[Freesurfer] MNIX/Y/Z coordinates in mri_glmfit-sim .summary file
Hi list, I noticed that, while the wiki refers to Talairach coordinates named TalX/Y/Z (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary), the header in my .summary files reads something like: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLowCWPHi NVtxs Annot could someone confirm what atlas space the MINX/MINY/MNIZ coordinates are in? Is it Talairach, MNI152 or something else? Thanks in advance, Nicola ___ 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] Hyppocampal subfields v 6.0 on segmentations with prior versions
Hi List, quick question - can I run the new HyppoSubfields module (v.6.0) on the subject dirs produced by FS 5.3 and/or FS5.1? Or do I need to "re-recon-all" all using FS 6.0 beforehand? Thanks in advance, Nicola ___ 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] Error with mri_glmfit_sim (dev version f)
Hi List, I am getting a couple of strange error when running a 3-group F-test. WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin WARNING: 251446 NaNs found in volume analysis/Ftest/cache.th20.pos.sig.cluster.mgh... And as a result, I consistently get huge clusters: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLowCWPHi NVtxsWghtVtx Annot 1 inf 0 63247.45-38.8 -19.0 66.9 0.00010 0.0 0.00020 98722 inf precentral However, this doesn't happen when running t-tests on the same data. Still, I think my F-contrast is correct (see below). Thanks in advance for any advice! Nicola PS: my F-contrast looks like this: 1 -1 0 0 0 0 1 0 -1 0 0 0 and my design matrix looks like this: 0 0 1 1 179 110 0 0 1 1 193 103 0 0 1 1 176 108 0 0 1 1 198 94 0 1 0 1 186 87 0 1 0 1 217 83 . and my versions are # $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $ # $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $ ___ 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.
Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi,
here it is (I also pasted the mri_glmfit line):
/odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory//
//
//mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \//
//--C ${C1} \//
//--glmdir ${odir} --surf fsaverage ${h} ${surf}//
//
//*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir} --cache
${t} pos*//*
*/
Note: it is the same code i use for the t-tests, which appear to work fine.
The content of the file ${C1} is
1 -1 0 0 0 0
1 0 -1 0 0 0
Thanks in advance!
Nicola
On 7/21/2016 5:38 PM, Douglas N Greve wrote:
what is your mri_glmfit-sim command line?
On 07/20/2016 05:56 PM, Nicola Toschi wrote:
Hi List,
I am getting a couple of strange error when running a 3-group F-test.
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
WARNING: 251446 NaNs found in volume
analysis/Ftest/cache.th20.pos.sig.cluster.mgh...
And as a result, I consistently get huge clusters:
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
CWPLowCWPHi NVtxsWghtVtx Annot
1 inf 0 63247.45-38.8 -19.0 66.9 0.00010
0.0 0.00020 98722 inf precentral
However, this doesn't happen when running t-tests on the same data.
Still, I think my F-contrast is correct (see below).
Thanks in advance for any advice!
Nicola
PS:
my F-contrast looks like this:
1 -1 0 0 0 0
1 0 -1 0 0 0
and my design matrix looks like this:
0 0 1 1 179 110
0 0 1 1 193 103
0 0 1 1 176 108
0 0 1 1 198 94
0 1 0 1 186 87
0 1 0 1 217 83
.
and my versions are
# $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
# $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $
___
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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
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Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi,
thanks for your reply. The mri_glmfit-sim was pasted below, here it is
the dereferenced version:
/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
thanks again,
Nicola
On 7/21/2016 11:13 PM, Douglas N Greve wrote:
> That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
> please do not include variables, just the full command with all
> dereferenced args
>
> On 07/21/2016 03:28 PM, Nicola Toschi wrote:
>> Hi,
>>
>> here it is (I also pasted the mri_glmfit line):
>>
>> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory//
>> //
>> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \//
>> //--C ${C1} \//
>> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
>> //
>> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
>> --cache ${t} pos*//*
>> */
>> Note: it is the same code i use for the t-tests, which appear to work
>> fine.
>>
>> The content of the file ${C1} is
>>
>> 1 -1 0 0 0 0
>> 1 0 -1 0 0 0
>>
>>
>> Thanks in advance!
>>
>> Nicola
>>
>>
>>
>> On 7/21/2016 5:38 PM, Douglas N Greve wrote:
>>> what is your mri_glmfit-sim command line?
>>>
>>> On 07/20/2016 05:56 PM, Nicola Toschi wrote:
>>>> Hi List,
>>>>
>>>> I am getting a couple of strange error when running a 3-group F-test.
>>>>
>>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>> WARNING: 251446 NaNs found in volume
>>>> analysis/Ftest/cache.th20.pos.sig.cluster.mgh...
>>>>
>>>> And as a result, I consistently get huge clusters:
>>>>
>>>> # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
>>>> CWPLowCWPHi NVtxsWghtVtx Annot
>>>> 1 inf 0 63247.45-38.8 -19.0 66.9 0.00010
>>>> 0.0 0.00020 98722 inf precentral
>>>>
>>>> However, this doesn't happen when running t-tests on the same data.
>>>> Still, I think my F-contrast is correct (see below).
>>>>
>>>> Thanks in advance for any advice!
>>>>
>>>> Nicola
>>>>
>>>> PS:
>>>>
>>>> my F-contrast looks like this:
>>>>
>>>> 1 -1 0 0 0 0
>>>> 1 0 -1 0 0 0
>>>>
>>>> and my design matrix looks like this:
>>>>
>>>> 0 0 1 1 179 110
>>>> 0 0 1 1 193 103
>>>> 0 0 1 1 176 108
>>>> 0 0 1 1 198 94
>>>> 0 1 0 1 186 87
>>>> 0 1 0 1 217 83
>>>> .
>>>>
>>>> and my versions are
>>>>
>>>> # $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
>>>> # $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $
>>>>
>>>>
>>>>
>>>> ___
>>>> 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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi,
thanks - I tried using "abs" as well as a higher threshold, however the
large, whole-brain cluster (as well as the warning messages) still remains.
Do the warnings:
WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
WARNING: 251446 NaNs found in volume
give any clues?
The strange thing is that everything is fine (small clusters and no
warning) when I use t-tests )i.e. just the first or second line of the F
test).
Thanks a lot for your time,
Nicola
On 07/21/2016 11:53 PM, Douglas N Greve wrote:
> Try using abs instead of pos. abs (absolute) is more appropriate since
> an F test is unsigned. Also, I would go with a threshold of 2 and not
> 1.3. I'm just now finding out that such a low threshold can cause a
> lot of false postives on real data.
>
>
> On 07/21/2016 05:32 PM, Nicola Toschi wrote:
>> Hi,
>>
>> thanks for your reply. The mri_glmfit-sim was pasted below, here it
>> is the dereferenced version:
>>
>>
>> /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
>> design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
>>
>>
>> thanks again,
>>
>> Nicola
>>
>> On 7/21/2016 11:13 PM, Douglas N Greve wrote:
>>> That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
>>> please do not include variables, just the full command with all
>>> dereferenced args
>>>
>>> On 07/21/2016 03:28 PM, Nicola Toschi wrote:
>>>> Hi,
>>>>
>>>> here it is (I also pasted the mri_glmfit line):
>>>>
>>>> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory//
>>>> //
>>>> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \//
>>>> //--C ${C1} \//
>>>> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
>>>> //
>>>> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
>>>> --cache ${t} pos*//*
>>>> */
>>>> Note: it is the same code i use for the t-tests, which appear to
>>>> work fine.
>>>>
>>>> The content of the file ${C1} is
>>>>
>>>> 1 -1 0 0 0 0
>>>> 1 0 -1 0 0 0
>>>>
>>>>
>>>> Thanks in advance!
>>>>
>>>> Nicola
>>>>
>>>>
>>>>
>>>> On 7/21/2016 5:38 PM, Douglas N Greve wrote:
>>>>> what is your mri_glmfit-sim command line?
>>>>>
>>>>> On 07/20/2016 05:56 PM, Nicola Toschi wrote:
>>>>>> Hi List,
>>>>>>
>>>>>> I am getting a couple of strange error when running a 3-group
>>>>>> F-test.
>>>>>>
>>>>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>>>> WARNING: 251446 NaNs found in volume
>>>>>> analysis/Ftest/cache.th20.pos.sig.cluster.mgh...
>>>>>>
>>>>>> And as a result, I consistently get huge clusters:
>>>>>>
>>>>>> # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
>>>>>> CWPLowCWPHi NVtxsWghtVtx Annot
>>>>>> 1 inf 0 63247.45-38.8 -19.0 66.9 0.00010
>>>>>> 0.0 0.00020 98722 inf precentral
>>>>>>
>>>>>> However, this doesn't happen when running t-tests on the same data.
>>>>>> Still, I think my F-contrast is correct (see below).
>>>>>>
>>>>>> Thanks in advance for any advice!
>>>>>>
>>>>>> Nicola
>>>>>>
>>>>>> PS:
>>>>>>
>>>>>> my F-contrast looks like this:
>>>>>>
>>>>>> 1 -1 0 0 0 0
>>>>>> 1 0 -1 0 0 0
>>>>>>
>>>>>> and my design matrix looks like this:
>>>>>>
>>>>>> 0 0 1 1 179 110
>>>>>> 0 0 1 1 193 103
>>>>>> 0 0 1 1 176 108
>>>>>> 0 0 1 1 198 94
>>>>>> 0 1 0 1 186 87
>>>>>> 0 1 0 1 217 83
>>>>>> .
>>>>>>
>>>>>> and my versions are
>>>>>>
>>>>>> # $Id: mri_surfcluster.c,v 1.57 2014/03/06 17:02:46 greve Exp $
>>>>>> # $Id: mrisurf.c,v 1.776 2015/12/17 18:09:34 fischl Exp $
>>>>>>
>>>>>>
>>>>>>
>>>>>> ___
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>>>
>>>>>>
>>>>
>>>
>>
>>
>
___
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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.
Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi Again,
(apologies for the many posts): I should add that none of this happens
(and everything works fine - no warning and small clusters which look
reasonable) if I use version 5.3.
Thank you,
Nicola
On 7/22/2016 2:10 PM, Nicola Toschi wrote:
> Hi,
>
> thanks - I tried using "abs" as well as a higher threshold, however the
> large, whole-brain cluster (as well as the warning messages) still remains.
>
> Do the warnings:
>
> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
> WARNING: 251446 NaNs found in volume
>
> give any clues?
>
> The strange thing is that everything is fine (small clusters and no
> warning) when I use t-tests )i.e. just the first or second line of the F
> test).
>
> Thanks a lot for your time,
>
> Nicola
>
>
> On 07/21/2016 11:53 PM, Douglas N Greve wrote:
>> Try using abs instead of pos. abs (absolute) is more appropriate since
>> an F test is unsigned. Also, I would go with a threshold of 2 and not
>> 1.3. I'm just now finding out that such a low threshold can cause a
>> lot of false postives on real data.
>>
>>
>> On 07/21/2016 05:32 PM, Nicola Toschi wrote:
>>> Hi,
>>>
>>> thanks for your reply. The mri_glmfit-sim was pasted below, here it
>>> is the dereferenced version:
>>>
>>>
>>> /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
>>> design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
>>>
>>>
>>> thanks again,
>>>
>>> Nicola
>>>
>>> On 7/21/2016 11:13 PM, Douglas N Greve wrote:
>>>> That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
>>>> please do not include variables, just the full command with all
>>>> dereferenced args
>>>>
>>>> On 07/21/2016 03:28 PM, Nicola Toschi wrote:
>>>>> Hi,
>>>>>
>>>>> here it is (I also pasted the mri_glmfit line):
>>>>>
>>>>> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output directory//
>>>>> //
>>>>> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \//
>>>>> //--C ${C1} \//
>>>>> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
>>>>> //
>>>>> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
>>>>> --cache ${t} pos*//*
>>>>> */
>>>>> Note: it is the same code i use for the t-tests, which appear to
>>>>> work fine.
>>>>>
>>>>> The content of the file ${C1} is
>>>>>
>>>>> 1 -1 0 0 0 0
>>>>> 1 0 -1 0 0 0
>>>>>
>>>>>
>>>>> Thanks in advance!
>>>>>
>>>>> Nicola
>>>>>
>>>>>
>>>>>
>>>>> On 7/21/2016 5:38 PM, Douglas N Greve wrote:
>>>>>> what is your mri_glmfit-sim command line?
>>>>>>
>>>>>> On 07/20/2016 05:56 PM, Nicola Toschi wrote:
>>>>>>> Hi List,
>>>>>>>
>>>>>>> I am getting a couple of strange error when running a 3-group
>>>>>>> F-test.
>>>>>>>
>>>>>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>>>>> WARNING: 251446 NaNs found in volume
>>>>>>> analysis/Ftest/cache.th20.pos.sig.cluster.mgh...
>>>>>>>
>>>>>>> And as a result, I consistently get huge clusters:
>>>>>>>
>>>>>>> # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
>>>>>>> CWPLowCWPHi NVtxsWghtVtx Annot
>>>>>>>1 inf 0 63247.45-38.8 -19.0 66.9 0.00010
>>>>>>> 0.0 0.00020 98722 inf precentral
>>>>>>>
>>>>>>> However, this doesn't happen when running t-tests on the same data.
>>>>>>> Still, I think my F-contrast is correct (see below).
>>>>>>>
>>>>>>> Thanks in advance for any advice!
>>>>>>>
>>>>>>> Nicola
>>>>>>>
>>>>>>> PS:
>>>>>>>
>>>>>>> my F-contrast looks like this:
>>>>>>>
>>>>>>> 1 -1 0 0 0 0
>>>>>>> 1 0 -1 0
Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi,
I have uploaded it and the link should be
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
Thanks!
Nicola
On 7/22/2016 6:31 PM, Douglas N Greve wrote:
> Can you tar up the glmdir and send it to me on our filedrop? The first
> warning is not a problem. Not sure about the 2nd.
> doug
>
> On 07/22/2016 08:10 AM, Nicola Toschi wrote:
>> Hi,
>>
>> thanks - I tried using "abs" as well as a higher threshold, however
>> the large, whole-brain cluster (as well as the warning messages)
>> still remains.
>>
>> Do the warnings:
>>
>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>> WARNING: 251446 NaNs found in volume
>>
>> give any clues?
>>
>> The strange thing is that everything is fine (small clusters and no
>> warning) when I use t-tests )i.e. just the first or second line of
>> the F test).
>>
>> Thanks a lot for your time,
>>
>> Nicola
>>
>>
>> On 07/21/2016 11:53 PM, Douglas N Greve wrote:
>>> Try using abs instead of pos. abs (absolute) is more appropriate
>>> since an F test is unsigned. Also, I would go with a threshold of 2
>>> and not 1.3. I'm just now finding out that such a low threshold can
>>> cause a lot of false postives on real data.
>>>
>>>
>>> On 07/21/2016 05:32 PM, Nicola Toschi wrote:
>>>> Hi,
>>>>
>>>> thanks for your reply. The mri_glmfit-sim was pasted below, here it
>>>> is the dereferenced version:
>>>>
>>>>
>>>> /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
>>>> design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
>>>>
>>>>
>>>> thanks again,
>>>>
>>>> Nicola
>>>>
>>>> On 7/21/2016 11:13 PM, Douglas N Greve wrote:
>>>>> That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
>>>>> please do not include variables, just the full command with all
>>>>> dereferenced args
>>>>>
>>>>> On 07/21/2016 03:28 PM, Nicola Toschi wrote:
>>>>>> Hi,
>>>>>>
>>>>>> here it is (I also pasted the mri_glmfit line):
>>>>>>
>>>>>> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output
>>>>>> directory//
>>>>>> //
>>>>>> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix} \//
>>>>>> //--C ${C1} \//
>>>>>> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
>>>>>> //
>>>>>> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
>>>>>> --cache ${t} pos*//*
>>>>>> */
>>>>>> Note: it is the same code i use for the t-tests, which appear to
>>>>>> work fine.
>>>>>>
>>>>>> The content of the file ${C1} is
>>>>>>
>>>>>> 1 -1 0 0 0 0
>>>>>> 1 0 -1 0 0 0
>>>>>>
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> Nicola
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 7/21/2016 5:38 PM, Douglas N Greve wrote:
>>>>>>> what is your mri_glmfit-sim command line?
>>>>>>>
>>>>>>> On 07/20/2016 05:56 PM, Nicola Toschi wrote:
>>>>>>>> Hi List,
>>>>>>>>
>>>>>>>> I am getting a couple of strange error when running a 3-group
>>>>>>>> F-test.
>>>>>>>>
>>>>>>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>>>>>> WARNING: 251446 NaNs found in volume
>>>>>>>> analysis/Ftest/cache.th20.pos.sig.cluster.mgh...
>>>>>>>>
>>>>>>>> And as a result, I consistently get huge clusters:
>>>>>>>>
>>>>>>>> # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP
>>>>>>>> CWPLowCWPHi NVtxsWghtVtx Annot
>>>>>>>> 1 inf 0 63247.45-38.8 -19.0 66.9 0.00010
>>>>>>>> 0.0 0.00020 98722 inf precentral
>>>>>>>>
>>>>>>>> However, this doesn't happen when running t-tests on the same
&g
Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi,
it's a dev version downloaded on Jan 17th 2016.
As mentioned in my other mail, I have uploaded a full glmdir at
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
thanks for your time,
Nicola
On 7/22/2016 6:35 PM, Douglas N Greve wrote:
> what version does it fail on? If a dev version, when did you download it?
>
> On 07/22/2016 12:15 PM, Nicola Toschi wrote:
>> Hi Again,
>>
>> (apologies for the many posts): I should add that none of this
>> happens (and everything works fine - no warning and small clusters
>> which look reasonable) if I use version 5.3.
>>
>> Thank you,
>>
>> Nicola
>>
>> On 7/22/2016 2:10 PM, Nicola Toschi wrote:
>>> Hi,
>>>
>>> thanks - I tried using "abs" as well as a higher threshold, however the
>>> large, whole-brain cluster (as well as the warning messages) still
>>> remains.
>>>
>>> Do the warnings:
>>>
>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>> WARNING: 251446 NaNs found in volume
>>>
>>> give any clues?
>>>
>>> The strange thing is that everything is fine (small clusters and no
>>> warning) when I use t-tests )i.e. just the first or second line of
>>> the F
>>> test).
>>>
>>> Thanks a lot for your time,
>>>
>>> Nicola
>>>
>>>
>>> On 07/21/2016 11:53 PM, Douglas N Greve wrote:
>>>> Try using abs instead of pos. abs (absolute) is more appropriate since
>>>> an F test is unsigned. Also, I would go with a threshold of 2 and not
>>>> 1.3. I'm just now finding out that such a low threshold can cause a
>>>> lot of false postives on real data.
>>>>
>>>>
>>>> On 07/21/2016 05:32 PM, Nicola Toschi wrote:
>>>>> Hi,
>>>>>
>>>>> thanks for your reply. The mri_glmfit-sim was pasted below, here it
>>>>> is the dereferenced version:
>>>>>
>>>>>
>>>>> /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
>>>>> design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
>>>>>
>>>>>
>>>>> thanks again,
>>>>>
>>>>> Nicola
>>>>>
>>>>> On 7/21/2016 11:13 PM, Douglas N Greve wrote:
>>>>>> That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
>>>>>> please do not include variables, just the full command with all
>>>>>> dereferenced args
>>>>>>
>>>>>> On 07/21/2016 03:28 PM, Nicola Toschi wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> here it is (I also pasted the mri_glmfit line):
>>>>>>>
>>>>>>> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output
>>>>>>> directory//
>>>>>>> //
>>>>>>> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X ${matrix}
>>>>>>> \//
>>>>>>> //--C ${C1} \//
>>>>>>> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
>>>>>>> //
>>>>>>> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
>>>>>>> --cache ${t} pos*//*
>>>>>>> */
>>>>>>> Note: it is the same code i use for the t-tests, which appear to
>>>>>>> work fine.
>>>>>>>
>>>>>>> The content of the file ${C1} is
>>>>>>>
>>>>>>> 1 -1 0 0 0 0
>>>>>>> 1 0 -1 0 0 0
>>>>>>>
>>>>>>>
>>>>>>> Thanks in advance!
>>>>>>>
>>>>>>> Nicola
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 7/21/2016 5:38 PM, Douglas N Greve wrote:
>>>>>>>> what is your mri_glmfit-sim command line?
>>>>>>>>
>>>>>>>> On 07/20/2016 05:56 PM, Nicola Toschi wrote:
>>>>>>>>> Hi List,
>>>>>>>>>
>>>>>>>>> I am getting a couple of strange error when running a 3-group
>>>>>>>>> F-test.
>>>>>>>>>
>>>>>>>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>
Re: [Freesurfer] Error with mri_glmfit_sim (dev version f)
Hi Doug,
thank you - using this new version changed everything back to "normal"
(small clusters, few results), so it may indeed have been a problem with
that particular version.
Thanks again,
Nicola
On 7/22/2016 8:22 PM, Douglas N Greve wrote:
>
> That version may have had a bug. Try this one
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit
> btw, you should not be using the dev version of recon-all
>
> On 07/22/2016 02:01 PM, Nicola Toschi wrote:
>> Hi,
>>
>> it's a dev version downloaded on Jan 17th 2016.
>>
>> As mentioned in my other mail, I have uploaded a full glmdir at
>>
>> http://gate.nmr.mgh.harvard.edu/filedrop2/?p=akbem4mthlv
>>
>> thanks for your time,
>>
>> Nicola
>>
>> On 7/22/2016 6:35 PM, Douglas N Greve wrote:
>>> what version does it fail on? If a dev version, when did you
>>> download it?
>>>
>>> On 07/22/2016 12:15 PM, Nicola Toschi wrote:
>>>> Hi Again,
>>>>
>>>> (apologies for the many posts): I should add that none of this
>>>> happens (and everything works fine - no warning and small clusters
>>>> which look reasonable) if I use version 5.3.
>>>>
>>>> Thank you,
>>>>
>>>> Nicola
>>>>
>>>> On 7/22/2016 2:10 PM, Nicola Toschi wrote:
>>>>> Hi,
>>>>>
>>>>> thanks - I tried using "abs" as well as a higher threshold,
>>>>> however the
>>>>> large, whole-brain cluster (as well as the warning messages) still
>>>>> remains.
>>>>>
>>>>> Do the warnings:
>>>>>
>>>>> WARNING: unrecognized mri_glmfit cmd option mri_glmfit.bin
>>>>> WARNING: 251446 NaNs found in volume
>>>>>
>>>>> give any clues?
>>>>>
>>>>> The strange thing is that everything is fine (small clusters and no
>>>>> warning) when I use t-tests )i.e. just the first or second line of
>>>>> the F
>>>>> test).
>>>>>
>>>>> Thanks a lot for your time,
>>>>>
>>>>> Nicola
>>>>>
>>>>>
>>>>> On 07/21/2016 11:53 PM, Douglas N Greve wrote:
>>>>>> Try using abs instead of pos. abs (absolute) is more appropriate
>>>>>> since
>>>>>> an F test is unsigned. Also, I would go with a threshold of 2 and
>>>>>> not
>>>>>> 1.3. I'm just now finding out that such a low threshold can cause a
>>>>>> lot of false postives on real data.
>>>>>>
>>>>>>
>>>>>> On 07/21/2016 05:32 PM, Nicola Toschi wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> thanks for your reply. The mri_glmfit-sim was pasted below, here it
>>>>>>> is the dereferenced version:
>>>>>>>
>>>>>>>
>>>>>>> /usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir
>>>>>>> design_3groups_AgeGenderIq_area_lh_fwhm0_pial --cache 1.3 pos
>>>>>>>
>>>>>>>
>>>>>>> thanks again,
>>>>>>>
>>>>>>> Nicola
>>>>>>>
>>>>>>> On 7/21/2016 11:13 PM, Douglas N Greve wrote:
>>>>>>>> That is the mri_glmfit command, I need the mri_glmfit-sim. Also,
>>>>>>>> please do not include variables, just the full command with all
>>>>>>>> dereferenced args
>>>>>>>>
>>>>>>>> On 07/21/2016 03:28 PM, Nicola Toschi wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> here it is (I also pasted the mri_glmfit line):
>>>>>>>>>
>>>>>>>>> /odir=${prefix}_${meas}_${h}_fwhm${s}_${surf} #name output
>>>>>>>>> directory//
>>>>>>>>> //
>>>>>>>>> //mri_glmfit --y ${h}.fwhm${s}.${list}.${meas}.mgh --X
>>>>>>>>> ${matrix} \//
>>>>>>>>> //--C ${C1} \//
>>>>>>>>> //--glmdir ${odir} --surf fsaverage ${h} ${surf}//
>>>>>>>>> //
>>>>>>>>> //*/usr/local/freesurfer6dev/bin/mri_glmfit-sim --glmdir ${odir}
>>>>>>>>> --cache
[Freesurfer] Error with .license after upgrading to 5.2
Hi list, after upgrading to 5.2 (from 5.1), I am consistently getting a license error (see below). The strange thing is that my .license is the same file I was using on 5.1 and worked fine. I have also tried multiple modifications of file permission/owners (its a local install so I can be root) but no luck. Thanks in advance, Nicola ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. ___ 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.
Re: [Freesurfer] Error with .license after upgrading to 5.2
Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applications/freesurfer then echo each line of the licence. Let me know In thanks chikku ___ 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.
Re: [Freesurfer] Error with .license after upgrading to 5.2
Hi, that is exactly what I did (see my first message) - that's why I'm so puzzled! Nicola On 03/22/2013 05:05 PM, Lingqiang Kong wrote: > Just use the license file from your previous version (or you can apply for > a new license for free, but this is redundant). > > cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license > where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, > respectively. > > Lingqiang > > >> Hi - no luck unfortunately (I had already tried changing permissions) >> >> On 03/22/2013 04:09 PM, Varghese Chikku wrote: >>> Hi Nicola, >>> Can you try this command,and echo the license.It may ask for >>> password.I have similar issues with 5.2 and this how i sorted. >>> sudo chmod -R a+rwX /Applications/freesurfer >>> then >>> echo each line of the licence. >>> Let me know >>> In thanks >>> chikku >> ___ >> 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] License invalid after upgrading OS (opensuse) - still not working
Hi List, with reference to my below messages, I have now determined that the license file is considered invalid by freesurfer executables since i have upgraded from opensuse 12.2 to 12.3. The upgrade to freesurfer 5.2 had nothing to do with it - in fact, setting the proper environments variables and running 5.1 from by backed up, untouched, old install dir and .license file changes nothing (i.e. not even 5.1 is working now). Any idea what my be going on here? I have tried every combination of file permissions and contents I could think of. Much appreciated Nicola On 3/22/2013 5:36 PM, Nicola Toschi wrote: > Hi, > > that is exactly what I did (see my first message) - that's why I'm so > puzzled! > > Nicola > > On 03/22/2013 05:05 PM, Lingqiang Kong wrote: >> Just use the license file from your previous version (or you can apply for >> a new license for free, but this is redundant). >> >> cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license >> where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, >> respectively. >> >> Lingqiang >> >> >>> Hi - no luck unfortunately (I had already tried changing permissions) >>> >>> On 03/22/2013 04:09 PM, Varghese Chikku wrote: >>>> Hi Nicola, >>>> Can you try this command,and echo the license.It may ask for >>>>password.I have similar issues with 5.2 and this how i sorted. >>>> sudo chmod -R a+rwX /Applications/freesurfer >>>> then >>>> echo each line of the licence. >>>> Let me know >>>> In thanks >>>> chikku >>> ___ >>> 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
[Freesurfer] Libray/tool used to read license file - cannot checkout source code
Hi List, could anyone point out to me which tool/library is used by freesurfer binaries to read the .license file? I am positive my .license file is correct (I have used the same file before) and have tried every combination of permissions, but on my Opensuse 12.3 Distro I keep getting: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license So I'm thinking ti must be OS -related. Also, I have not been able to checkout the source code, the error message is: Could not map memory to RCS archive /usr/fscvsroot/dev/distribution/average/fsaverage.tar.gz Thanks in advance for any pointers. Nicola On 3/26/2013 7:28 PM, Nicola Toschi wrote: > Hi List, > > with reference to my below messages, I have now determined that the > license file is considered invalid by freesurfer executables since i > have upgraded from opensuse 12.2 to 12.3. > > The upgrade to freesurfer 5.2 had nothing to do with it - in fact, > setting the proper environments variables and running 5.1 from by backed > up, untouched, old install dir and .license file changes nothing (i.e. > not even 5.1 is working now). > > Any idea what my be going on here? I have tried every combination of > file permissions and contents I could think of. > > Much appreciated > > Nicola > > On 3/22/2013 5:36 PM, Nicola Toschi wrote: >> Hi, >> >> that is exactly what I did (see my first message) - that's why I'm so >> puzzled! >> >> Nicola >> >> On 03/22/2013 05:05 PM, Lingqiang Kong wrote: >>> Just use the license file from your previous version (or you can apply for >>> a new license for free, but this is redundant). >>> >>> cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license >>> where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, >>> respectively. >>> >>> Lingqiang >>> >>> >>>> Hi - no luck unfortunately (I had already tried changing permissions) >>>> >>>> On 03/22/2013 04:09 PM, Varghese Chikku wrote: >>>>> Hi Nicola, >>>>> Can you try this command,and echo the license.It may ask for >>>>> password.I have similar issues with 5.2 and this how i sorted. >>>>> sudo chmod -R a+rwX /Applications/freesurfer >>>>> then >>>>> echo each line of the licence. >>>>> Let me know >>>>> In thanks >>>>> chikku >>>> ___ >>>> 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Libray/tool used to read license file - cannot checkout source code
Hi Zeke, thank you for your reply. I've tried that - the system keeps sending me the same license file (it's probably tied to the email address). Also, I've tried other (working) license files from other installations - no luck. As for the checkout, I have tried multiple times After login, I am using cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev Seems I'm out of luck with FS these days! Thanks Nicola On 4/2/2013 11:53 AM, zkauf...@nmr.mgh.harvard.edu wrote: > Nicola, > > Perhaps it is worth getting a new license file: > > https://surfer.nmr.mgh.harvard.edu/registration.html > > As to checking out the source code, I too received that error during > checkout and by simply reissuing the checkout command I was able to > get the checkout finish to completion. (It even may have taken a > couple tries) > > -Zeke > > > On 04/02/2013 12:44 PM, Nicola Toschi wrote: >> Hi List, >> >> could anyone point out to me which tool/library is used by freesurfer >> binaries to read the .license file? I am positive my .license file is >> correct (I have used the same file before) and have tried every >> combination of permissions, but on my Opensuse 12.3 Distro I keep >> getting: >> >> ERROR: Invalid FreeSurfer license key found in license file >> /usr/local/freesurfer/.license >> >> So I'm thinking ti must be OS -related. Also, I have not been able to >> checkout the source code, the error message is: >> >> Could not map memory to RCS archive >> /usr/fscvsroot/dev/distribution/average/fsaverage.tar.gz >> >> Thanks in advance for any pointers. >> >> Nicola >> >> >> On 3/26/2013 7:28 PM, Nicola Toschi wrote: >>> Hi List, >>> >>> with reference to my below messages, I have now determined that the >>> license file is considered invalid by freesurfer executables since i >>> have upgraded from opensuse 12.2 to 12.3. >>> >>> The upgrade to freesurfer 5.2 had nothing to do with it - in fact, >>> setting the proper environments variables and running 5.1 from by >>> backed >>> up, untouched, old install dir and .license file changes nothing (i.e. >>> not even 5.1 is working now). >>> >>> Any idea what my be going on here? I have tried every combination of >>> file permissions and contents I could think of. >>> >>> Much appreciated >>> >>> Nicola >>> >>> On 3/22/2013 5:36 PM, Nicola Toschi wrote: >>>> Hi, >>>> >>>> that is exactly what I did (see my first message) - that's why I'm so >>>> puzzled! >>>> >>>> Nicola >>>> >>>> On 03/22/2013 05:05 PM, Lingqiang Kong wrote: >>>>> Just use the license file from your previous version (or you can >>>>> apply for >>>>> a new license for free, but this is redundant). >>>>> >>>>> cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license >>>>> where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, >>>>> respectively. >>>>> >>>>> Lingqiang >>>>> >>>>> >>>>>> Hi - no luck unfortunately (I had already tried changing >>>>>> permissions) >>>>>> >>>>>> On 03/22/2013 04:09 PM, Varghese Chikku wrote: >>>>>>> Hi Nicola, >>>>>>> Can you try this command,and echo the license.It may ask for >>>>>>> password.I have similar issues with 5.2 and this how i >>>>>>> sorted. >>>>>>> sudo chmod -R a+rwX /Applications/freesurfer >>>>>>> then >>>>>>> echo each line of the licence. >>>>>>> Let me know >>>>>>> In thanks >>>>>>> chikku >>>>>> ___ >>>>>> 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 >> >> ___ >> 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
Re: [Freesurfer] Libray/tool used to read license file - cannot checkout source code
Hi Zeke, thanks for you email. Unfortunately nothing has changed for me (neither on the license, nor on the checkout front). I've tried the checkout from 3 machines, al linux (ContOS, Suse, Mint). Please let me know if i can provide you with more specific info. Best, Nicola On 4/2/2013 2:08 PM, zkauf...@nmr.mgh.harvard.edu wrote: > Nicola, Akio, and others, > > The issues you experienced with checking out the freesurfer source > code from the CVS repository should be solved. Please let me know if > this is not the case. > > -Zeke > > > > On 04/02/2013 01:00 PM, Nicola Toschi wrote: >> Hi Zeke, >> >> thank you for your reply. I've tried that - the system keeps sending me >> the same license file (it's probably tied to the email address). Also, >> I've tried other (working) license files from other installations - no >> luck. >> >> As for the checkout, I have tried multiple times After login, I am >> using >> >> cvs -d :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot >> checkout -P dev >> >> Seems I'm out of luck with FS these days! >> >> Thanks >> >> Nicola >> >> On 4/2/2013 11:53 AM, zkauf...@nmr.mgh.harvard.edu wrote: >>> Nicola, >>> >>> Perhaps it is worth getting a new license file: >>> >>> https://surfer.nmr.mgh.harvard.edu/registration.html >>> >>> As to checking out the source code, I too received that error during >>> checkout and by simply reissuing the checkout command I was able to >>> get the checkout finish to completion. (It even may have taken a >>> couple tries) >>> >>> -Zeke >>> >>> >>> On 04/02/2013 12:44 PM, Nicola Toschi wrote: >>>> Hi List, >>>> >>>> could anyone point out to me which tool/library is used by freesurfer >>>> binaries to read the .license file? I am positive my .license file is >>>> correct (I have used the same file before) and have tried every >>>> combination of permissions, but on my Opensuse 12.3 Distro I keep >>>> getting: >>>> >>>> ERROR: Invalid FreeSurfer license key found in license file >>>> /usr/local/freesurfer/.license >>>> >>>> So I'm thinking ti must be OS -related. Also, I have not been able to >>>> checkout the source code, the error message is: >>>> >>>> Could not map memory to RCS archive >>>> /usr/fscvsroot/dev/distribution/average/fsaverage.tar.gz >>>> >>>> Thanks in advance for any pointers. >>>> >>>> Nicola >>>> >>>> >>>> On 3/26/2013 7:28 PM, Nicola Toschi wrote: >>>>> Hi List, >>>>> >>>>> with reference to my below messages, I have now determined that the >>>>> license file is considered invalid by freesurfer executables since i >>>>> have upgraded from opensuse 12.2 to 12.3. >>>>> >>>>> The upgrade to freesurfer 5.2 had nothing to do with it - in fact, >>>>> setting the proper environments variables and running 5.1 from by >>>>> backed >>>>> up, untouched, old install dir and .license file changes nothing >>>>> (i.e. >>>>> not even 5.1 is working now). >>>>> >>>>> Any idea what my be going on here? I have tried every combination of >>>>> file permissions and contents I could think of. >>>>> >>>>> Much appreciated >>>>> >>>>> Nicola >>>>> >>>>> On 3/22/2013 5:36 PM, Nicola Toschi wrote: >>>>>> Hi, >>>>>> >>>>>> that is exactly what I did (see my first message) - that's why >>>>>> I'm so >>>>>> puzzled! >>>>>> >>>>>> Nicola >>>>>> >>>>>> On 03/22/2013 05:05 PM, Lingqiang Kong wrote: >>>>>>> Just use the license file from your previous version (or you can >>>>>>> apply for >>>>>>> a new license for free, but this is redundant). >>>>>>> >>>>>>> cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license >>>>>>> where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, >>>>>>> respectively. >>>>>>> >>>>>>> Lingqiang >>>>>>> >>>>>
[Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Hi Nick, hi List, I have been having the exact same problem (also posted it on this list) with every freesurfer version on Opensuse 12.3, and haven't been able to sort it out. Any luck with it? Any pointers would be highly appreciated. Thanks in advance, Nicola On 5/1/2013 4:42 PM, Nick Jones wrote: > Hi, > > I've run into a license problem with the latest version of Freesurfer on > OpenSuse 12.3. 64 bit. > > FREESURFER_HOME: /usr/freesurfer > Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > Kernel info: Linux 3.7.10-1.1-desktop x86_64 > > When running a test: > > /usr/freesurfer>echo $shell > /bin/tcsh > > /usr/freesurfer>source SetUpFreeSurfer.csh > freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/freesurfer > FSFAST_HOME /usr/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/freesurfer/subjects > MNI_DIR /usr/freesurfer/mni > FSL_DIR /usr/fsl > > /usr/freesurfer>tkmedit bert orig.mgz > -- > ERROR: Invalid FreeSurfer license key found in license file > /usr/freesurfer/.license > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -- > > /usr/freesurfer>cat .license > hotm...@hotmail.com > 14743 > *C5.JPynIz8mt > /usr/freesurfer> > > This license file has been obfuscated. > > /usr/freesurfer>ll -a .license > -rw-r--r-- 1 root root 46 Apr 29 09:38 .license > > /usr/freesurfer>cat VERSION > freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 > > /usr/freesurfer>zypper targetos > openSUSE-12.3-x86_64 > > /usr/freesurfer>uname -a > Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 UTC 2013 > (82d3f21) x86_64 x86_64 x86_64 GNU/Linux > > Name: tcl > Version: 8.5.12-3.1.3 > Name: tk > Version: 8.5.12-3.1.1 > > Thanks to anyone who can provide some insight or workaround. I'm also > curious if anyone knows the reasoning behind using this type of license > mechanism, as opposed to agreeing to a license prior to downloading, like FSL > or 3DSlicer? > > Nick > ___ > 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
Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Hi Nick, sorry - I should have been more specific. I get the same error with *any* FS command or script (recon-all, mri_glmfit), so in effect ever since the upgrade I am not able to use FS at all. The tkmedit patch you posted is only missing a library on my system though, which I can fix - so maybe that's a pointer towards the root of the problem? Thanks again, Nicola On 5/7/2013 2:57 PM, Nick Jones wrote: > Hi Nick, > > It complains about libtix8.1.8.4.so missing. I add > $FREESURFER_HOME/lib/tcltktixblt/lib/ to the LD_LIBRARY_PATH variable, > but it still complains about the license and does not open bert. > > Tried the dev build and 5.3 beta, which also fail at the license. > > Why not remove the requirement and have people agree to a license > prior to downloading? Lots of folks probably enter bogus information > into the registration form anyway. > Just trying to be constructive. > > Thanks very much for your help > > Nick > > On 05/07/2013 12:14 PM, Nick Schmansky wrote: >> Nicola and Nick, >> >> Can you try the tkmedit.bin found here: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ >> >> >> >> copy it to the freesurfer/tktools directory (the wrapper script >> 'tkmedit' in the bin dir calls the binary in the tktools dir). >> >> I'm hoping the problem you are seeing is the same one that others have >> seen on Fedora 19 and Ubuntu 13 which is fixed for the upcoming 5.3 >> release. >> >> Nick >> >> >> >> On Tue, 2013-05-07 at 12:15 -0400, Nicola Toschi wrote: >>> Hi Nick, hi List, >>> >>> I have been having the exact same problem (also posted it on this list) >>> with every freesurfer version on Opensuse 12.3, and haven't been >>> able to >>> sort it out. >>> >>> Any luck with it? Any pointers would be highly appreciated. >>> >>> Thanks in advance, >>> >>> Nicola >>> >>> On 5/1/2013 4:42 PM, Nick Jones wrote: >>>> Hi, >>>> >>>> I've run into a license problem with the latest version of >>>> Freesurfer on OpenSuse 12.3. 64 bit. >>>> >>>> FREESURFER_HOME: /usr/freesurfer >>>> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 >>>> Kernel info: Linux 3.7.10-1.1-desktop x86_64 >>>> >>>> When running a test: >>>> >>>> /usr/freesurfer>echo $shell >>>> /bin/tcsh >>>> >>>> /usr/freesurfer>source SetUpFreeSurfer.csh >>>> freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 >>>> Setting up environment for FreeSurfer/FS-FAST (and FSL) >>>> FREESURFER_HOME /usr/freesurfer >>>> FSFAST_HOME /usr/freesurfer/fsfast >>>> FSF_OUTPUT_FORMAT nii.gz >>>> SUBJECTS_DIR /usr/freesurfer/subjects >>>> MNI_DIR /usr/freesurfer/mni >>>> FSL_DIR /usr/fsl >>>> >>>> /usr/freesurfer>tkmedit bert orig.mgz >>>> -- >>>> >>>> ERROR: Invalid FreeSurfer license key found in license file >>>> /usr/freesurfer/.license >>>> If you are outside the NMR-Martinos Center, >>>> go to http://surfer.nmr.mgh.harvard.edu to >>>> get a valid license file (it's free). >>>> If you are inside the NMR-Martinos Center, >>>> make sure to source the standard environment. >>>> -- >>>> >>>> >>>> /usr/freesurfer>cat .license >>>> hotm...@hotmail.com >>>> 14743 >>>> *C5.JPynIz8mt >>>> /usr/freesurfer> >>>> >>>> This license file has been obfuscated. >>>> >>>> /usr/freesurfer>ll -a .license >>>> -rw-r--r-- 1 root root 46 Apr 29 09:38 .license >>>> >>>> /usr/freesurfer>cat VERSION >>>> freesurfer-x86_64-unknown-linux-gnu-stable5-20130226 >>>> >>>> /usr/freesurfer>zypper targetos >>>> openSUSE-12.3-x86_64 >>>> >>>> /usr/freesurfer>uname -a >>>> Linux adams 3.7.10-1.1-desktop #1 SMP PREEMPT Thu Feb 28 15:06:29 >>>> UTC 2013 (82d3f21) x86_64 x86_64 x86_64 GNU/Linux >>>> >>>> Name: tcl >>>> Version: 8.5.12-3.1.
Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Hi Nick (Schmansky), sorry to jump back in on this thread - I have exactly the same issue (license file not valid) on the same OS (and not on others) with *all* fs commands. I have tried multiple license files from other working installations. Is there anything else i can try? Thanks a lot nicola On 5/8/2013 3:09 PM, Nick Schmansky wrote: > Nick > > Can you email me the .license file that is being used? > > Thanks, > > N. > > > On Wed, 2013-05-08 at 13:21 -0500, Nick Jones wrote: >> Hi Nick, >> >> Truncated the email. I'm getting a license error for both the mri_convert >> command and the tkmedit command that you provided. The original also yields >> a license error (no segfault). You are right, my earlier test called >> tkmedit.bin directly. >> >> Thanks >> >> Nick >> >> On 05/08/2013 12:07 PM, Nick Schmansky wrote: >>> Nick, >>> >>> Hi, I found what might the source of the problem and posted new versions >>> of mri_convert and tkmedit.bin to this directory: >>> >>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ >>> >>> before trying the new mri_convert though, can you try the following? >>> >>> cd >>> mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz >>> >>> I'm guessing it will segfault or print the license problem. >>> >>> Now copy the new mri_convert (from the ftp link above) to the >>> freesurfer/bin directory and try again. It should work. You can then >>> also try the new tkmedit.bin. Remember to copy the tkmedit.bin to the >>> freesurfer/tktools directory and leave freesurfer/bin/tkmedit untouched >>> (its a wrapper-script that sets-up paths to the tcl/tk/tix/blt libs, so >>> tkmedit.bin cannot be run directly) >>> >>> Thanks, >>> >>> Nick >>> >>> >>> >> > > > > 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
Re: [Freesurfer] UNRESOLVED: Re: Freesurfer License issue/bug on Opensuse 12.3
Thanks Nick, well that did change something... here is what i get now with any fs command: /bin/tcsh: /lib64/libfreebl3.so: version `NSSRAWHASH_3.12.3' not found (required by /work2/rootbackup/usr/local/freesurfer/lib/libcrypt.so.1) Should I update/substitute /lib64/libfreebl3.so al well? thanks a lot, Nicola PS when running ldd ./mri_convert inside the bin dir, I get "not a dynamic executable" On 05/09/2013 06:02 AM, Nick Schmansky wrote: > Nicola and Nick, > > Hi, its Nick (the other Nick :)). This looks like a new issue we haven't > seen before that is specific to opensuse. Can you try downloading the > file libcrypt.so.1 from this location: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ > > copy it to your freesurfer/lib dir, then set a lib path prior to > setting-up (sourcing) freesurfer, like this: > > setenv FREESURFER_HOME > setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > this libcrypt lib is from centos6, and i'm thinking that possibly opensuse > implements crypt differently (working theory anyway). > > you can confirm that mri_convert is using this new lib by typing: > > cd $FREESURFER_HOME/bin > ldd ./mri_convert > > and you should see libcrypt in the list with a path to the freesurfer/lib > dir. > > Nick > > >> Hi Nick (Schmansky), >> >> sorry to jump back in on this thread - I have exactly the same issue >> (license file not valid) on the same OS (and not on others) with *all* >> fs commands. I have tried multiple license files from other working >> installations. >> >> Is there anything else i can try? >> >> Thanks a lot >> >> nicola >> >> On 5/8/2013 3:09 PM, Nick Schmansky wrote: >>> Nick >>> >>> Can you email me the .license file that is being used? >>> >>> Thanks, >>> >>> N. >>> >>> >>> On Wed, 2013-05-08 at 13:21 -0500, Nick Jones wrote: Hi Nick, Truncated the email. I'm getting a license error for both the mri_convert command and the tkmedit command that you provided. The original also yields a license error (no segfault). You are right, my earlier test called tkmedit.bin directly. Thanks Nick On 05/08/2013 12:07 PM, Nick Schmansky wrote: > Nick, > > Hi, I found what might the source of the problem and posted new > versions > of mri_convert and tkmedit.bin to this directory: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/ > > before trying the new mri_convert though, can you try the following? > > cd > mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz > > I'm guessing it will segfault or print the license problem. > > Now copy the new mri_convert (from the ftp link above) to the > freesurfer/bin directory and try again. It should work. You can then > also try the new tkmedit.bin. Remember to copy the tkmedit.bin to the > freesurfer/tktools directory and leave freesurfer/bin/tkmedit > untouched > (its a wrapper-script that sets-up paths to the tcl/tk/tix/blt libs, > so > tkmedit.bin cannot be run directly) > > Thanks, > > Nick > > > >>> >>> >>> 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
[Freesurfer] freesurfer@nmr.mgh.harvard.edu
Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola ___ 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] Downsampling/decimating overlays (not surfaces)
Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola PS apologies for the repost - my subject line was incorrect the first time around. ___ 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] Downsampling/decimating overlays (not surfaces)
Hello list, is there a quick way to decimate an overlay /while respecting surface geomery)? I am looking to downsample by about a factor 100. Alternatively, I know I can use mris_decimate to downsample a surface, but I would have to project my highres overlays onto the downsampled surface (which may not be straightforward). Thanks a lot in advance, Nicola PS apologies for the repost - my subject line was incorrect the first time around. ___ 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.
Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)
Hi Alex and Bruce, thanks a lot for your help. Will play around with MNE - looks like it does what I am looking for. Nicola On 01/24/2013 07:54 AM, Alexandre Gramfort wrote: > hi, > > what we do with MEG in the MNE package is indeed store downsampled > overlays (that actually have a temporal dimension). More specifically we > store the values e.g. only at the vertices of the ico5 subdivision and > store the ico 5 vertex indices and overlay values. Then to display them > on the high resolution freesurfer surface we basically use a > smoothing/diffusion > process to fill the missing values. For this downsampling to be valid > you'll need to make sure the data are smooth enough in order to avoid > aliasing. > > let me know if you need more details > > hope this helps, > > Alex > > On Thu, Jan 24, 2013 at 3:47 AM, Bruce Fischl > wrote: >> Hi Nicola >> >> I think this gets done in the MEG analysis stream, but perhaps Matti >> (ccd) can comment. >> cheers >> BruceOn Thu, 24 Jan 2013, Nicola Toschi wrote: >> >>> Hello list, >>> >>> is there a quick way to decimate an overlay /while respecting surface >>> geomery)? I am looking to downsample by about a factor 100. >>> >>> Alternatively, I know I can use mris_decimate to downsample a surface, but I >>> would have to project my highres overlays onto the downsampled surface >>> (which may not be straightforward). >>> >>> Thanks a lot in advance, >>> >>> Nicola >>> >>> PS apologies for the repost - my subject line was incorrect the first time >>> around. >>> >>> >> ___ >> 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
Re: [Freesurfer] Downsampling/decimating overlays (not surfaces)
Thank you Rudolph, what I would like to have as an end product is a list of overlay values at each vertex of the decimated surface (i.e. I don't want to synthesize anything into ROIs). The overlays are all freesurfer-specific (curvature, thickness, LGI, etc). I cannot recompute these on the new (decimated) surface, as they will be significantly different and less accurate (they are specific to the geometry of the original surface). Rather, I was looking to downsample highres overlays after smoothing. So i am not sure your suggestion would work - please let me know if I misunderstood something. Thanks again for your reprly, Nicola On 01/24/2013 04:01 PM, Rudolph Pienaar wrote: > If you specifically want to project overlays onto 'mris_decimate'd > surfaces, you won't be able to do that. You could, however, generate > new overlays using the decimated surface, if that's helpful, using > 'mris_curvature_stats' and feeding it the newly downsampled/demicated > surface as input. > > FWIW. > > Best > -=R > > On 1/23/13 18:07 , Nicola Toschi wrote: >> Hello list, >> >> is there a quick way to decimate an overlay /while respecting surface >> geomery)? I am looking to downsample by about a factor 100. >> >> Alternatively, I know I can use mris_decimate to downsample a >> surface, but I would have to project my highres overlays onto the >> downsampled surface (which may not be straightforward). >> >> Thanks a lot in advance, >> >> Nicola >> >> PS apologies for the repost - my subject line was incorrect the first >> time around. >> >> >> ___ >> 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] Adding low-res T2 and PD images in the recon-all stream - any advantages?
Hello List, on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually acquire T2 and PD images - however they are at 1x1x5 mm resolution. Would you recommend passing these (T2+PD) to the recon-all stream anyway - would they add value/accuracy to the segmentation/parcellation (or would they possibly decrease accuracy)? Thanks in advance, Nicola ___ 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] Interpretation of pcc.mgh for negative contrasts
External Email - Use Caution Hi List, a dimple question about using partial correlation (pcc.mgh) as effect size measure. I am running multivariate regression and setting positive and negative contrasts one variable at a time, e.g. a design matrix with columns like Intercept Age Gender Fact1 Fact2 and a bunch of contrasts like 0 0 010 0 0 0-10 Now let's say the second contrast gives me a significant results after MC correction in a certain cluster, what sign should i expect in PCC in that cluster (on average)? Thank you very much in advance, Nicola ___ 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.
Re: [Freesurfer] Interpretation of pcc.mgh for negative contrasts
External Email - Use Caution Thank you Doug, that was exactly the question... it may be a trivial one but I have been messing aroung with several effects size calculation for a while and just wanted to make sure. So negative contrast (-1), negative beta.mgh, positive (?) gamma.mgh, and negative pcc.mgh withing the same significant cluster? Thanks!!! nicola On 09/13/2018 07:39 PM, Douglas N. Greve wrote: > not sure what your question is. The pcc should have the same sign as the > contrast. > > On 09/13/2018 12:20 PM, Nicola Toschi wrote: >> External Email - Use Caution >> >> Hi List, >> >> a dimple question about using partial correlation (pcc.mgh) as effect >> size measure. I am running multivariate regression and setting positive >> and negative contrasts one variable at a time, e.g. a design matrix with >> columns like >> >> Intercept Age Gender Fact1 Fact2 >> >> and a bunch of contrasts like >> >> 0 0 010 >> >> 0 0 0-10 >> >> Now let's say the second contrast gives me a significant results after >> MC correction in a certain cluster, what sign should i expect in PCC in >> that cluster (on average)? >> >> Thank you very much in advance, >> >> Nicola >> >> >> ___ >> 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
[Freesurfer] Workshop on Artificial Intelligence in NMR/MRI and Neuroscience
External Email - Use Caution Dear Freesurfer users, I hope this message is not out of place in this list. If it is, please ignore! I am writing to let you know about a high-level workshop we have organized titled "/The promises and Dark Sides of Artificial Intelligence in NMR, MRI and Neuroscience/", which is now online at https://secure-web.cisco.com/16ixw_i6BPFmKCirvs3yOpFZBsOe6rAcNXR8zplPC_9eTpxf0M8Fd5lx5d6Bw3a0kMz84SKsm92ef26jJ62Yt3mxREJKSu1mP2zgnUJiPln2lL7wScrD8iUOmiBMPCbttZBe5G1zDXMBxf1NF3z4rG-7mc8ZGyVeZsvmwbRokfAalUlVgq5-PQYHa8fAjad8700PcRJEFruZxEs84AZb_Tv3TlGgT0PeeCx15KGw23Ph2aKuofxFO_RPu4qgTdQlcQC4Y4lcYkPJ8Z56BbfB4YQ/https%3A%2F%2Fgidrm2020.uniroma2.it%2F (complete info are available on the website). We are particularly glad to have recruited _eminent speakers both from the scientific field and from Industry_ (e.g. Philips, Siemens, Amazon Web Services etc.) and to have been able to include talks on e.g. regulatory and ethical aspects as well as sections on e_xplainability, clinical applications and precision medicine_. The format is both asynchronous (until *March 31st*) and synchronous (*live *session on Feb *19th, 2021*). ** The registration *deadline *is *Feb 14th. *The workshop also carries 30 ECM credits.* * In the hope that this initiative may be of interest for you, your group (Empirical Inference) and Institute (MPI for Intelligent Systems), I would be most grateful if you could relay this scientific and educational resource among your local community as well as professional networks. Please, do not hesitate to contact me for more information. Best Regards, Nicola Toschi PS below you can find some social media posts of this annoucement for fast sharing: Twitter: https://secure-web.cisco.com/19wfe8NTs6BcghR1QgJE7XIPjlhtSJM-4phbv197Rde3id2yeia7qfxcDFaC55P4zo-MbUho1TZU1PzjDv-SuM2I4v0FtWYzDIHkj6yTJaMLN3Hn5UXKusdvokTXjB_PVJzaQrFlAXu1lSKuKqLXf04MqcAYeGAEHwIDZP6R6f1D755iVEwkxeov2QSmRT4lBuk7qgrYoiTr7dCvyo5TfNW95Rf2Cg6serTSch2_nq-fsw6ha6VceE2yYvvkTVWnKe65K4qN0R78PHaNH6Q8gPg/https%3A%2F%2Ftwitter.com%2FMedPhysTorVe%2Fstatus%2F1351684619788296192 Facebook: https://secure-web.cisco.com/1OFTx4jTf9EvgHOq_35AESclP5jtClp-vlijK5-rZTcxRqmPeha8L7unF90HwbG-LX0SBppZaqyASJc2Qt9SBSy3MwO-OArgPPLmK4fnVpvdAWsC6WlWlcRdkqj8pgPZJwUEHpVDkLrb4NEAm-hmXfFj5BlS2gLdLJpeRB18NQuNeZ6pwpYKcOv0k9lrBSs7C-iI9SotFH7YDhyIPzejuCZI_81cuot78KO2FJmSoXBz_ovY0z26oxq0g0gylwns7bG-Xht4eh7erk4cTgd5XIA/https%3A%2F%2Fwww.facebook.com%2F102581041868297%2Fposts%2F102592848533783%2F%3Fsfnsn%3Dscwshmo Instagram: https://secure-web.cisco.com/1USByxHXPJfIKKfcItZcYfTBdK3Fp7j9UmzaXhDIGQ1q1Kn99kepVoo6ka3a9LxO56PtbSKTElPmWaqoA4Ix2zfkujyrbvMnSaUAoepEqJDNwQQK_bE5gUECtnqkluX_NK65JToQTFSMBJBVbCboLyVXmFwv5klHJTGwlW79_h3qz5y8AtzjWatIJIo2B0c-o_pWtXiyBYpFYF7LiV0nRL1jlabVR6JiYfEPpbdHoQdOzWIeGW9hPm0sc_mT0tvu6SbRKWhJYuIs3k3wpyPotMQ/https%3A%2F%2Fwww.instagram.com%2Fp%2FCK7Z1Xlj416%2F%3Figshid%3Drtp5uwhaufph LinkedIn: https://secure-web.cisco.com/1viCIXQ0B_0IOfzus-8CBV-CbnJCh0nGG_2mS547pV27-8vCWksRdoilpGtFBc5qYoZaeyxOes_2LmYAmzqFOjH8-qFDwRBbmEtg_A_sZEGH_g82AJec778x6deSKOzz5vuucj6seExGodl9p46jk7550votefaaewvQ_EUUYOZtjot-IYhsAHwx963oeFAxtqgnqSpbhTHfP1lDiQ3Xro3Y-hCmK_SLMnaPaWvFKvQeo4esGMxhEGRKvNsf7tfLSVKwmgyeSrsCBSDt8v-okEg/https%3A%2F%2Fwww.linkedin.com%2Fposts%2Fnicola-toschi-5680923_physicists-computerscientist-engineers-activity-6757793367284969472-9IKh -- Prof. Nicola Toschi Associate Professor of Medical Physics Medical Physics Section - Department of Biomedicine and Prevention University of Rome "Tor Vergata" Via Montpellier 1 - 00133 Rome (IT) tos...@med.uniroma2.it Research Staff, Associate Investigator A.A. Martinos Center for Biomedical Imaging - Harvard Medical School/MGH 149 13th street, 02129 Boston (MA), USA nic...@nmr.mgh.harvard.edu -- This email has been checked for viruses by Avast antivirus software. https://secure-web.cisco.com/1jkaGBfKYYGqr5hk9GieAti-oND1hcigV7en69WTwpsQZb6YSOeMAvWqhEiSJYgFtR3LbLAQSYmmvQkVJhRljZqva_b1t0kmaFVdE0TqNxRfEqPzuaw8Oy2bEsn1GwCVunSKVE9T9ZHTEC5LbodAT9ZwT3VZgbrOW4UEYHSSMNQoshdABkdu1Ah3RkdPinL0lBJ0PPRjAG7Lk2Bo5v4rJwKL3jXg7oDS7rjO2purehy0WxUPZ_QG3Sj37YBchgxA2mtLODCw2b0G4mdtaozpC7Q/https%3A%2F%2Fwww.avast.com%2Fantivirus ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
