Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview? Thanks. All the best. Rujing Zha
the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote:
Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview? Thanks. All the best. Rujing Zha
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug, sig.mgh is my result for two group t-test on pial thickness of whole brain. So I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex by vertex. Thanks. All the best. Rujing Zha 2014-03-12
charujing123
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2014-03-12 00:16 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote:
Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview? Thanks. All the best. Rujing Zha
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/
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But what is in rh.ttest.thickness.10.mgh? Is it a stack of all your subjects (the file you passed with --y to mri_glmfit)? If so, then add "-t rh.ttest.thickness.10.mgh" to your tksurfer command line. Ruopeng just added something to freeview to do it, but you'd have to get a new version
doug
On 3/11/14 9:46 PM, charujing123 wrote:
Hi doug, sig.mgh is my result for two group t-test on pial thickness of whole brain. So I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex by vertex. Thanks. All the best. Rujing Zha 2014-03-12
charujing123
*???:*Douglas N Greve greve@nmr.mgh.harvard.edu *????:*2014-03-12 00:16 *??:*Re: [Freesurfer] view time course in freeview *???:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *??:* the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote:
Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview?
Thanks. All the best. Rujing Zha
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 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
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Hi doug, Thanks very much doug. rh.ttest.thickness.10.mgh is created from the mris_preproc to merge all the subjects' thickness into one file. Then group t-test can be done. I try tksurfer -t rh.ttest.thickness.10.mgh, but the command window echoes its usage. Just as you told me freeview has a new version to see time course for this file. I wonder where I can download it. Thanks doug, All the best. Rujing Zha
2014-03-13
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-03-12 22:57 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
But what is in rh.ttest.thickness.10.mgh? Is it a stack of all your subjects (the file you passed with --y to mri_glmfit)? If so, then add "-t rh.ttest.thickness.10.mgh" to your tksurfer command line. Ruopeng just added something to freeview to do it, but you'd have to get a new version
doug
On 3/11/14 9:46 PM, charujing123 wrote:
Hi doug, sig.mgh is my result for two group t-test on pial thickness of whole brain. So I want to see the time course of thickness of rh.ttest.thickness.10.mgh vertex by vertex. Thanks. All the best. Rujing Zha 2014-03-12
charujing123
发件人：Douglas N Greve greve@nmr.mgh.harvard.edu 发送时间：2014-03-12 00:16 主题：Re: [Freesurfer] view time course in freeview 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
the time course of what? On 03/11/2014 07:18 AM, charujing123 wrote:
Hi FS experts, For the sig.mgh, can I see the time course vertex by vertex in freeview? Thanks. All the best. Rujing Zha
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/
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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
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
I typed 1.3 but it is still not working.
Any other ideas???
Thanks for your help.
DH
Date: Thu, 13 Mar 2014 12:20:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
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
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.
are you puttting it in quotes? If so, don't doug
On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
Dear Doug,
I typed 1.3 but it is still not working.
Any other ideas???
Thanks for your help.
DH
Date: Thu, 13 Mar 2014 12:20:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding
values from Qdec
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
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
The information in this e-mail is intended only for the person to
whom it is
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the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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Dear Doug, no, I did not put it in quotes. I just typed the mentioned command, but it is still not working. I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation. Sorry for asking so many questions, but it is still not working. What should I do next? Best regards, DH
Date: Thu, 13 Mar 2014 15:15:23 -0400 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec
are you puttting it in quotes? If so, don't doug
On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
Dear Doug,
I typed 1.3 but it is still not working.
Any other ideas???
Thanks for your help.
DH
Date: Thu, 13 Mar 2014 12:20:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding
values from Qdec
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
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
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.
-- 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/
I think Doug meant the 1.3. Therefore the line should be something like:
mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg
What exactly did you type? (try separating it with lines instead of quotes)
HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote:
Dear Doug,
no, I did not put it in quotes. I just typed the mentioned command, but it is still not working. I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation. Sorry for asking so many questions, but it is still not working. What should I do next?
Best regards,
DH
Date: Thu, 13 Mar 2014 15:15:23 -0400 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec
are you puttting it in quotes? If so, don't doug
On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
Dear Doug,
I typed 1.3 but it is still not working.
Any other ideas???
Thanks for your help.
DH
Date: Thu, 13 Mar 2014 12:20:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding
values from Qdec
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
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
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.
-- 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
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.
I did type the same line es mentioned in your Email and I did not put the 1.3 in quotes.
However, it is still not working:-( Any other ideas???
Thanks.
DH
Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec From: dgwakeman@gmail.com Date: Thu, 13 Mar 2014 18:28:32 -0400 CC: greve@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
I think Doug meant the 1.3. Therefore the line should be something like:
mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg
What exactly did you type? (try separating it with lines instead of quotes)
HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote:
Dear Doug,
no, I did not put it in quotes. I just typed the mentioned command, but it is still not working. I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation. Sorry for asking so many questions, but it is still not working. What should I do next?
Best regards,
DH
Date: Thu, 13 Mar 2014 15:15:23 -0400 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec
are you puttting it in quotes? If so, don't doug
On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
Dear Doug,
I typed 1.3 but it is still not working.
Any other ideas???
Thanks for your help.
DH
Date: Thu, 13 Mar 2014 12:20:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding
values from Qdec
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster.
I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache "1,3" --sim-sign neg"
However, I got the ERROR: thresh = 1.3 not completely converted
What am I doing wrong? Any other ideas?
Is the pdf.dat file the right one to use???
Thanks!
DH
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
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.
-- 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
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.
Run it with --debug as the first option and send me the terminal output doug
On 3/14/14 3:44 AM, Dusan Hirjak wrote:
I did type the same line es mentioned in your Email and I did not put the 1.3 in quotes. However, it is still not working:-( Any other ideas???
Thanks.
DH
Subject: Re: [Freesurfer] Extracting thickness, area and folding
values from Qdec
From: dgwakeman@gmail.com Date: Thu, 13 Mar 2014 18:28:32 -0400 CC: greve@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com
I think Doug meant the 1.3. Therefore the line should be something like:
mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg
What exactly did you type? (try separating it with lines instead of
quotes)
HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote:
Dear Doug,
no, I did not put it in quotes. I just typed the mentioned
command, but it is still not working.
I can not find the file comprising the thickness, area or folding
values at peak maxima after Monte Carlo simulation.
Sorry for asking so many questions, but it is still not working. What should I do next?
Best regards,
DH
Date: Thu, 13 Mar 2014 15:15:23 -0400 From: greve@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding
values from Qdec
are you puttting it in quotes? If so, don't doug
On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
Dear Doug,
I typed 1.3 but it is still not working.
Any other ideas???
Thanks for your help.
DH
Date: Thu, 13 Mar 2014 12:20:57 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and
folding
values from Qdec
Use 1.3 not 1,3
doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: > Dear Freesurfer Experts, > > I did a correlational analysis in qdec and found several
significant
> clusters after Monte-Carlo simulation (0.05). > Now, I would like to extract the mean cortical thickness,
area and
> folding values (peak maximum) of each study subject above the > significant cluster. > > I tried to run "mri_glmfit-sim --glmdir
mc-z.neg.th13.pdf.dat --cache
> "1,3" --sim-sign neg" > > However, I got the ERROR: thresh = 1.3 not completely
converted
> > What am I doing wrong? Any other ideas? > > Is the pdf.dat file the right one to use??? > > Thanks! > > DH > > > > _______________________________________________ > 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
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-- 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/
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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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charujing123 -
dgw -
Douglas Greve -
Douglas N Greve
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Dusan Hirjak