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.
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 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
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.
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 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
* 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.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
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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>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
From: freesurfer-bounces@nmr.mgh.harvard.edu 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.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
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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 $FREESURFER/bin To run, add --spatial-sum to the command line On 1/26/2021 12:56 PM, Na, Xiaoxu wrote:
External Email - Use Caution To make it clear, I would like to extract the area of each subject in the cluster. May I know if this is the correct way? If not, it's appreciated if you would point it out. Thanks!
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Na, Xiaoxu Sent: Tuesday, January 26, 2021 11:44 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution Dear Freesurfer Experts,
As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers?
Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot!
ClusterNo
Max
VtxMax
Size(mm^2)
MNIX
MNIY
MNIZ
CWP
CWPLow
CWPHi
NVtxs
WghtVtx
1
-4.8321
40067
444.11
-58.1
-16.6
-23.9
0.0002
0
0.0004
670
-2784.11
Regards, Xiaoxu
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Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated:
/xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum// //cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir// //SURFACE: fsaverage rh// //Unmatched `./
Even if I run --help, only some of the lines appear:
/mri_glmfit-sim --help// // // --glmdir glmdir// // --cwp cwthresh : cluster-wise p-value threshold (.05)// // //Use pre-computed z-based monte-carlo simulations (see mri_mcsim)// // --mczsim vwthreshold sign// //If you have run your own simulations (mri_mcsim), then specify // // --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor// // --mczsim-label label : default is cortex// // //Use permutation simulation// // --perm nsim CFT sign : permutation simulation with nsim iterations// //Unmatched ".// /
Do you have any idea why this might be? Like Xiaoxu before me, I have already tried to convert the file with dos2unix. However, without the desired effect.
I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.
I would be very grateful for any tips.
Best regards
sven
I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sven Kühn Sent: Sunday, February 4, 2024 12:09 PM To: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution
Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated:
xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir SURFACE: fsaverage rh Unmatched `.
Even if I run --help, only some of the lines appear:
mri_glmfit-sim --help
--glmdir glmdir --cwp cwthresh : cluster-wise p-value threshold (.05)
Use pre-computed z-based monte-carlo simulations (see mri_mcsim) --mczsim vwthreshold sign If you have run your own simulations (mri_mcsim), then specify --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor --mczsim-label label : default is cortex
Use permutation simulation --perm nsim CFT sign : permutation simulation with nsim iterations Unmatched ".
Do you have any idea why this might be? Like Xiaoxu before me, I have already tried to convert the file with dos2unix. However, without the desired effect.
I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.
I would be very grateful for any tips.
Best regards
sven
External Email - Use Caution
Many thanks for the answer! Sorry, there seems to be some context missing. I was replying to an old post from the archives and thought it would attach itself there. I copied the script for mri_glmfit-sim from that post. Here is the link to it:
https://secure-web.cisco.com/15BtKLUwfY0w8EfmB_-A7ZDaRheinuB5VHF9HK_Z18GRANE...
I think the mistake is that I didn't convert it into a script properly. Could you perhaps provide me with the script as a file? I would like to get the volume of each subject from the ocn.dat by adding --spatial-sum to the command line. Exactly as described in the post.
Best
Sven
Am 06.02.24 um 15:16 schrieb Huang, Yujing:
I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints.
Best,
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu *On Behalf Of *Sven Kühn *Sent:* Sunday, February 4, 2024 12:09 PM *To:* Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
* External Email - Use Caution *
Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated:
/xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir SURFACE: fsaverage rh Unmatched `./
Even if I run --help, only some of the lines appear:
/mri_glmfit-sim --help
--glmdir glmdir --cwp cwthresh : cluster-wise p-value threshold (.05)
Use pre-computed z-based monte-carlo simulations (see mri_mcsim) --mczsim vwthreshold sign If you have run your own simulations (mri_mcsim), then specify --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor --mczsim-label label : default is cortex
Use permutation simulation --perm nsim CFT sign : permutation simulation with nsim iterations Unmatched "./
Do you have any idea why this might be? Like Xiaoxu before me, I have already tried to convert the file with dos2unix. However, without the desired effect.
I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.
I would be very grateful for any tips.
Best regards
sven
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dOpF92NtrTpxumyDbAlH8IN1EBeFBZrxV_obr2KSDtkHnx... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1EYZzzWWmgh3TVmqWgTDozSTTXs8FNuPvTMSrbRc7cLIAGW... https://secure-web.cisco.com/1EYZzzWWmgh3TVmqWgTDozSTTXs8FNuPvTMSrbRc7cLIAGWR_mfoBX1FZX2Zoxru0z8d1195za8JcdynO5g7Fo1wxptjBxg2NLFSAn6pcJ-pnuru3VhMXJU98rA3Vd1SP1VP6Z7_14gtytrVa0B_vgG4VyRYS-BI8-EBeGMH8sDcvelrt0M_CK-6GMJQVvPTBftTqUIWAv9daYyNoZSXvcaiVIaLK-VVWORCMdTY7xozFECDJbQ4aoOVwzDcmQAwiQVc-NP4BEZXA77CJz0UJk4KpNZIWeP4_3azckePccY2oQ0VLL1G87uwIJMWyt7X-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
I see the problem.
In ‘usage_exit:’ section, you will notice several echo statements are split into two lines. Fix those lines and try again. ‘“tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help” will help you identify those lines.
Best,
Yujing
From: Sven Kühn svkuehn@gmx.de Sent: Saturday, February 10, 2024 5:09 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Huang, Yujing YHUANG43@mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution
Many thanks for the answer! Sorry, there seems to be some context missing. I was replying to an old post from the archives and thought it would attach itself there. I copied the script for mri_glmfit-sim from that post. Here is the link to it:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg68973.htmlhttps://secure-web.cisco.com/1C0tWp9a2AtgW6pz_K_YQQcl2gRLBm9YoGcFQf6OVnEWfU4xw_g9pNGtHahFmsjDHViYZcmLpx46sC-hnSXa_-HO_SWPh8Rn69JL37CIR4BjCC2U3i4xsmKBMaXA4_fmUDv9NRW_O_bKJKzfaVrQC37KFNK6gZM67pA5BkW2Ex3X4Q5zL3-hcBKuwPldhBY6uZ4u0mS_5yi_DNx3l0Te4GrqRDFTtFiqWBLEESSTbjtSiQQqKooQRy9pyYoJ61tWb3JVMXq7WAbovDlQzXcpt-kYgTcG3RPZ3ywYqskFJEZhEebype-G7ouR1yX1s4lLa/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68973.html
I think the mistake is that I didn't convert it into a script properly. Could you perhaps provide me with the script as a file? I would like to get the volume of each subject from the ocn.dat by adding --spatial-sum to the command line. Exactly as described in the post.
Best
Sven
Am 06.02.24 um 15:16 schrieb Huang, Yujing: I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Sven Kühn Sent: Sunday, February 4, 2024 12:09 PM To: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
External Email - Use Caution
Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated:
xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir SURFACE: fsaverage rh Unmatched `.
Even if I run --help, only some of the lines appear:
mri_glmfit-sim --help
--glmdir glmdir --cwp cwthresh : cluster-wise p-value threshold (.05)
Use pre-computed z-based monte-carlo simulations (see mri_mcsim) --mczsim vwthreshold sign If you have run your own simulations (mri_mcsim), then specify --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor --mczsim-label label : default is cortex
Use permutation simulation --perm nsim CFT sign : permutation simulation with nsim iterations Unmatched ".
Do you have any idea why this might be? Like Xiaoxu before me, I have already tried to convert the file with dos2unix. However, without the desired effect.
I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.
I would be very grateful for any tips.
Best regards
sven
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Thank you very much! Everything went well. I went through the script and was able to find some lines that were split. After I found them all, everything worked.
Thanks again!
Am 14.02.24 um 21:56 schrieb Huang, Yujing:
I see the problem.
In ‘usage_exit:’ section, you will notice several echo statements are split into two lines. Fix those lines and try again. ‘“tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help” will help you identify those lines.
Best,
Yujing
*From:* Sven Kühn svkuehn@gmx.de *Sent:* Saturday, February 10, 2024 5:09 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu; Huang, Yujing YHUANG43@mgh.harvard.edu *Subject:* Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat
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Many thanks for the answer! Sorry, there seems to be some context missing. I was replying to an old post from the archives and thought it would attach itself there. I copied the script for mri_glmfit-sim from that post. Here is the link to it:
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I think the mistake is that I didn't convert it into a script properly. Could you perhaps provide me with the script as a file? I would like to get the volume of each subject from the ocn.dat by adding --spatial-sum to the command line. Exactly as described in the post.
Best
Sven
Am 06.02.24 um 15:16 schrieb Huang, Yujing:
I can’t reproduce the error here with FS 6.0. Not sure where you downloaded the script. Can you run this “tcsh -x $FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give some hints. Best, Yujing *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Sven Kühn *Sent:* Sunday, February 4, 2024 12:09 PM *To:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> <mailto:DGREVE@mgh.harvard.edu>; freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* Re: [Freesurfer] Unit of the Numbers in cache.th40.neg.y.ocn.dat * External Email - Use Caution * Hi Dr. Greve, hi all I have tried your code. I copied it from the website into a text file and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is executable but aborts after a few lines with no indication of a cause. The following output is generated: /xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir rh.volume.DCS.10.glmdir SURFACE: fsaverage rh Unmatched `./ Even if I run --help, only some of the lines appear: /mri_glmfit-sim --help --glmdir glmdir --cwp cwthresh : cluster-wise p-value threshold (.05) Use pre-computed z-based monte-carlo simulations (see mri_mcsim) --mczsim vwthreshold sign If you have run your own simulations (mri_mcsim), then specify --mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor --mczsim-label label : default is cortex Use permutation simulation --perm nsim CFT sign : permutation simulation with nsim iterations Unmatched "./ Do you have any idea why this might be? Like Xiaoxu before me, I have already tried to convert the file with dos2unix. However, without the desired effect. I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0. I would be very grateful for any tips. 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Douglas N. Greve -
Huang, Yujing -
Na, Xiaoxu -
Sven Kühn