Dear Bruce,
The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right?
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
no, not necessarily. The blue area is just the suprathreshold region. Are the numbers reported in the overlay reasonable? You can email us the sig.mgh and we'll take a look if you want (email us the label also)
On Wed, 18 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce,
The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right?
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you.
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，上午3:50，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
no, not necessarily. The blue area is just the suprathreshold region. Are the numbers reported in the overlay reasonable? You can email us the sig.mgh and we'll take a look if you want (email us the label also)
On Wed, 18 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce,
The overlay was sig.mgh,which was the result of thickness between patient and control. The line must be within the area of blue, right?
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug.
cheers Bruce
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you.
Dear Bruce,
I creat the file of label according to the manual of free surfer. The website was http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File --> Save Label.
Thank you very much.
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，下午9:45，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug.
cheers Bruce
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you.
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
using tksurfer? On what fsaverage?
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File --> Save Label.
Thank you very much.
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，下午9:45，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce
No, I used QDEC to create label. It should be fsaverage.
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，下午10:00，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
using tksurfer? On what fsaverage?
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview.
(1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File --> Save Label. Thank you very much.
Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce
I used QDEC to create the label. It should be fsaverage.
Thank you
2014-06-19 22:04 GMT+08:00 wangkangcheng_gmail kangchengwang0808@gmail.com :
Dear Bruce
No, I used QDEC to create label. It should be fsaverage.
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，下午10:00，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
using tksurfer? On what fsaverage?
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas
http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview.
(1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File --> Save Label. Thank you very much.
Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing,
400715,P.R.China
在 2014年6月19日，下午9:45，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi all, I am analyzing functional data using fsfast 5.3 with the error: Error using==> basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.h...), but I can't find answer in the discussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue
what is your command line and terminal output
On 6/19/14 4:36 PM, Xiaomin Yue wrote:
Hi all,
I am analyzing functional data using fsfast 5.3 with the error: Error using==> basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.h...), but I can't find answer in the discussion thread in the above link.
Any suggestions? Thanks,
Xiaomin Yue
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug Thanks for you response. The command line is: selxavg3-sess -s subject_0101 -d . -analysis DoD_looming_lh. I checked the basename function in the matlab installed in my computer, which is 2010b. It seems that the basename in the 2010b matlab only accepts one parameter. I tried two ways to avoid the problem. First, I replaced the matlab's basename function with my own basename function. Second, I removed the motion regressor from the analysis.info. The two method indeed avoided the basename function error, but new errors were created as the following: Error using ==> fmri_hemodynToo many input argument. Error in ==> flac_ev2irf at 74xirf = fmri_hemodync(tirf, delay, tau, alpha); Error in ==> flac_desmat at 66[xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur); Error in ==> flac_customize at 356flacnew = flac_desmat(flacnew); Error in ==> fast_selxavg3 at 65flac0=flac_customize(flac0);
I suspected that the errors was caused by matlab? if so, what version is required to run 5.3 version correctly?
Thanks for your help! Xiaomin Date: Thu, 19 Jun 2014 20:41:28 +0200 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Basename error
what is your command line and terminal output
On 6/19/14 4:36 PM, Xiaomin Yue wrote:
Hi all,
I am analyzing functional data using fsfast 5.3 with the error: Error using==> basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.h...), but I can't find answer in the discussion thread in the above link.
Any suggestions? Thanks,
Xiaomin Yue
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
If it is not using the basename.m in freesurfer it may fail. Try putting $FREESURFER_HOME/fsfast/toolbox first in your matlab path
On 06/22/2014 02:52 PM, Xiaomin Yue wrote:
Hi Doug
Thanks for you response. The command line is: selxavg3-sess -s subject_0101 -d . -analysis DoD_looming_lh.
I checked the basename function in the matlab installed in my computer, which is 2010b. It seems that the basename in the 2010b matlab only accepts one parameter. I tried two ways to avoid the problem. First, I replaced the matlab's basename function with my own basename function. Second, I removed the motion regressor from the analysis.info. The two method indeed avoided the basename function error, but new errors were created as the following:
Error using ==> fmri_hemodyn Too many input argument.
Error in ==> flac_ev2irf at 74 xirf = fmri_hemodync(tirf, delay, tau, alpha);
Error in ==> flac_desmat at 66 [xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur);
Error in ==> flac_customize at 356 flacnew = flac_desmat(flacnew);
Error in ==> fast_selxavg3 at 65 flac0=flac_customize(flac0);
I suspected that the errors was caused by matlab? if so, what version is required to run 5.3 version correctly?
Thanks for your help!
Xiaomin
Date: Thu, 19 Jun 2014 20:41:28 +0200 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Basename error
what is your command line and terminal output
On 6/19/14 4:36 PM, Xiaomin Yue wrote:
Hi all, I am analyzing functional data using fsfast 5.3 with the error: Error using==> basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html), but I can't find answer in the discussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks very much for the information. I will try it. XIaomin
Date: Mon, 23 Jun 2014 09:19:20 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Basename error
If it is not using the basename.m in freesurfer it may fail. Try putting $FREESURFER_HOME/fsfast/toolbox first in your matlab path
On 06/22/2014 02:52 PM, Xiaomin Yue wrote:
Hi Doug
Thanks for you response. The command line is: selxavg3-sess -s subject_0101 -d . -analysis DoD_looming_lh.
I checked the basename function in the matlab installed in my computer, which is 2010b. It seems that the basename in the 2010b matlab only accepts one parameter. I tried two ways to avoid the problem. First, I replaced the matlab's basename function with my own basename function. Second, I removed the motion regressor from the analysis.info. The two method indeed avoided the basename function error, but new errors were created as the following:
Error using ==> fmri_hemodyn Too many input argument.
Error in ==> flac_ev2irf at 74 xirf = fmri_hemodync(tirf, delay, tau, alpha);
Error in ==> flac_desmat at 66 [xirf tirf] = flac_ev2irf(ev, TER, flac, RefEventDur);
Error in ==> flac_customize at 356 flacnew = flac_desmat(flacnew);
Error in ==> fast_selxavg3 at 65 flac0=flac_customize(flac0);
I suspected that the errors was caused by matlab? if so, what version is required to run 5.3 version correctly?
Thanks for your help!
Xiaomin
Date: Thu, 19 Jun 2014 20:41:28 +0200 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Basename error
what is your command line and terminal output
On 6/19/14 4:36 PM, Xiaomin Yue wrote:
Hi all, I am analyzing functional data using fsfast 5.3 with the error: Error using==> basename. It seems that the same problem was reported before in the mail list (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021898.html), but I can't find answer in the discussion thread in the above link. Any suggestions? Thanks, Xiaomin Yue _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce
No, I used QDEC to create label. It should be fsaverage.
Wang Kangcheng
Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
在 2014年6月19日，下午10:00，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
using tksurfer? On what fsaverage?
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview.
(1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File --> Save Label. Thank you very much.
Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fischl@nmr.mgh.harvard.edu 写道：
hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug.
cheers Bruce
On Thu, 19 Jun 2014, wangkangcheng_gmail wrote:
I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you.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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas Greve -
Douglas N Greve
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wangkangcheng_gmail -
Xiaomin Yue -
王康程