External Email - Use Caution
Hi Dr. Steve,
I figured this out by using dos2unix, since I found this file has "with CRLF line terminators" while checking with command line "file". In case, anyone may need this as well. I got exactly what I need for further analysis in the cache.th40.neg.y.ocn.dat now. Thanks so much for your reply and explanations!
Cheers!
Regards, Xiaoxu
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Na, Xiaoxu Sent: Wednesday, January 27, 2021 9:58 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution Dr. Steve, I gave it all the permissions, but still not working. By the way, is there an excutable file coming with this, like mri_glmfit?
$ls -l /home/xiaoxu/freesurfer/bin/mri_glmfit-sim -rwxrwxrwx 1 root 1590 39574 Jan 27 09:19 /home/xiaoxu/freesurfer/bin/mri_glmfit-sim
$ mri_glmfit-sim --help : Command not found. : Command not found. : Command not found. : Command not found. set: Variable name must begin with a letter.
Regards, Xiaoxu
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 Douglas N. Greve Sent: Wednesday, January 27, 2021 9:44 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
Try making it executable with chmod a+x $FREESURFER/bin/mri_glmfit-sim On 1/27/2021 10:41 AM, Na, Xiaoxu wrote:
External Email - Use Caution Hi Dr. Greve,
Thanks for your reply. However, it shows me the command line error when I try to run it after having the file replaced. Please kindly see below. Is there any other settings I should run before that? Even the - -help can't be passed. Thanks a lot!
$ mri_glmfit-sim --glmdir sAnalysis/lh.area.g2v2CSHQ.10.glmdir --cache 4 neg --cwp 0.05 --2spaces --spatial-sum : Command not found. : Command not found. : Command not found. : Command not found. set: Variable name must begin with a letter. $mri_glmfit-sim --help : Command not found. : Command not found. : Command not found. : Command not found. set: Variable name must begin with a letter.
Regards, Xiaoxu
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 Douglas N. Greve Sent: Tuesday, January 26, 2021 6:08 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
By default, mri_glmfit-sim will compute a spatial average inside of a cluster to create the OCN table, so the values do not agree with the table below. In he case of area or volume inputs, it needs to compute the sum instead of the average. I have just modified this program to do this. I've attached this new version. Copy it to $FREESURFER/bin To run, add --spatial-sum to the command line On 1/26/2021 12:56 PM, Na, Xiaoxu wrote:
External Email - Use Caution To make it clear, I would like to extract the area of each subject in the cluster. May I know if this is the correct way? If not, it's appreciated if you would point it out. Thanks!
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 Na, Xiaoxu Sent: Tuesday, January 26, 2021 11:44 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution Dear Freesurfer Experts,
As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers?
Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot!
ClusterNo
Max
VtxMax
Size(mm^2)
MNIX
MNIY
MNIZ
CWP
CWPLow
CWPHi
NVtxs
WghtVtx
1
-4.8321
40067
444.11
-58.1
-16.6
-23.9
0.0002
0
0.0004
670
-2784.11
Regards, Xiaoxu
________________________________ Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/188WcQA2AsaU60YMRy5Djhmlw0N14Ibx9zXyjtgRRyHTsnL...https://secure-web.cisco.com/1AecDJe40eU82ZVq4BWV-4vh_tbk8w_Mu1jTQ4UciLKD-ignhsZ-j4pC2-RGgCDvJ69OnXzz1dXzM2IURsPyr0aH8QeUihwpUPx6-5ov4R_yH8YISugRPwvdAK6AaI8VhfjzSfndJXOXoVOGT7iR1qYERgv5GDVhGGgC_MdRi2uX4GXRHWYa7WUD-wkjttxOo4zis67jHvGgQDCzaOfJn6JnJCUGbQRyg5jYQqNmBroFrsf1J6cJxb9LH5FnBXhOqdAW58kdbq3rX7Kk-EMZVCg/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_13IWCtFrBNHonXeeyPITDinreohTeqytYJ6nztnQFd4yhk3nXN4Bkq9QSBAeyfqOwlJMFYlzjAIlaB4QWtxF-5Fv582Q7byRiq2OFn-2DOKoyQSUQ2e4IOHjCSCK4ClWGcGvQTA5kIQLLrpxgXcFkVmb7Ya1X5AcRONaAjfmFbzSNz7D237RUSPEdhlqBuwaliM-5Fpb6qDDq8C9kr8k31kJ3bYfQYwgYkJN5pMlRThjir7kwI8z4g-5FvjpGWkPs4aFTs9QzGc-5FtH4PH0jYTOyzldK4K0A_https-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fsecure-2D2Dweb.cisco.com-5F1QXsCNNhFh-2D2DbrzaSzrnEamNpivI0Re19RGx6G6Pz4-2D5FOp9HZvOFtXm0uZq4uIq0Ou3oilQGEQGR24qDidwNgmf3pw5mzlWRoAYx5Nt-2D2D3chsypA3aeWoYIOPb1Cfa-2D5F39n43048YT3O1YnJIFNwfwwHPRlHhUP7hlNdvD0oy1iFaWlr-2D2DcBV4GO3qCsTxpLpQPx48HR8rIGKWq-2D5FYKmqKmUhYvYvHl7G79wa-2D5F0iQSgSmXl-2D5FvcuX27JCj4u5jFralxilx6C0XG9hdpAB-2D2D4QAGg9cGBW0Q-5Fhttps-2D253A-2D252F-2D252Furldefense.proofpoint.com-2D252Fv2-2D252Furl-2D253Fu-2D253Dhttps-2D2D3A-2D5F-2D5Fmail.nmr.mgh.harvard.edu-2D5Fmailman-2D5Flistinfo-2D5Ffreesurfer-2D2526d-2D253DDwMD-2D2Dg-2D2526c-2D253D27AKQ-2D2DAFTMvLXtgZ7shZqsfSXu-2D2DFwzpqk4BoASshREk-2D2526r-2D253DAQ0GBw0jN0YsxXpbOoM-2D2DtQ-2D2526m-2D253D4Eo1ALvsVtjqO7fGNobj1xKwfESo-2D2DW1SEAGN3n3R8Z0-2D2526s-2D253DKD108hEcj1K5YPOiXoc2jhCZDIeF18F0qWdIq8Wrq8Y-2D2526e-2D253D-2526d-253DDwMD-2Dg-2526c-253D27AKQ-2DAFTMvLXtgZ7shZqsfSXu-2DFwzpqk4BoASshREk-2526r-253DAQ0GBw0jN0YsxXpbOoM-2DtQ-2526m-253DYcOJDRQ1D9o8a7bu7m8-2D3xYcD6G6rcJYTW1MA8xDD-5FY-2526s-253Dtl9TVzbtl5t-2D3xI-5FYpINSd2-2DnbU1MqWTBNRic6xIU-5FU-2526e-253D%26d%3DDwMFAg%26c%3D27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk%26r%3DAQ0GBw0jN0YsxXpbOoM-tQ%26m%3D3Nv61Vuo-iNbXy_YMkpRegaT5pP5ia_Z1BzvL4HQhKM%26s%3DGLu65HxqP-CX_LUS-enVwtl19o5xszoezNseC5KknDI%26e%3D
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/188WcQA2AsaU60YMRy5Djhmlw0N14Ibx9zXyjtgRRyHTsnL...https://secure-web.cisco.com/1PhUEQBF8VjG4uJzGax4fBiG0hLl31AberFu9UEFoyuz25zs0oqCNh7kgQdxJ9Dv02JhVq5SGWoW4lfDOs8Hg1xMaqHQewnSGCMKpfUcifqouWFPJe4_6-qhTOY9n4686hGynZuyBCIQlEdLpnxX7BqWfakg-4al520LuSeJ97leH9VHmIk_vFlKnresuWGVZn9rVcewvg-4dz9FdIdN1tWGOnkxoUJNXSx09ZSKxnXl_5Jpf0O7FI9Pvid5BktXM20UOAeL1nw2ZhIqugFq-bw/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1TVzIfGr9UlEHNf-5FhLd9iKxXjt0lfVA1KK-2DQi0Zwd-5FW3q3h1Hv2sqCvdo0EBS4NFGZWZWAsZ8N-2Dwy-2DfeQasZjciNE0YGd3rlLb6t1Mo9vGMyc1yrjh-2DAP2OvGOdIco6d9OnY0ciV0E-5FSsQPs30dUgXE4zkhBaDOYx-2DLSK3Ls4FF9fxA-5FReZoGX-2DITx9w1yYR9ULMRt1aAn4jgF11j3V475zjSYTA-5FukHTZdC9gKTI-2DvV2uMAgtTpahWJthyr84d7aHM58FkYbiSZQ9QKZG7RaGA_https-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fmail.nmr.mgh.harvard.edu-5Fmailman-5Flistinfo-5Ffreesurfer-2526d-253DDwMD-2Dg-2526c-253D27AKQ-2DAFTMvLXtgZ7shZqsfSXu-2DFwzpqk4BoASshREk-2526r-253DAQ0GBw0jN0YsxXpbOoM-2DtQ-2526m-253DYcOJDRQ1D9o8a7bu7m8-2D3xYcD6G6rcJYTW1MA8xDD-5FY-2526s-253D2jXNXhDGhKLmbChpPDz8nDXYof4-2DMxMl30czWaYT3xU-2526e-253D%26d%3DDwMFAg%26c%3D27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk%26r%3DAQ0GBw0jN0YsxXpbOoM-tQ%26m%3D3Nv61Vuo-iNbXy_YMkpRegaT5pP5ia_Z1BzvL4HQhKM%26s%3DRYNGJvAwoxd1Ndhg-wdMrpTQF2-FjTYyivpH3NEgtTE%26e%3D