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.s...@duke-nus.edu.sg <mailto:beatrice....@duke-nus.edu.sg>
Web: www.neuroimaginglab.or <http://www.neuroimaginglab.org/>g
On 20/2/18, 12:06 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
fis...@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.s...@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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>>
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