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
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