[Freesurfer] Convert TAL coordinates to surface RAS coordinates
Dear experts, I have a set of Talairach coordinates that I want to convert to the individual subject surf RAS coordinates. How can I do this? Thank you very much. Ines ___ 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] Convert TAL coordinates to surface RAS coordinates
Dear Douglas,
I've been looking a that page for a while now and I am very confused...
Are you referring to this example?
2. I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS"
from tksurfer) and want to compute the MNI305 RAS that corresponds to
this point:
MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info
--vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz
So, is it the case that I just do the equation like this:
[tkrR tkrA tkrS 1]' = [X Y Z (in MNIspace)] / TalXFM*Norig*inv(Torig)
Thank you,
ines
On Fri, Dec 11, 2015 at 4:12 PM, Douglas Greve
wrote:
>
> See if this helps
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
>
> On 12/11/15 10:23 AM, Inês Violante wrote:
>> Dear experts,
>>
>> I have a set of Talairach coordinates that I want to convert to the
>> individual subject surf RAS coordinates.
>> How can I do this?
>>
>> Thank you very much.
>>
>> Ines
>> ___
>> 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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Re: [Freesurfer] Convert TAL coordinates to surface RAS coordinates
Using the previous equation I tried to calculate [tkrR tkrA tkrS] for
MNI = [43 -69 47]. Which are ~ MNI coordinates for P4 (electrode 10-20
system)
[43 -69 47 1]/(TalXFM*Norig*inv(Torig))
This resulted in [46.0541 -7.9735 -4.1630]. However, this
coordinates in RAS surface space are not even near the place where
they were supposed to be, taking into account the projection of P4 to
the cortex.
Any ideas about what could be wrong?
Thank you very much,
ines
On Fri, Dec 11, 2015 at 4:20 PM, Inês Violante wrote:
> Dear Douglas,
>
> I've been looking a that page for a while now and I am very confused...
>
> Are you referring to this example?
>
> 2. I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS"
> from tksurfer) and want to compute the MNI305 RAS that corresponds to
> this point:
>
> MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'
>
> TalXFM: subject/orig/transforms/talairach.xfm Norig: mri_info
> --vox2ras orig.mgz Torig: mri_info --vox2ras-tkr orig.mgz
>
> So, is it the case that I just do the equation like this:
>
> [tkrR tkrA tkrS 1]' = [X Y Z (in MNIspace)] / TalXFM*Norig*inv(Torig)
>
>
> Thank you,
>
> ines
>
> On Fri, Dec 11, 2015 at 4:12 PM, Douglas Greve
> wrote:
>>
>> See if this helps
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>>
>>
>> On 12/11/15 10:23 AM, Inês Violante wrote:
>>> Dear experts,
>>>
>>> I have a set of Talairach coordinates that I want to convert to the
>>> individual subject surf RAS coordinates.
>>> How can I do this?
>>>
>>> Thank you very much.
>>>
>>> Ines
>>> ___
>>> 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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[Freesurfer] MNI to Surf RAS problems
Hi, I am trying to convert MNI coordinates to a subject's anatomical space surf coordinates. While this MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' works fine from surf coordinates to MNI I don't know how to make it work correctly the other way around... i.e., knowing MNI305RAS and wanting to know [tkrR tkrA tkrS]. Could anyone help me with this? Thank you! Ines ___ 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] accuracy of cerebellar segmenation
Dear all, Does anyone have information on the accuracy of cerebellar segmenation into GM and WM? Thank you very much. ines ___ 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] lobar WM volumes
Dear all, I need to obtain the white matter volume per lobe for a given numer of subjects. I started by using the following: mri_annotation2label --subject --hemi rh --lobesStrict lobe mri_aparc2aseg --s --labelwm --annot lobe and now I have a lobe+aseg.mgz file. How can I create a stats file containing the wm volume for each lobe? Thank you, ines ___ 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] lobar WM volumes
Dear all, I need to obtain the white matter volume per lobe for a given numer of subjects. I started by using the following: mri_annotation2label --subject --hemi rh --lobesStrict lobe mri_aparc2aseg --s --labelwm --annot lobe and now I have a lobe+aseg.mgz file. How can I create a stats file containing the wm volume for each lobe? Thank you, ines ___ 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] lobar WM volumes
Hi Doug, Thanks for your reply. However, I was not able to succeed. Can you give me an extra help? I created a new color table and I tried the following command: mri_segstats --seg $SUBJECTS_DIR/Subjid/mri/lobe+aseg.mgz --pv $SUBJECTS_DIR/Subjid/mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask $SUBJECTS_DIR/Subjid/mri/brainmask.mgz --in $SUBJECTS_DIR/Subjid/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject Subjid --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT_lobe.txt --sum Subjid.aseg.sum But it only makes calculations for temporal and parietal lobes and they don't seem like valid numbers. This is what is shown in the command line: Loading /home/user/Projects/Freesurfer/AC/mri/lobe+aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 224173 rh white matter volume 229757 Loading /home/user/Projects/Freesurfer/AC/mri/norm.mgz Loading /home/user/Projects/Freesurfer/AC/mri/norm.mgz Loading /home/user/Projects/Freesurfer/AC/mri/brainmask.mgz # nbrainmaskvoxels 1506513 # brainmaskvolume 1506513.0 # nbrainsegvoxels 232396 # brainsegvolume 232396.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 7 segmentations Computing statistics for each segmentation 1 1 frontal 0 2 2 cingulate 0 3 3 occipital 0 4 4 temporal 3706 3706 5 5 parietal 247 247 6 6 insula 0 Reporting on 2 segmentations Hope you can help. Thank you very much, ines On Mon, Apr 2, 2012 at 6:38 PM, Douglas N Greve wrote: > use mri_segstats. You can look in subjid/scripts/recon-all.log for > example command lines (look for the one with wmparc). The command will > require a color table. The ones in the log file will use the default > table, but this will not have the numbers/names of your lobar regions, > so you'll need to create a new color table (or add to the one that is > there). > doug > > On 04/02/2012 12:58 PM, Inês Violante wrote: >> Dear all, >> >> I need to obtain the white matter volume per lobe for a given numer of >> subjects. >> I started by using the following: >> >> mri_annotation2label --subject --hemi rh --lobesStrict lobe >> >> mri_aparc2aseg --s --labelwm --annot lobe >> >> and now I have a lobe+aseg.mgz file. How can I create a stats file >> containing the wm volume for each lobe? >> >> Thank you, >> >> ines >> >> ___ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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] lGI differences without variation in other cortical morphometric variables
Dear all, I am comparing a group of patients with controls. I extracted: cortical volume, surface area, cortical thickness and gyrification index for each subject's lobe. Comparisons between this variables with Total Intracranial Volume as a covariate indicated a difference in frontal and temporal lobes lGI. However, differences were not significant for any of the other variables. I can´t understand these results from a biological perspective. I was expecting that if a difference exist in lGI it would also manifest in surface area or volume. Can someone help me with an explanation for this? Thank you. ines ___ 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] lGI differences without variation in other cortical morphometric variables
Hi, Thank you so much for your reply. I am going to read the paper. However, if the increase in head size obscures the lGI, why this is not an overall variation? Meaning, why is only for the frontal and temporal lobes? thank you ines On Tue, May 15, 2012 at 4:30 PM, j janssen wrote: > Hi, > >> I am comparing a group of patients with controls. I extracted: >> cortical volume, surface area, cortical thickness and gyrification >> index for each subject's lobe. >> Comparisons between this variables with Total Intracranial Volume as a >> covariate indicated a difference in frontal and temporal lobes lGI. > > > what happens if you do not adjust for intracranial volume? if your patients > have abnormal sized lobes then this may be obscured by controlling for head > size. > >> >> However, differences were not significant for any of the other >> variables. >> >> I can´t understand these results from a biological perspective. I was >> expecting that if a difference exist in lGI it would also manifest in >> surface area or volume. > > > this paper: http://www.ncbi.nlm.nih.gov/pubmed/18267953 > > tells us that it is possible for smaller sized brains to have higher folding > compared to bigger sized brains. however, it also states that it's much more > probable for bigger sized brains to have a higher degree of folding, indeed > a strong relationship is shown between brain volume, cortical surface and > folding (Figs. 3 and 4c) over large parts of the cortex. > > hth, > -joost > > >> >> Can someone help me with an explanation for this? >> >> Thank you. >> >> ines >> >> ___ >> 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] average lGI for each subject's hemipshere
Dear all, How can I obtain an average lGI for each subject's hemipshere? I've tried: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh but I had the following error: ERROR: stating file .../label/lh.aparc.annot It calculates the lgi for each gyri label but it does not give average values for the hemisphere. Thanks a lot. ines ___ 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] average lGI for each subject's hemipshere
I think I got it, but it would be great if someone could tell me if this is wright: mris_anatomical_stats -l lh.cortex.label -t lh.pial_lgi -log file.txt SUBJECT lh pial thanks, ines On Tue, May 15, 2012 at 6:58 PM, Inês Violante wrote: > Dear all, > > How can I obtain an average lGI for each subject's hemipshere? > > I've tried: > > mris_anatomical_stats -mgz -f > lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ > lgi.annot.ctab -t pial_lgi > $SUBJECT lh > > but I had the following error: > > ERROR: stating file .../label/lh.aparc.annot > > It calculates the lgi for each gyri label but it does not give average > values for the hemisphere. > > Thanks a lot. > > ines ___ 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] Surface Area aparc from pial surface
Hi, I need to know the surface area of the structures in the aparc file but I want to obtain this measurement from the pial surface and not the white matter surface. How can I do that? Thank you a lot for your help. ines ___ 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] Surface Area aparc from pial surface
Hi, Thanks Michael. However, when I try to do this using the aparc.annot file: mris_anatomical_stats -l CS/label/lh.aparc.annot -b CS lh pial I receive this error: mris_anatomical_stats: could not scan # of lines from CS/label/lh.aparc.annot I imagine this happens because the mris_anatomical_stats is waiting for a .label file What I aim is the output of the aparcstats2table for the surface area using the pial surface. Perhaps I am not using the correct command Thanks for the help. ines On Fri, May 18, 2012 at 3:41 PM, Michael Harms wrote: > > The last argument of mris_anatomical_stats allows you to specify the > surface to use (pial in your case) > > cheers, > -MH > > > NAME > mris_anatomical_stats > > SYNOPSIS > mris_anatomical_stats [options] > [] > > > On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote: >> Hi, >> >> I need to know the surface area of the structures in the aparc file >> but I want to obtain this measurement from the pial surface and not >> the white matter surface. >> How can I do that? >> >> Thank you a lot for your help. >> >> ines >> ___ >> 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] Surface Area aparc from pial surface
Thank you. I've tried this command: mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial Would this be appropriate? ines On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve wrote: > And you can get the full command line from the > $subject/scripts/recon-all.log file > doug > > On 05/18/2012 10:41 AM, Michael Harms wrote: >> The last argument of mris_anatomical_stats allows you to specify the >> surface to use (pial in your case) >> >> cheers, >> -MH >> >> >> NAME >> mris_anatomical_stats >> >> SYNOPSIS >> mris_anatomical_stats [options] >> [] >> >> >> On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote: >>> Hi, >>> >>> I need to know the surface area of the structures in the aparc file >>> but I want to obtain this measurement from the pial surface and not >>> the white matter surface. >>> How can I do that? >>> >>> Thank you a lot for your help. >>> >>> ines >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>> error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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] Surface Area aparc from pial surface
Hi, It repeats this several times and MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 775162420 i=2E340A34, in_array_size=157940 annot file: CS/label/lh.aparc.annot (...) ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray! On Fri, May 18, 2012 at 4:53 PM, Douglas N Greve wrote: > Hi Ines, this is a good thing to post to the list since there are others > that might know better than me. Also, please include the full terminal > output. > thanks > doug > > > > > On 05/18/2012 11:51 AM, Inês Violante wrote: >> >> Thanks a lot! >> >> Just another question: >> I get this message for one of my subjects using the previous command: >> >> ERROR: Too many out-of-range vertex indices in >> MRISreadAnnotationIntoArray! >> >> I must have done something wrong. Is there a way to correct this >> without having to run the whole recon-all again? >> >> All the best, >> >> ines >> >> >> On Fri, May 18, 2012 at 4:46 PM, Douglas N Greve >> wrote: >>> >>> yes, but you might want to change the name of the stats file so that you >>> don't overwrite the one that is there >>> doug >>> >>> >>> On 05/18/2012 11:39 AM, Inęs Violante wrote: >>>> >>>> Thank you. >>>> >>>> I've tried this command: >>>> >>>> mris_anatomical_stats -f AC/stats/lh.aparc.stats -b -a >>>> AC/label/lh.aparc.annot -c ./aparc.annot.ctab AC lh pial >>>> >>>> Would this be appropriate? >>>> >>>> >>>> ines >>>> >>>> On Fri, May 18, 2012 at 4:32 PM, Douglas N Greve >>>> wrote: >>>>> >>>>> And you can get the full command line from the >>>>> $subject/scripts/recon-all.log file >>>>> doug >>>>> >>>>> On 05/18/2012 10:41 AM, Michael Harms wrote: >>>>>> >>>>>> The last argument of mris_anatomical_stats allows you to specify the >>>>>> surface to use (pial in your case) >>>>>> >>>>>> cheers, >>>>>> -MH >>>>>> >>>>>> >>>>>> NAME >>>>>> mris_anatomical_stats >>>>>> >>>>>> SYNOPSIS >>>>>> mris_anatomical_stats [options] >>>>>> [] >>>>>> >>>>>> >>>>>> On Fri, 2012-05-18 at 15:18 +0100, Inęs Violante wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I need to know the surface area of the structures in the aparc file >>>>>>> but I want to obtain this measurement from the pial surface and not >>>>>>> the white matter surface. >>>>>>> How can I do that? >>>>>>> >>>>>>> Thank you a lot for your help. >>>>>>> >>>>>>> ines >>>>>>> ___ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> The information in this e-mail is intended only for the person to >>>>>>> whom >>>>>>> it is >>>>>>> addressed. If you believe this e-mail was sent to you in error and >>>>>>> the >>>>>>> e-mail >>>>>>> contains patient information, please contact the Partners Compliance >>>>>>> HelpLine at >>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>>>>>> you >>>>>>> in error >>>>>>> but does not contain patient information, please contact the sender >>>>>>> and >>>>>>> properly >>>>>>> dispose of the e-mail. >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> ___ >>>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
