotropic FLAIR series in addition to the 1mm 
isotropic T1 series, rather than using the T1 series alone.

Regards
Ole Johan Sørhaug
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[Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields

[Ole Johan Evjenth Sørhaug]

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Dear freesurfer experts,

I'm interested in doing subfield segmentations of the hippocampus in
version 6.0. What I am specifically interested in, is that if I can expect
better segmentations if I use a 1mm isotropic FLAIR series in addition to
the 1mm isotropic T1 series, rather than using the T1 series alone.

Regards
Ole Johan Sørhaug
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[Freesurfer] AAL and freesurfer atlas concordance

[Venkateswaran Rajagopalan]

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Dear All

I have seen posts discussing about bringing AAL to freesurfer etc.

I am wondering whether anyone has created a table of concordance between
the regions in AAL to the freesurfer or the vice versa. If so can you
please share with me.
For my work I just want to know the mapping between the two atlases.

 Or is there any software or website (like the brain atlas concordance one)
from where I can find the concordance between the two atlas regions

Any help is greatly appreciated

Thanks
Venkat
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