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Hi Jinyoung

Sorry for the slow response but I'm traveling these days

I believe this is a bug that was fixed in the dev version 2-3 weeks ago. Would you mind trying the latest dev, and checking whether that solves the problem?

Cheers

Eugenio

Sent from my phone, please excuse brevity and typos

---

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 오진영 <jinyoung.oh555@gmail.com>
Sent: Wednesday, September 5, 2018 6:13:48 AM
To: Freesurfer support list
Subject: [Freesurfer] amygdala segmentation using additional scan error

 

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Hello, freesurfer experts

I'm trying to run segmentation of hippocampal subfields and nuclei of amygdala with additional scan.

I already ran segmentation of hippocampal subfields and nuclei of amygdala with only T1 image, using segmentHA_T1.sh command and succeeded.

After success of segmentation of amygdala with T1 image, I tried to run segmentation again with additional scan(T2 image) to get more reliable results.

However, when I use command segmentHA_T2.sh, I got the following error:

Error in segmentSubjectT1T2_autoEstimateAlveusML (line 2628)

And the last few lines before the error are below:

Fitting mesh to image data mask took 264.2808 seconds

Transforming points

Transforming points

Wrote image to file image1.mgz

Wrote image to file image2.mgz

INFO: dst volume info differs from the one stored in lta.  gets modified now.

volume geometry:

extent  : (232, 469, 208)

voxel   : ( 0.3333,  0.3333,  0.3333)

x_(ras) : ( 0.0000, -1.0000,  0.0000)

y_(ras) : ( 0.0000,  0.0000, -1.0000)

z_(ras) : ( 1.0000,  0.0000,  0.0000)

c_(ras) : (-21.1788, -1.8961,  3.8447)

file    : T2isotropic.mgz

volume geometry:

extent  : (256, 256, 256)

voxel   : ( 1.0000,  1.0000,  1.0000)

x_(ras) : ( 0.0000, -1.0000,  0.0000)

y_(ras) : ( 0.0000,  0.0000, -1.0000)

z_(ras) : ( 1.0000,  0.0000,  0.0000)

c_(ras) : ( 2.3212,  8.6039, -21.1553)

file    : /Users/mnd_mac/Desktop/JY_surfer/sub_05_T2.nii

Constructing image-to-world transform from header information (asmr1.mgz)

Constructing image-to-world transform from header information (/Users/mnd_mac/Desktop/JY_surfer//recon_sub_05/tmp/hippoSF_T1T2_v21_T2_left/imageDump.mgz)

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

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 segmentSubjectT1T2_autoEstimateAlveusML (line 2628)

MATLAB:subsassignnumelmismatch

Darwin MnD-macui-iMac.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64

and I have no idea how to solve this problem out.

I use the dev version of freesurfer.

T1 scan image and T2 scan image of participant were taken on the same day.

If you have any recommendations, please send me the email back.

Thanks!

Jinyoung

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