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.edu 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.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.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Na, Xiaoxu *Sent:* Tuesday, January 26, 2021 11:44 AM *To:* freesurfer@nmr.mgh.harvard.edu <mailto: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.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1QXsCNNhFh-brzaSzrnEamNpivI0Re19RGx6G6Pz4_Op9HZvOFtXm0uZq4uIq0Ou3oilQGEQGR24qDidwNgmf3pw5mzlWRoAYx5Nt-3chsypA3aeWoYIOPb1Cfa_39n43048YT3O1YnJIFNwfwwHPRlHhUP7hlNdvD0oy1iFaWlr-cBV4GO3qCsTxpLpQPx48HR8rIGKWq_YKmqKmUhYvYvHl7G79wa_0iQSgSmXl_vcuX27JCj4u5jFralxilx6C0XG9hdpAB-4QAGg9cGBW0Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer%26d%3DDwMD-g%26c%3D27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk%26r%3DAQ0GBw0jN0YsxXpbOoM-tQ%26m%3D4Eo1ALvsVtjqO7fGNobj1xKwfESo-W1SEAGN3n3R8Z0%26s%3DKD108hEcj1K5YPOiXoc2jhCZDIeF18F0qWdIq8Wrq8Y%26e%3D>
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