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

 

 

 

 

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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

 

 

 

Try making it executable with
chmod a+x $FREESURFER/bin/mri_glmfit-sim

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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:

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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 <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
Subject: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat

 

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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

 

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