Hi Bruce,

Thanks for your email. I am using Freesurfer version 6 and the command I used to run is this:

qsub -m n -o o -e e -V recon-all -subjid ${Z}_${Image}_fs -i ${step1LocalDir}/$T1 -FLAIR ${step1LocalDir}/${FLAIR} -FLAIRpial -all

Best Regards,

Shim Hee Youn Research Assistant Multimodal Neuroimaging in Neuropsychiatric Disorders Laboratory | Center for Cognitive Neuroscience | Neuroscience and Behavioral Disorders Program | Duke-NUS Medical School, Singapore Address: 8 College Road, #06-15, Singapore 169857 Tel: (65) 6516 4339 or (65) 6516 7590 Fax: (65) 6221 8685 Email: heeyoun.shim@duke-nus.edu.sg mailto:beatrice.loo@duke-nus.edu.sg Web: www.neuroimaginglab.or http://www.neuroimaginglab.org/g

On 20/2/18, 12:06 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

Hi Shim Hee

we need to know what commands you ran, the full screen output from them, and what version of FS you are using (at least!)

cheers Bruce

On Mon, 19 Feb 2018, Shim Hee Youn wrote:

...

Hi Freesurfer team,

I am currently using ADNI dataset to run Freesurfer Recon all for MPRAGE, SPGR and SPGR accelerated sequences.

For SPGR sequences (including SPGR accelerated), I have ran recon all with FLAIR images as I thought it would improve the output; however, it seems to aggravate the output. Any ideas on know why this is the case?

I have attached the images in this email.

Hope to hear from you soon. Thank you!

Best Regards,

Shim Hee Youn

Research Assistant

Multimodal Neuroimaging in Neuropsychiatric Disorders Laboratory | Center for Cognitive Neuroscience |

Neuroscience and Behavioral Disorders Program | Duke-NUS Medical School, Singapore

Address: 8 College Road, #06-15, Singapore 169857

Tel: (65) 6516 4339 or (65) 6516 7590 Fax: (65) 6221 8685 Email: heeyoun.shim@duke-nus.edu.sg

Web: MailScanner has detected a possible fraud attempt from "www.neuroimaginglab.org" claiming to be www.neuroimaginglab.org

---

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Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

________________________________

Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

Hi Bruce,

This is the sequence details:

- Axial FLAIR: Plane=AXIAL; Acquisition Type=2D; Coil=8HRBRAIN; Field Strength=3.0 tesla; Flip Angle=90.0 degree; Manufacturer=GE MEDICAL SYSTEMS; Matrix X=256.0 pixels; Matrix Y=256.0 pixels; Matrix Z=42.0 ; Mfg Model=Signa HDxt; Pixel Spacing X=0.8593999743461609 mm; Pixel Spacing Y=0.8593999743461609 mm; Pulse Sequence=SE/IR; Slice Thickness=5.0 mm; TE=153.91200256347656 ms; TI=2250.0 ms; TR=11002.0 ms; Weighting=T2;

- Sag IR-SPGR: Acquisition Plane=SAGITTAL; Acquisition Type=3D; Coil=8HRBRAIN; Field Strength=3.0 tesla; Flip Angle=11.0 degree; Manufacturer=GE MEDICAL SYSTEMS; Matrix X=256.0 pixels; Matrix Y=256.0 pixels; Matrix Z=196.0 ; Mfg Model=Signa HDxt; Pixel Spacing X=1.0155999660491943 mm; Pixel Spacing Y=1.0155999660491943 mm; Pulse Sequence=GR; Slice Thickness=1.2000000476837158 mm; TE=2.8480000495910645 ms; TI=400.0 ms; TR=6.984000205993652 ms; Weighting=T1;

Best Regards,

Shim Hee Youn Research Assistant Multimodal Neuroimaging in Neuropsychiatric Disorders Laboratory | Center for Cognitive Neuroscience | Neuroscience and Behavioral Disorders Program | Duke-NUS Medical School, Singapore Address: 8 College Road, #06-15, Singapore 169857 Tel: (65) 6516 4339 or (65) 6516 7590 Fax: (65) 6221 8685 Email: heeyoun.shim@duke-nus.edu.sg mailto:beatrice.loo@duke-nus.edu.sg Web: www.neuroimaginglab.or http://www.neuroimaginglab.org/g

On 21/2/18, 12:11 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

and can you give us details of your FLAIR acquisition? What are the voxel sizes? What sequence? On Tue, 20 Feb 2018, Shim Hee Youn wrote:

...

Hi Bruce,

Thanks for your email. I am using Freesurfer version 6 and the command I used to run is this:

qsub -m n -o o -e e -V recon-all -subjid ${Z}_${Image}_fs -i ${step1LocalDir}/$T1 -FLAIR ${step1LocalDir}/${FLAIR} -FLAIRpial -all

Best Regards,

Shim Hee Youn Research Assistant Multimodal Neuroimaging in Neuropsychiatric Disorders Laboratory | Center for Cognitive Neuroscience | Neuroscience and Behavioral Disorders Program | Duke-NUS Medical School, Singapore Address: 8 College Road, #06-15, Singapore 169857 Tel: (65) 6516 4339 or (65) 6516 7590 Fax: (65) 6221 8685 Email: heeyoun.shim@duke-nus.edu.sg mailto:beatrice.loo@duke-nus.edu.sg Web: www.neuroimaginglab.or http://www.neuroimaginglab.org/g

On 20/2/18, 12:06 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:

...

Hi Shim Hee

we need to know what commands you ran, the full screen output from them, and what version of FS you are using (at least!)

cheers Bruce

On Mon, 19 Feb 2018, Shim Hee Youn wrote:

...

Hi Freesurfer team,

I am currently using ADNI dataset to run Freesurfer Recon all for MPRAGE, SPGR and SPGR accelerated sequences.

For SPGR sequences (including SPGR accelerated), I have ran recon all with FLAIR images as I thought it would improve the output; however, it seems to aggravate the output. Any ideas on know why this is the case?

I have attached the images in this email.

Hope to hear from you soon. Thank you!

Best Regards,

Shim Hee Youn

Research Assistant

Multimodal Neuroimaging in Neuropsychiatric Disorders Laboratory | Center for Cognitive Neuroscience |

Neuroscience and Behavioral Disorders Program | Duke-NUS Medical School, Singapore

Address: 8 College Road, #06-15, Singapore 169857

Tel: (65) 6516 4339 or (65) 6516 7590 Fax: (65) 6221 8685 Email: heeyoun.shim@duke-nus.edu.sg

Web: MailScanner has detected a possible fraud attempt from "www.neuroimaginglab.org" claiming to be www.neuroimaginglab.org

---

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Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.

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Important: This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately; you should not copy or use it for any purpose, nor disclose its contents to any other person. Thank you.