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Hi Anastasia,

Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 degrees around y axis and the last 2 are top and bottom.

Thanks,

-Matt

On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia AYENDIKI@mgh.harvard.edu wrote:

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of an FA map that looked truncated, with slices missing from the bottom of the brain (which explains why the error happened for the ILF, which would go through that missing part of the brain). Does dmri/dwi.nii.gz look like that?

Best,

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek < matt@grecsek.com> *Sent:* Thursday, September 20, 2018 2:00:11 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

    External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T.

---

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700

Do the raw images look like that too?

From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Matthew Grecsek <m...@grecsek.com<mailto:m...@grecsek.com m...@grecsek.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

    External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags.

---

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks!

a.y

---

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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.

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Attached are the dwi_orig.nii screenshots with same orientations as before...

Thanks!

-Matt

On Fri, Sep 21, 2018 at 12:27 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Thank you. Can you also send screenshots of your original DWIs, if they don't look like this?

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek < matt@grecsek.com> *Sent:* Friday, September 21, 2018 10:27:37 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

    External Email - Use Caution

Hi Anastasia,

Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 degrees around y axis and the last 2 are top and bottom.

Thanks,

-Matt

On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia < AYENDIKI@mgh.harvard.edu> wrote:

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of an FA map that looked truncated, with slices missing from the bottom of the brain (which explains why the error happened for the ILF, which would go through that missing part of the brain). Does dmri/dwi.nii.gz look like that?

Best,

a.y

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek < matt@grecsek.com> *Sent:* Thursday, September 20, 2018 2:00:11 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

    External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T.

---

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700

Do the raw images look like that too?

From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Matthew Grecsek <m...@grecsek.com<mailto:m...@grecsek.com m...@grecsek.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

    External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags.

---

Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks!

a.y

---

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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 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.

Hi Matt – If your original DWIs are also truncated (which is what it looks like from the screenshots you sent), then it’s not tracula that’s truncating them. Any tracts that go through the truncated part of the brain (like the ILF, which is where you were getting the error, if I remember correctly) will not be reconstructed. You can still run tracula but use a configuration file and specify the pathlist so that it doesn’t include the tracts that go through the truncated part of the brain.

Best, a.y

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.commailto:matt@grecsek.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, September 25, 2018 at 9:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

I posted a reply with the dwi_orig.nii screenshots on Friday, but they did not show up on the list.

Yes, the dwi_orig.nii images appear the same as the dwi.nii.gz images.

Also, I ran them through TrackVis/DTK and they came out correct, so it seems to be something within Tracula that is not working for me as expected.

On Fri, Sep 21, 2018 at 12:27 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Thank you. Can you also send screenshots of your original DWIs, if they don't look like this?

________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.commailto:matt@grecsek.com> Sent: Friday, September 21, 2018 10:27:37 AM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Hi Anastasia,

Please see attached screenshots from dwi.nii.gz. The first 4 are rotated 90 degrees around y axis and the last 2 are top and bottom.

Thanks,

-Matt

On Thu, Sep 20, 2018 at 7:19 PM Yendiki, Anastasia <AYENDIKI@mgh.harvard.edumailto:AYENDIKI@mgh.harvard.edu> wrote:

Hi Matt - I am asking about the raw diffusion images. You sent a screenshot of an FA map that looked truncated, with slices missing from the bottom of the brain (which explains why the error happened for the ILF, which would go through that missing part of the brain). Does dmri/dwi.nii.gz look like that?

Best,

a.y

________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <matt@grecsek.commailto:matt@grecsek.com> Sent: Thursday, September 20, 2018 2:00:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

If you are referring to the T1 raw images, no they appear normal and the standard Freesurfer pipeline generates correct volumes.

If you are referring to the DTI raw images off the scanner, they also don't appear to have brain parts missing, although some appear more noisy and pixelated than others.

This is a mTBI subject with no other anatomical brain anomalies scanned with a Siemens 3T.

------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 13:20:02 -0700

Do the raw images look like that too?

From: <freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Matthew Grecsek <m...@grecsek.commailto:m...@grecsek.commailto:m...@grecsek.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, September 19, 2018 at 4:07 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault

External Email - Use Caution

Yes, a part of the brain appears missing. See attached screenshot.

I did not use a configuration file, I simply accepted all defaults and kicked off the process with -s and -i flags.

------------------------------------------------ Re: [Freesurfer] Freesurfer 6.0 - Tracula - Segmentation fault Yendiki, Anastasia Wed, 19 Sep 2018 09:02:47 -0700

Hi Matt – It looks like some sort of registration issue. When you display the FA map (dmri/dtifit_FA) and structural segmentation in diffusion space (label/diff/aparc+aseg), do they look fine? Is there any part of the brain that is cut off from any of the images? Also, can you attach your config file? Thanks!

a.y

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.