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Hello Bruce,

Thanks for the quick answer! I attached the recon-all.log file and a visualization of the subjects problem. How can I run only one hemisphere?

Thanks,

Alina

Am 06.07.2020 um 16:32 schrieb Fischl, Bruce BFISCHL@mgh.harvard.edu:

What is the error? You should be able to run through to the surface generation, then only run the hemi you want

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alina Rojas Sent: Monday, July 6, 2020 10:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Lesioned hemisphere

   External Email - Use Caution        

Hello Freesurfer experts,

I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the cortical thickness from the healthy one. Is there a possibility to only run one hemisphere through freesurfer? Or to project the healthy one on to the lesioned to have an intact brain and run recon-all succesfully?

Thanks,

Alina

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hello Bruce,

I let it run with recon-all -sd ${TARGET_FOLDER} -subjid $SUBJECTID -i $T1 -T2 $T2 -qcache -all -3T -T2pial -hemi lh died it died unexpected and searching for the surf rh.white… I attached you the recon-log file. Thanks so much for your help!

Am 06.07.2020 um 17:23 schrieb Alina Rojas alinacolora@gmail.com:

Hello Bruce,

Thanks for the quick answer! I attached the recon-all.log file and a visualization of the subjects problem. How can I run only one hemisphere?

Thanks,

Alina

<recon-all.log> <PastedGraphic-1.pdf>

...

Am 06.07.2020 um 16:32 schrieb Fischl, Bruce <BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu>:

What is the error? You should be able to run through to the surface generation, then only run the hemi you want

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alina Rojas Sent: Monday, July 6, 2020 10:22 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Lesioned hemisphere

   External Email - Use Caution        

Hello Freesurfer experts,

I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the cortical thickness from the healthy one. Is there a possibility to only run one hemisphere through freesurfer? Or to project the healthy one on to the lesioned to have an intact brain and run recon-all succesfully?

Thanks,

Alina

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hello Bruce,

I followed your instructions and it failed at the stats: " ERROR: you must include rh white and pial surfaces", is it a way to do the lh/rh aparc? Thank you!!

Am 09.07.2020 um 18:51 schrieb Douglas N. Greve dgreve@mgh.harvard.edu:

Use -lh instead of -hemi lh

On 7/9/2020 12:16 PM, Alina Rojas wrote:

...

    External Email - Use Caution        

Hello Bruce,

I let it run with recon-all -sd ${TARGET_FOLDER} -subjid $SUBJECTID -i $T1 -T2 $T2 -qcache -all -3T -T2pial -hemi lh died it died unexpected and searching for the surf rh.white… I attached you the recon-log file. Thanks so much for your help!

...

Am 06.07.2020 um 17:23 schrieb Alina Rojas <alinacolora@gmail.com mailto:alinacolora@gmail.com>:

Hello Bruce,

Thanks for the quick answer! I attached the recon-all.log file and a visualization of the subjects problem. How can I run only one hemisphere?

Thanks,

Alina

<recon-all.log> <PastedGraphic-1.pdf>

...

Am 06.07.2020 um 16:32 schrieb Fischl, Bruce <BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu>:

What is the error? You should be able to run through to the surface generation, then only run the hemi you want

Cheers Bruce

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alina Rojas Sent: Monday, July 6, 2020 10:22 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Lesioned hemisphere

   External Email - Use Caution        

Hello Freesurfer experts,

I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the cortical thickness from the healthy one. Is there a possibility to only run one hemisphere through freesurfer? Or to project the healthy one on to the lesioned to have an intact brain and run recon-all succesfully?

Thanks,

Alina

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer