Groups

Automated Fiber Quantification (AFQ)

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Avantika Mathur, Jason Yeatman3

Apr 23

Plotting individual AFQ ROIs

Thanks for your reply, I am using matlab version of AFQ. On Wednesday, April 23, 2025 at 4:39:25 PM

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Plotting individual AFQ ROIs

Thanks for your reply, I am using matlab version of AFQ. On Wednesday, April 23, 2025 at 4:39:25 PM

Apr 23

9/20/24

afq.mat file not appear in afq output

Hi everyone, After running pyAFQ, I do not have a nodes.csv or a afq.mat folder in the afq output

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afq.mat file not appear in afq output

Hi everyone, After running pyAFQ, I do not have a nodes.csv or a afq.mat folder in the afq output

9/20/24

Zhongrui Huang, Maryana Daood2

3/6/24

Error in running "AFQ_example.m"

Hello ZhongruiHuang, Were you able to solve this problem? I'm encountering the same problem when

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Error in running "AFQ_example.m"

Hello ZhongruiHuang, Were you able to solve this problem? I'm encountering the same problem when

3/6/24

9/21/23

Dentatorubrothalamic Tract data

Hi all, I need to extract along-tract fractional anisotropy values for patients'

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Dentatorubrothalamic Tract data

Hi all, I need to extract along-tract fractional anisotropy values for patients'

9/21/23

Luie Wang, Rosie Zhou2

2/17/23

Missing/Incorrect Tract Segmentation

Dear Sir， I have whole brain tractography from Mrtrix and I'm trying to use AFQ to segment it.

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Missing/Incorrect Tract Segmentation

Dear Sir， I have whole brain tractography from Mrtrix and I'm trying to use AFQ to segment it.

2/17/23

Xuan Bu, hec...@gmail.com2

11/1/22

NaN for FA value but tractography is OK

Hello, Were you able to find a solution to this issue? On Tuesday, April 6, 2021 at 9:18:40 AM UTC-5

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NaN for FA value but tractography is OK

Hello, Were you able to find a solution to this issue? On Tuesday, April 6, 2021 at 9:18:40 AM UTC-5

11/1/22

caiwan...@gmail.com, … 刘不言4

8/28/22

Error in dtiRoiClean

Hello, when I am running AFQ_run.m, I met the same question，could you tell me how you solve this

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Error in dtiRoiClean

Hello, when I am running AFQ_run.m, I met the same question，could you tell me how you solve this

8/28/22

3/28/22

dMRI data is only roughly aligned with the T1 data

Hello experts and users of AFQ, I use mrAnatAverageAcpcNifti to ac-pc align the T1 anatomy and then

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dMRI data is only roughly aligned with the T1 data

Hello experts and users of AFQ, I use mrAnatAverageAcpcNifti to ac-pc align the T1 anatomy and then

3/28/22

aava...@gmail.com, Jason Yeatman2

11/23/21

Fiber Density Units

There are 2 options Either raw count if fibers in each voxel. Or that value can be normalized to

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Fiber Density Units

There are 2 options Either raw count if fibers in each voxel. Or that value can be normalized to

11/23/21

3/22/21

Does this SLF have erroneous fibers?

Hi AFQers, The figure below is depicting left SLF(tractnum=15). I wonder to know whether this SLF

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Does this SLF have erroneous fibers?

Hi AFQers, The figure below is depicting left SLF(tractnum=15). I wonder to know whether this SLF

3/22/21

3/21/21

Is there any other multiple correction method that can be used in AFQ apart from FWE?

Hi AFQers, I have performed AFQ_MultiCompCorrectionPartialCorr (permutation+ p< 0.05, FWE

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Is there any other multiple correction method that can be used in AFQ apart from FWE?

Hi AFQers, I have performed AFQ_MultiCompCorrectionPartialCorr (permutation+ p< 0.05, FWE

3/21/21

Naeim Bahrami, … Ted Turesky7

10/20/20

Corpus Callosum

Thank you, Jason!! On Tuesday, October 20, 2020 at 11:48:23 AM UTC-4 Jason wrote: Dougherty, RF,

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Corpus Callosum

Thank you, Jason!! On Tuesday, October 20, 2020 at 11:48:23 AM UTC-4 Jason wrote: Dougherty, RF,

10/20/20

Luie Wang, … Maria Economou7

10/6/20

Ques about Automatic Segmentation and Incomplete Whole Brain Tractography

Thanks both for the tips! On Saturday, October 3, 2020 at 5:25:48 AM UTC+2 luie...@gmail.com wrote:

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Ques about Automatic Segmentation and Incomplete Whole Brain Tractography

Thanks both for the tips! On Saturday, October 3, 2020 at 5:25:48 AM UTC+2 luie...@gmail.com wrote:

10/6/20

Jason Yeatman, … Chris Wertz6

10/1/20

Estimating fiber endpoints on the cortical surface

Yeah something like the command you cited should work. It all depends on the registration of the

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Estimating fiber endpoints on the cortical surface

Yeah something like the command you cited should work. It all depends on the registration of the

10/1/20

xiuxiu liu, … Maria Economou3

9/28/20

AFQ analysis problem of children aged 6 to 8

Hi, Were you able to solve this problem? I am struggling with AFQ analysis on a pediatric dataset as

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AFQ analysis problem of children aged 6 to 8

Hi, Were you able to solve this problem? I am struggling with AFQ analysis on a pediatric dataset as

9/28/20

8/26/20

Incorrect/incomplete whole-brain tractography result

Hi all, I'm using a Philips multi-shell dataset with 119 volumes, pre-processed in FSL (eddy,

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Incorrect/incomplete whole-brain tractography result

Hi all, I'm using a Philips multi-shell dataset with 119 volumes, pre-processed in FSL (eddy,

8/26/20

anegu...@gmail.com

8/21/20

Template Mori ROIs location?

Dear AFQ experts, In which directory are the Mori ROIs for located? According to the documentation (

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Template Mori ROIs location?

Dear AFQ experts, In which directory are the Mori ROIs for located? According to the documentation (

8/21/20

Sebastian Miguel Toescu3

6/19/20

Undefined function or variable 'spm_normalise'.

I emailed the SPM developers who replied: "this is due to spm_normalise being an old function

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Undefined function or variable 'spm_normalise'.

I emailed the SPM developers who replied: "this is due to spm_normalise being an old function

6/19/20

Zachary Anderson, Jason Yeatman5

6/3/20

ROI to ROI tractography

Yeah, you can either (a) switch your code in for the warping code or (b) warp the ROIs yourself and

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ROI to ROI tractography

Yeah, you can either (a) switch your code in for the warping code or (b) warp the ROIs yourself and

6/3/20

Steven Meisler, Jason Yeatman8

5/13/20

AFQ_RenderFibers works for individual fiber groups, but not for whole brain

Not sure how that file name ended up like that but I'll fix it as soon as I have time to test

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AFQ_RenderFibers works for individual fiber groups, but not for whole brain

Not sure how that file name ended up like that but I'll fix it as soon as I have time to test

5/13/20

Marie J. Prioris

4/14/20

AFQ MultiCompCorrection with crawford t-test

Dear AFQ experts I have a problem with AFQ_MultiCompCorrection scrip (permutation method). I´m

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AFQ MultiCompCorrection with crawford t-test

Dear AFQ experts I have a problem with AFQ_MultiCompCorrection scrip (permutation method). I´m

4/14/20

Steven Meisler, … Jason Yeatman10

4/9/20

AFQ_WholeBrainTractography image looks sparse

Image may have not sent as first, so I am attaching it here.

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AFQ_WholeBrainTractography image looks sparse

Image may have not sent as first, so I am attaching it here.

4/9/20

3/21/20

Hi, I am not familiar with AFQ. just learn to use Matlab script to perform group AFQ analysis.

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Hi, I am not familiar with AFQ. just learn to use Matlab script to perform group AFQ analysis.

3/21/20

2/28/20

Transforming Fibers to MNI space

Hi all, I would like to normalize each subject's fiber group to MNI space so I can make a average

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Transforming Fibers to MNI space

Hi all, I would like to normalize each subject's fiber group to MNI space so I can make a average

2/28/20

Jason Yeatman, Loxlan Kasa2

2/28/20

AFQ now supports normalization with ANTs

Great tool Jason and the AFQ team. A quick question, am trying to transform the MNI ROIs to native

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AFQ now supports normalization with ANTs

Great tool Jason and the AFQ team. A quick question, am trying to transform the MNI ROIs to native

2/28/20

Qi Yang, Jason Yeatman10

2/13/20

Binarizing cleaned and clipped streamlines

Yes there are many automated alignment tools that would probably work fine. Also many image

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Binarizing cleaned and clipped streamlines

Yes there are many automated alignment tools that would probably work fine. Also many image

2/13/20

Sebastian Miguel Toescu, … Changfu Zou10

2/12/20

MEX-file error with AFQ_example.m

Hi Changfu, It will depend on what Matlab version you're running etc. Open terminal; Navigate to

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MEX-file error with AFQ_example.m

Hi Changfu, It will depend on what Matlab version you're running etc. Open terminal; Navigate to

2/12/20

Alica Rogojin, Jason Yeatman2

2/11/20

Permutation method not working properly for correlation analysis?

I never actually tested this but what you report is exactly what would be expected. Neighboring nodes

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Permutation method not working properly for correlation analysis?

I never actually tested this but what you report is exactly what would be expected. Neighboring nodes

2/11/20

1/28/20

Callosum Segmentation

Hi Jason, Can you please help me with that? Thanks, Yildir On Friday, January 10, 2020 at 3:40:37 PM

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Callosum Segmentation

Hi Jason, Can you please help me with that? Thanks, Yildir On Friday, January 10, 2020 at 3:40:37 PM

1/28/20

1/21/20

Questions about dtiInit parameters

Hi AFQ Community, I'm using dtiInit function to align my DWI (obtained from Siemens scanner) to

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Questions about dtiInit parameters

Hi AFQ Community, I'm using dtiInit function to align my DWI (obtained from Siemens scanner) to

1/21/20

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