Hi all,
I am getting an error that seems common for people running LGI where it crashes due to a topological defect.
I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good.
Any advice on any other steps I can take? I have already tried rerunning recon-all.
Thank you! Tara
Hi Tara,
Did you try to run the recon-all with the randomness flag? If you don't add this flag, your surfaces will not change much with the new recon-all and you'll probably get the same problem again when running LGI.
Let me know if you still have trouble,
Marie
On Aug 22, 2014, at 7:07 PM, Tara Miskovich miskovi2@uwm.edu wrote:
Hi all,
I am getting an error that seems common for people running LGI where it crashes due to a topological defect.
I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good.
Any advice on any other steps I can take? I have already tried rerunning recon-all.
Thank you! Tara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
Hi all, I have a question about hemispheric asymmetry analyses. The example given in the wiki shows how to compare lh and rh using a paired t-test. Is it right? But how can I calculate (and then compare groups) the laterality index (L-R)/(L+R)? Thank you very much for any help
Angela
You can use --paired-diff-norm instead of --paired-diff, this will compute
(L-R)/((L+R)/2)
You can then divide the output by 2, eg,
fscalc output.mgh div 2 -o output.div2.mgh
doug
On 8/24/14 9:52 AM, angela.favaro@unipd.it wrote:
Hi all, I have a question about hemispheric asymmetry analyses. The example given in the wiki shows how to compare lh and rh using a paired t-test. Is it right? But how can I calculate (and then compare groups) the laterality index (L-R)/(L+R)? Thank you very much for any help
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thank you! Angela
You can use --paired-diff-norm instead of --paired-diff, this will compute
(L-R)/((L+R)/2)
You can then divide the output by 2, eg,
fscalc output.mgh div 2 -o output.div2.mgh
doug
On 8/24/14 9:52 AM, angela.favaro@unipd.it wrote:
Hi all, I have a question about hemispheric asymmetry analyses. The example given in the wiki shows how to compare lh and rh using a paired t-test. Is it right? But how can I calculate (and then compare groups) the laterality index (L-R)/(L+R)? Thank you very much for any help
Angela
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.
Hi Doug, is there a way to perform asymmetry analyses for local gyrification index? In my xhemi folders there is no LGI surface.
thank you Angela
You can use --paired-diff-norm instead of --paired-diff, this will compute
(L-R)/((L+R)/2)
You can then divide the output by 2, eg,
fscalc output.mgh div 2 -o output.div2.mgh
doug
On 8/24/14 9:52 AM, angela.favaro@unipd.it wrote:
Hi all, I have a question about hemispheric asymmetry analyses. The example given in the wiki shows how to compare lh and rh using a paired t-test. Is it right? But how can I calculate (and then compare groups) the laterality index (L-R)/(L+R)? Thank you very much for any help
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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You can copy the rh gyrification index to xhemi/surf/lh gyrification index, ie, copy it to xhemi/surf, but change the name so that it appears to be lh instead of rh doug
On 8/27/14 5:47 AM, angela.favaro@unipd.it wrote:
Hi Doug, is there a way to perform asymmetry analyses for local gyrification index? In my xhemi folders there is no LGI surface.
thank you Angela
You can use --paired-diff-norm instead of --paired-diff, this will compute
(L-R)/((L+R)/2)
You can then divide the output by 2, eg,
fscalc output.mgh div 2 -o output.div2.mgh
doug
On 8/24/14 9:52 AM, angela.favaro@unipd.it wrote:
Hi all, I have a question about hemispheric asymmetry analyses. The example given in the wiki shows how to compare lh and rh using a paired t-test. Is it right? But how can I calculate (and then compare groups) the laterality index (L-R)/(L+R)? Thank you very much for any help
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2.0 abs
printf: 2.0: not completely converted ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean? I am using a MacOSX 10.6.8 thank you for your help
Angela
Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
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.
I think this has something to do with the unix LOCALE because it is interpreting the "2.0" as "2,0" using the comma "," instead of the "." I actually don't know how to fix this. If you run
echo $LANG
does it return
en_US.UTF-8
if not, as a test, try setenv LANG en_US.UTF-8
Then run mri_glmfit-sim
doug
On 8/24/14 1:00 PM, angela.favaro@unipd.it wrote:
Hi Doug, already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2.0 abs
printf: 2.0: not completely converted ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean? I am using a MacOSX 10.6.8 thank you for your help
Angela
Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
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.
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thank you! that solved my problem!
I think this has something to do with the unix LOCALE because it is interpreting the "2.0" as "2,0" using the comma "," instead of the "." I actually don't know how to fix this. If you run
echo $LANG
does it return
en_US.UTF-8
if not, as a test, try setenv LANG en_US.UTF-8
Then run mri_glmfit-sim
doug
On 8/24/14 1:00 PM, angela.favaro@unipd.it wrote:
Hi Doug, already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2.0 abs
printf: 2.0: not completely converted ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean? I am using a MacOSX 10.6.8 thank you for your help
Angela
Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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HI all, I have another problem with mri_glmfit-sim. It looks for something that is not available in my FS (see below the error message) How can I solve this problem? thank you! Angela
mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces cmdline mri_glmfit --y /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/y.mgh --fsgd /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/qdec.fsgd dods --glmdir /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled --surf fsaverage lh --label /Users/angelafavaro/Desktop/risonanze/studyfree/fsaverage/label/lh.aparc.label --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Diff-1-3-Intercept-pial_lgi.mat SURFACE: fsaverage lh log file is qdec/Untitled/cache.mri_glmfit-sim.log
cd /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Mon Sep 1 12:00:58 CEST 2014 Darwin MacBook-Pro-di-Angela-Favaro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 angelafavaro setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/y.mgh --fsgd /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/qdec.fsgd dods --glmdir /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled --surf fsaverage lh --label /Users/angelafavaro/Desktop/risonanze/studyfree/fsaverage/label/lh.aparc.label --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Diff-1-3-Intercept-pial_lgi.mat
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 37.845465 ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm38/abs/th13/mc-z.csd
I think this has something to do with the unix LOCALE because it is interpreting the "2.0" as "2,0" using the comma "," instead of the "." I actually don't know how to fix this. If you run
echo $LANG
does it return
en_US.UTF-8
if not, as a test, try setenv LANG en_US.UTF-8
Then run mri_glmfit-sim
doug
On 8/24/14 1:00 PM, angela.favaro@unipd.it wrote:
Hi Doug, already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2.0 abs
printf: 2.0: not completely converted ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean? I am using a MacOSX 10.6.8 thank you for your help
Angela
Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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.
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The final FWHM is larger than the maximum that the correction has been computed for. This often happens with lGI because lGI naturally has a large amount of spatial correlation. Did you smooth it prior to running mri_glmfit? If so, try it without smoothing.
doug
On 9/2/14 11:47 AM, angela.favaro@unipd.it wrote:
HI all, I have another problem with mri_glmfit-sim. It looks for something that is not available in my FS (see below the error message) How can I solve this problem? thank you! Angela
mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces cmdline mri_glmfit --y /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/y.mgh --fsgd /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/qdec.fsgd dods --glmdir /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled --surf fsaverage lh --label /Users/angelafavaro/Desktop/risonanze/studyfree/fsaverage/label/lh.aparc.label --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Diff-1-3-Intercept-pial_lgi.mat SURFACE: fsaverage lh log file is qdec/Untitled/cache.mri_glmfit-sim.log
cd /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/mri_glmfit-sim --glmdir qdec/Untitled --cwpvalthresh .05 --cache 1.3 abs --2spaces
$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $ Mon Sep 1 12:00:58 CEST 2014 Darwin MacBook-Pro-di-Angela-Favaro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 angelafavaro setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree FREESURFER_HOME /Applications/freesurfer
Original mri_glmfit command line: cmdline mri_glmfit --y /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/y.mgh --fsgd /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/qdec.fsgd dods --glmdir /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled --surf fsaverage lh --label /Users/angelafavaro/Desktop/risonanze/studyfree/fsaverage/label/lh.aparc.label --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Avg-Intercept-pial_lgi.mat --C /Users/angelafavaro/Desktop/risonanze/studyfree/qdec/Untitled/contrasts/lh-Diff-1-3-Intercept-pial_lgi.mat
DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 37.845465 ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm38/abs/th13/mc-z.csd
I think this has something to do with the unix LOCALE because it is interpreting the "2.0" as "2,0" using the comma "," instead of the "." I actually don't know how to fix this. If you run
echo $LANG
does it return
en_US.UTF-8
if not, as a test, try setenv LANG en_US.UTF-8
Then run mri_glmfit-sim
doug
On 8/24/14 1:00 PM, angela.favaro@unipd.it wrote:
Hi Doug, already done!
mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2.0 abs
printf: 2.0: not completely converted ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
what does it mean? I am using a MacOSX 10.6.8 thank you for your help
Angela
Try using --cache 2.0 abs
On 8/24/14 9:41 AM, angela.favaro@unipd.it wrote:
Hi all, I am having a problem with mri_glmfit-sim:
my command was: mri_glmfit-sim --glmdir glm.lh.lh-rh.thickness.sm10 --cwpvalthresh .5 --cache 2 abs
and this is the only output:
ERROR: thresh = 2,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
I am not able to understand which is the source of this error. Can somebody help me?
thank you
Angela
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Dear all, Is there a way to visualize brains in QDEC (or tksurfer or freeview) with a white background? thank you for any help
Angela
Hi Angela,
sorry, I'm afraid not, although it is a pretty common request, so maybe Ruopeng can add it to freeview Bruce
On Sat, 6 Sep 2014, angela.favaro@unipd.it wrote:
Dear all, Is there a way to visualize brains in QDEC (or tksurfer or freeview) with a white background? thank you for any help
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can set background color in freeview from Preferences.
Ruopeng
On Sep 6, 2014, at 9:57 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Angela,
sorry, I'm afraid not, although it is a pretty common request, so maybe Ruopeng can add it to freeview Bruce
On Sat, 6 Sep 2014, angela.favaro@unipd.it wrote:
Dear all, Is there a way to visualize brains in QDEC (or tksurfer or freeview) with a white background? thank you for any help
Angela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Tara try: recon-all -s <subject> -randomness -all
Jon
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Tara Miskovich miskovi2@uwm.edu Sent: Friday, August 22, 2014 12:07 PM To: Freesurfer support list Subject: [Freesurfer] LGI Topological Defect
Hi all,
I am getting an error that seems common for people running LGI where it crashes due to a topological defect.
I have run mris_euler_number and everything looks fine. Plus, I went through each slice and made sure the surfaces looked good.
Any advice on any other steps I can take? I have already tried rerunning recon-all.
Thank you! Tara
freesurfer@nmr.mgh.harvard.edu
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angela.favaro＠unipd.it -
Bruce Fischl -
Douglas Greve -
Jon Alan Wieser -
Marie Schaer -
Ruopeng Wang -
Tara Miskovich