Thank you Doug,
Kindly one more question regarding mri_segstats:
The following two mri_segstats command lines:
mri_segstats --seg ${out1}/${i}/mri/aseg.mgz --sum
${out1}/${i}/stats/aseg.stats --pv ${out1}/${i}/mri/norm.mgz --empty
--excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in
${out1}/${i}/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR
--etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab
/usr/local/freesurfer/stable5_1_0/ASegStatsLUT.txt --subject ${i}
and
mri_segstats --seg${out1}/${i}/mri/aseg.mgz --ctab
/usr/local/freesurfer/stable5_3_0/FreeSurferColorLUT.txt --i
${out1}/${i}/fa.anat.mgh --sum ${out1}/${i}/fa.aseg.stats
Why in the second command line the output "aseg.stats" contains left and right
hemispheric white matter stats while in the first command line I don't have any
stats regarding left and right hemispheric white matter?
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 13, 2015 4:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats flags
maybe zeke can help you sort it out
On 04/13/2015 04:24 PM, Alshikho, Mohamad J. wrote:
> I got
>
> /usr/local/freesurfer/stable5_1_0/bin/mri_segstats
>
> and this is really weird because I thought that I am using FS 5.0.3.
>
> I am sourcing routinely the following script before I start FS
>
> #!/bin/tcsh
> setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0
> setenv USE_STABLE5_3_0
> setenv LD_LIBRARY_PATH /usr/lib64/GLoverride:/usr/lib/GLoverride
> setenv FSENV_KEEP_PROMPT
> setenv SUBJECTS_DIR /autofs/cluster/transcend/malshikho/2015/orig_data/recons
> setenv FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast
> setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.6
> setenv FSF_OUTPUT_FORMAT nii.gz
>
> source /usr/local/freesurfer/stable5_3_0
> source /usr/pubsw/packages/fsl/5.0.6
>
>
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, April 13, 2015 4:16 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats flags
>
> Are you sure you're using the new version?
> what do you get if you type
> which mri_segstats
>
>
>
>
> On 04/13/2015 03:41 PM, Alshikho, Mohamad J. wrote:
>> Hi Doug,
>> My system is Linux Centos 7
>>
>> I tried to run it and I got:
>>
>> [malshikh@glia 002201]$ mri_segstats --seg mri/aseg.mgz --sum
>> stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm
>> --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>> --seg-erode 2 --ctab /usr/local/freesurfer/stable5_1_0/ASegStatsLUT.txt
>> --subject 002201
>>
>> ERROR: Option --seg-erode unknown
>>
>>
>>
>>
>> ________________________________________
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Monday, April 13, 2015 3:22 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats flags
>>
>> Try this one
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
>>
>> This is for linux. If that is not your system, tell me what your system is
>>
>> doug
>>
>> On 04/13/2015 02:22 PM, Alshikho, Mohamad J. wrote:
>>> Hi Doug,
>>>
>>> Kindly I have the following questions regarding the command mri_segstats:
>>>
>>> ·I wanted to use the flag --seg-erode 2 in the command mri_segstats
>>> but I am receiving an error message that this flag is not available (
>>> I am using FreeSurfer 5.3.0 ).
>>>
>>> ·When the command recon-all finish. I don’t see the right or left
>>> cerebral white matter volumes in “aseg.stats”. Do I need to use
>>> specific flags in order to generate the statistics related to left and
>>> right hemispheric white matter. My command is like this:
>>>
>>> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>>> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
>>> --subcortgray --in mri/norm.mgz --in-intensity-name norm
>>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
>>> --totalgray --ctab /usr/local/freesurfer/stable5_1_0/ASegStatsLUT.txt
>>> --subject 075801
>>>
>>> Bests,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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