Re: [Freesurfer] How to compute area of subcortical structures

[Ruopeng Wang]

Hi Anirudh,

Lee was right. Label stats shown in freeview is for volume labels. It shows the 
stats of the underlying volume slice in that label.  It should not be compared 
with surface area.

Best,
Ruopeng

> On Nov 11, 2015, at 5:57 AM, anirudh nihalani  
> wrote:
> 
> Hi Bruce,
> 
>Sorry I forgot to attach the files mentioned in my last email. PFA the 
> files here. Thank you.
> 
> Regards,
> Anirudh
> 
> On Wed, 11 Nov 2015 at 16:18 anirudh nihalani  > wrote:
> Hi Bruce,
> 
> Thank you very much for your quick reply. Sorry I hadn't been able to 
> reply faster as I was trying to figure out the below mentioned issue from two 
> days.
> 
>  I have computed surface area of left-hippocampus using the commands 
> mri_tessellate and mris_info. However I found that in freeview by selecting 
> Tools->show label stats, I am able to display area of any label (PFA a 
> screenshot) but these area stats do not match with the areas obtained using 
> mri_tessellate and mris_info. I have two queries regarding this:
> 
> 1) Surface areas of labels displayed in freeview doesn't match with 
> subcortical structures' areas obtained by running mri_tesselate and 
> mris_info. For example the attached screenshot shows that area of 
> left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info 
> found the area for left-hippocampus to be 3586 (PFA the output of 
> mris_tessellate and mris_info). Why is there a mismatch?
> 
> 2) Based on your reply I thought area stats are not calculated for 
> subcortical structures during "recon-all". If that is the case, how is 
> freeview displaying area stats for subcortical areas? Also which file does 
> freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask 
> because even cortical structures' areas displayed by freeview are not 
> matching with what is stored in these files.
> 
> Please let me know. Thank you.
> 
> Regards,
> Anirudh
> ___
> 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.

Re: [Freesurfer] How to compute area of subcortical structures

[anirudh nihalani]

Hi Lee/Ruopeng,

Thank you for the information.

Regards,
Anirudh

On Thu, 12 Nov 2015 at 19:12 Ruopeng Wang 
wrote:

> Hi Anirudh,
>
> Lee was right. Label stats shown in freeview is for volume labels. It
> shows the stats of the underlying volume slice in that label.  It should
> not be compared with surface area.
>
> Best,
> Ruopeng
>
> On Nov 11, 2015, at 5:57 AM, anirudh nihalani 
> wrote:
>
> Hi Bruce,
>
>Sorry I forgot to attach the files mentioned in my last email. PFA the
> files here. Thank you.
>
> Regards,
> Anirudh
>
> On Wed, 11 Nov 2015 at 16:18 anirudh nihalani 
> wrote:
>
>> Hi Bruce,
>>
>> Thank you very much for your quick reply. Sorry I hadn't been able
>> to reply faster as I was trying to figure out the below mentioned issue
>> from two days.
>>
>>  I have computed surface area of left-hippocampus using the commands
>> mri_tessellate and mris_info. However I found that in freeview by selecting
>> Tools->show label stats, I am able to display area of any label (PFA a
>> screenshot) but these area stats do not match with the areas obtained using
>> mri_tessellate and mris_info. I have two queries regarding this:
>>
>> 1) Surface areas of labels displayed in freeview doesn't match with
>> subcortical structures' areas obtained by running mri_tesselate and
>> mris_info. For example the attached screenshot shows that area of
>> left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info
>> found the area for left-hippocampus to be 3586 (PFA the output of
>> mris_tessellate and mris_info). Why is there a mismatch?
>>
>> 2) Based on your reply I thought area stats are not calculated for
>> subcortical structures during "recon-all". If that is the case, how is
>> freeview displaying area stats for subcortical areas? Also which file does
>> freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask
>> because even cortical structures' areas displayed by freeview are not
>> matching with what is stored in these files.
>>
>> Please let me know. Thank you.
>>
>> Regards,
>> Anirudh
>>
> 
> ___
>
>
> 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


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 the surface

[Ray Razlighi]

Dear All,
I can't find the mris_decimate command any more in the new freesurfer
distribution. I assume there is substitute. Would someone direct me to the
substitute.
Also, I remember using mris_decimate changed the vertices coordinates. I
was wondering if there is any way to downsample the surface in a way that
the new vertices on the downsampled surface always fall on one of the
original ones. I know this is not possible with exact downsample ratio;
However I do not need exact downsampling ratio.

-- 
Sincerely,
Ray
___
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 the surface

[Douglas N Greve]

Where did you get the distribution from? I put a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_decimate


On 11/12/2015 09:59 AM, Ray Razlighi wrote:
> Dear All,
> I can't find the mris_decimate command any more in the new freesurfer 
> distribution. I assume there is substitute. Would someone direct me to 
> the substitute.
> Also, I remember using mris_decimate changed the vertices coordinates. 
> I was wondering if there is any way to downsample the surface in a way 
> that the new vertices on the downsampled surface always fall on one of 
> the original ones. I know this is not possible with exact downsample 
> ratio; However I do not need exact downsampling ratio.
>
> -- 
> Sincerely,
> Ray
>
>
> ___
> 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


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] Freesurfer@nmr.mgh.harvard.edu

[Douglas N Greve]

/
really? So if you run

ls -l 
/Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz/

what do you get?

On 11/11/2015 07:59 PM, Heidi Foo wrote:
> Hi Dr Greve,
>
> Yes it does, for all base templates, there 
> are lh(rh).long.thickness-avg(pc1, rate, and 
> spc).fwhm0(5,10,20,25).fsaverage.mgh files.
>
> I did the following steps in preprocessing:
>
> 1. recon-all -all -s  -i path_to_tpN_dc m
> 2. recon-all -base  -tp  -tp  ... -all
> 3. recon-all -long   -all
> 4. long_mris_slopes --qdec 
> /Users/nnidementia/Documents/PDFS/long.qdec.table.txt --meas thickness 
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label 
> --time years --qcache fsaverage --sd /Users/nnidementia/Documents/PDFS
> 5. long_mris_slopes --qdec 
> /Users/nnidementia/Documents/PDFS/QDEC/long.qdec.table.txt --meas 
> thickness --hemi lh --sd /Users/nnidementia/Documents/PDFS --do-pc1 
> --do-label --generic-time --fwhm 10 --qcache fsaverage --stack-pc1 
> /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.thickness-pc1.stack.mgh
>  
> --isec-labels 
> /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.fsaverage.cortex.label
>
> Thanks.
>
> Regards,
> Heidi Foo
>
>
>
>
> On Wed, Nov 11, 2015 at 11:57 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> does that file exist? Did you run recon-all -qcache ?
>
>
> On 11/11/15 7:54 AM, Heidi Foo wrote:
>> Apologies, the error message should be /Error in
>> analyze: couldn't open
>> 
>> /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz
>> or .mgh file./
>>
>> On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo > > wrote:
>>
>> Hi Dr Greve,
>>
>> Thank you for your advice, it is deeply appreciated. I
>> removed the blank lines of wmh.levels and included a carriage
>> return at the end of the long.qdec.table.txt.
>>
>> However, there is still /error in analyze: Couldn't open
>> 
>> /Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz
>> or .mgh file./
>> /
>> /
>> I checked my qdec.table.txt (both cross and long) but I did
>> not see any fsaverage included in the list of subjects. Am I
>> missing something?
>>
>> Thank you.
>>
>> Regards,
>> Heidi Foo
>> /
>> /
>>
>> On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve
>> > > wrote:
>>
>> Also, try removing the blank line at the end of
>> wmh.levels, and make sure you have a carriage return at
>> the end of long.qdec.table.txt. This may fix the 2nd error
>>
>> On 11/09/2015 10:38 PM, Heidi Foo wrote:
>>
>> Dear Dr Greve,
>>
>> Thanks for your reply. I have already linked
>> fsaverage to my SUBJECTS_DIR but the error still
>> persists.
>>
>> Attached is my qdec (long and cross) files.
>>
>> Thanks.
>>
>> Regards,
>> Heidi Foo
>>
>>
>>
>> On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve
>> > 
>> > >> wrote:
>>
>>
>>
>> On 11/06/2015 09:35 PM, Heidi Foo wrote:
>>
>> Dear FreeSurfer experts,
>>
>> I am trying to compare between stable WMH
>> group and rapid
>> progressed WMH group in regards to the
>> cortical thickness as
>> well as volume changes in the gray matter.
>> The nuisance
>> variable in my case is age. I ran my analysis
>> using QDEC but
>> encountered a few problems:
>>
>> 1. There is error in analyze: couldn't open file
>>
>> It looks like it cannot find fsaverage. Link it
>> to your
>> SUBJECTS_DIR if you have not already.
>>
>> 2. If this error doesn't appear, another one
>> does.
>> QdecGlmDesign::Create: zero factors!
>> (Attached the screenshot of the errors for
>> your perusal)
>>
>> please send the qdec file
>>
>>
>> I am hoping that you could give me a solution
>> to my problems.
>>
>> Thank you so much.
>>
>> Regards,
>> Heidi
>>
>>
>> -- Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@n

Re: [Freesurfer] Computing Statistics with Custom ROI Masks

[Douglas N Greve]

maybe you have a bad file? Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz


On 11/11/2015 08:46 PM, Shady El Damaty wrote:
> Hi FS-ers,
>
> I'm a bit stuck trying to compute cortical and subcortical statistics 
> using the Buckner 2011 Cerebellum mask.  I tried using mri_segstats to 
> generate the .stats file for the provided image:
>
> mri_segstats --seg
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --sum test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt
> --nonempty
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> cwd
> cmdline mri_segstats --seg
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> --sum test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt
> --nonempty
> sysname  Darwin
> hostname Apricot.local
> machine  x86_64
> user shady
> UseRobust  0
> Loading
> Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
> Segmentation fault: 11
>
>
> Clearly I am doing something wrong.  Can someone throw a pointer my 
> way about how I can go about computing statistics on my subjects (or 
> any arbitrary volume) using this mask?
>
> In the end I would like to be able to generate a .stats file for every 
> subject in my SUBJECTS_DIR using any custom mask.. how can I make this 
> possible?
>
> Your help would be very greatly appreciated!
>
>
> ___
> 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


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] group mean greater than X

[Douglas N Greve]

I don't think that will work because you'll have -5 in both groups which 
will then be removed when you take the group diff

On 11/11/2015 05:11 PM, Kirstie Whitaker wrote:
> Could you also just subtract 5 from all your input data? Then when you 
> test against zero (and only look at positive p values) you'll really 
> be testing whether the values are greater than 5?
>
> Kx
>
> On 11 November 2015 at 21:35, Douglas Greve  > wrote:
>
> I guess you could subtract 5 from the gamma.mgh, then recompute
> the t =
> gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t
> to a p
> or sig given the dof.
> doug
>
> ps. Please remember to include previous correspondences so we know the
> context of the question
>
> On 11/11/15 4:10 PM, Dace Apshvalka wrote:
> > Sorry, I was not very clear.
> >
> > I meant, how do I test whether the group mean is greater than 5, for
> > example.
> >
> > The default is 0, but can I change it somehow?
> >
> >
> > Dace
>
> ___
> 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.
>
>
>
>
> -- 
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> *Phone: *+44 7583 535 307
> *Website:* www.kirstiewhitaker.com 
>
>
> ___
> 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] 'mri_normalize' & 'mri_nu_correct', how do they work?

[Guido Orlando Pascariello]

Hi FS Experts

I'm bioengineering student and I'm working on my final project to get my
degree. it's about process neuroimaging (IRM) in order to cuantific some
parameter which could be helpful for medicine (clinical neurology).

I'm using FreeSurfer to process my data. It works realy good. But it will
be so much helpful to me if you can answer me a few question about it!

*FIRST ONE*:

I've been using 'mri_normalize' and I read the paper which describe it. But:


   1. In step 4: Discard outliers from the array: You suppose variation in
   intensity due to magnetic field inhomogeneities is smooth across space.
   But, field inhomogeneities are corrected in 'NuCorrect' module using N3.
   2. I understood the 1D normalization process. However the 3D
   normalization process works estimating a bias field like that which is
   corrected by 'NuCorrect' module.


Could you tell me why did you that? and what are diferences with
'NuCorrect' module?

*SECOND ONE*:

It's abuou 'mri_nu_correct':

I've read the description but I'm not sure about it. Does it use the N3
algorithm to work?

In the description is written that "changing the number of iterations
should be done carefully, because this can exacerbate artifacts". Could you
tell me what are these artifact? and why is the default number of iteration
four?

I'll be grateful if you can help
Being all for now, I await a reply

Guido PASCARIELLO
Facultad de Ingeniería - Universidad Nacional de Entre Ríos
Argentina
___
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] 'mri_normalize' & 'mri_nu_correct', how do they work?

[Douglas N Greve]

For n3/nu_correct, you should read the paper by Sled. For mri_normalize, 
it selects points that it strongly suspects are in 100% white matter. It 
is assumed that all WM is iso-intense, so any variation is bias field. 
It then uses soap bubble smoothing fill in the values between control 
points.

On 11/12/2015 10:45 AM, Guido Orlando Pascariello wrote:
> Hi FS Experts
>
> I'm bioengineering student and I'm working on my final project to get 
> my degree. it's about process neuroimaging (IRM) in order to cuantific 
> some parameter which could be helpful for medicine (clinical neurology).
>
> I'm using FreeSurfer to process my data. It works realy good. But it 
> will be so much helpful to me if you can answer me a few question 
> about it!
>
> *FIRST ONE*:
>
> I've been using 'mri_normalize' and I read the paper which describe 
> it. But:
>
>  1. In step 4: Discard outliers from the array: You suppose variation
> in intensity due to magnetic field inhomogeneities is smooth
> across space. But, field inhomogeneities are corrected in
> 'NuCorrect' module using N3.
>  2. I understood the 1D normalization process. However the 3D
> normalization process works estimating a bias field like that
> which is corrected by 'NuCorrect' module.
>
>
> Could you tell me why did you that? and what are diferences with 
> 'NuCorrect' module?
>
> *SECOND ONE*:
>
> It's abuou 'mri_nu_correct':
>
> I've read the description but I'm not sure about it. Does it use the 
> N3 algorithm to work?
>
> In the description is written that "changing the number of iterations 
> should be done carefully, because this can exacerbate artifacts". 
> Could you tell me what are these artifact? and why is the default 
> number of iteration four?
>
> I'll be grateful if you can help
> Being all for now, I await a reply
>
> Guido PASCARIELLO
> Facultad de Ingeniería - Universidad Nacional de Entre Ríos
> Argentina
>
>
> ___
> 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


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] aparcstats2table -- extracting multiple measures

[Eryilmaz, H. Hamdi]

Dear experts,

I am using aparcstats2table to extract values on a number of measures like 
thickness, curvature, folding index, and surface area for specific ROIs. Is it 
possible to create a table (using aparcstats2table)  with all these measures 
included or do I have to run it separately and create a separate table for each 
measure? Passing --meas flag multiple items did not work.

Thanks for your help!
Hamdi




___
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] aparcstats2table -- extracting multiple measures

[Douglas N Greve]

you have to run it separately

On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
> Dear experts,
>
> I am using aparcstats2table to extract values on a number of measures 
> like thickness, curvature, folding index, and surface area for 
> specific ROIs. Is it possible to create a table (using 
> aparcstats2table)  with all these measures included or do I have to 
> run it separately and create a separate table for each measure? 
> Passing --meas flag multiple items did not work.
>
> Thanks for your help!
> Hamdi
>
>
>
>
>
>
> ___
> 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


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] FreeSurfer question

[Tsapanou, Angeliki]

Hello,
I am dealing with a problem on FreeSurfer a couple of days now.
I want to fix the scull strip and I run the following commands:
cd /users/Angeliki/studyname
export SUBJECTS_DIR=studyname/subjid/session/T1/
recon-all -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas -subjid FreeSurfer

Then, the command works and the part of the cerebellum that I don't need turns 
brown.
I close it and I save the script with:  gedit 
~/FreeSurfer/Angeliki/run_reconalls_aut1.sh
And type at the script for echo: recon-all -autorecon2 -autorecon3 -subjid 
FreeSurfer
Finally, I submit it to the cluster with the command: 
~/FreeSurfer/Angeliki/run_reconalls_aut1.sh

The problem is that even though it runs properly (and I tried to add some 
control points and they work), the brown part of the cerebellum does not 
disappear, but remains there.

Is there something I have to change?

Thank you,
Best,
Angeliki Tsapanou


___
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 the surface

[Razlighi, Qolamreza R.]

Hi Doug,
It's missing from Mac version of the built v5.3.0. 
I just checked the Linux version for the same built and it is there. 
Is the one you sent compiled for Mac?
Also, I would really appreciate if you could kindly comment on my second 
question.

Thanks a lot

--
Ray Razlighi, Ph.D.
Assistant Professor
Quantitative Neuroimaging Laboratory
Division of Cognitive Neuroscience
Department of Neurology
Columbia University

Alt: razli...@gmail.com
Office Phone: 212-342-1352
Office Fax: 212-342-1838
Website: http://www.columbia.edu/cu/qnl/


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: Thursday, November 12, 2015 10:18 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Downsampling the surface

Where did you get the distribution from? I put a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_decimate


On 11/12/2015 09:59 AM, Ray Razlighi wrote:
> Dear All,
> I can't find the mris_decimate command any more in the new freesurfer
> distribution. I assume there is substitute. Would someone direct me to
> the substitute.
> Also, I remember using mris_decimate changed the vertices coordinates.
> I was wondering if there is any way to downsample the surface in a way
> that the new vertices on the downsampled surface always fall on one of
> the original ones. I know this is not possible with exact downsample
> ratio; However I do not need exact downsampling ratio.
>
> --
> Sincerely,
> Ray
>
>
> ___
> 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


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] aparcstats2table -- extracting multiple measures

[Eryilmaz, H. Hamdi]

Thanks Doug for the quick reply! Is there an option in aparcstats2table that 
allows to make a table with the folding index measure? If so, what variable 
should I use in the flag -meas? 

Best,
Hamdi



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: Thursday, November 12, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures

you have to run it separately

On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote:
> Dear experts,
>
> I am using aparcstats2table to extract values on a number of measures
> like thickness, curvature, folding index, and surface area for
> specific ROIs. Is it possible to create a table (using
> aparcstats2table)  with all these measures included or do I have to
> run it separately and create a separate table for each measure?
> Passing --meas flag multiple items did not work.
>
> Thanks for your help!
> Hamdi
>
>
>
>
>
>
> ___
> 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


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] 'mri_normalize' & 'mri_nu_correct', how do they work?

[Bruce Fischl]

Hi Guido

the nu_correct is a pretty gentle normalization and leaves a large 
residual bias field in some cases. We are much more aggressive in trying 
to flatten out the white matter over space, which improves our ability to 
recover thin gyri


cheers
Bruce
On Thu, 12 Nov 2015, Guido Orlando Pascariello wrote:


Hi FS Experts

I'm bioengineering student and I'm working on my final project to get my
degree. it's about process neuroimaging (IRM) in order to cuantific some
parameter which could be helpful for medicine (clinical neurology).

I'm using FreeSurfer to process my data. It works realy good. But it will be
so much helpful to me if you can answer me a few question about it!

FIRST ONE:

I've been using 'mri_normalize' and I read the paper which describe it. But:

 1. In step 4: Discard outliers from the array: You suppose variation in
intensity due to magnetic field inhomogeneities is smooth across space.
But, field inhomogeneities are corrected in 'NuCorrect' module using N3.
 2. I understood the 1D normalization process. However the 3D normalization
process works estimating a bias field like that which is corrected by
'NuCorrect' module.

Could you tell me why did you that? and what are diferences with 'NuCorrect'
module?

SECOND ONE:

It's abuou 'mri_nu_correct':

I've read the description but I'm not sure about it. Does it use the N3
algorithm to work?

In the description is written that "changing the number of iterations should
be done carefully, because this can exacerbate artifacts". Could you tell me
what are these artifact? and why is the default number of iteration four?

I'll be grateful if you can help
Being all for now, I await a reply

Guido PASCARIELLO
Facultad de Ingeniería - Universidad Nacional de Entre Ríos
Argentina
[mfLKTZL.gif]

___
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] recon-all error message

[Bruce Fischl]

I guess upload the dataset and we'll see if we can figure out what is going 
on
Bruce
On Thu, 12 Nov 
2015, Nicole Zurcher wrote:

>
> Hi Bruce/hi all,
>
> Yes I am sure that I did not run out of disk space and I still get this
> error message for mris_calc.
> Do you have any suggestions?
>
> Thanks in advance
> Nicole
>
>
>> Message: 1
>> Date: Mon, 9 Nov 2015 12:34:24 -0500 (EST)
>> From: Bruce Fischl 
>> Subject: Re: [Freesurfer] recon-all error message
>> To: Freesurfer support list 
>> Message-ID:
>>  
>> Content-Type: text/plain; charset=US-ASCII; format=flowed
>>
>> Hi Nicole
>>
>> that's a very strange error. Are you sure that you didn't run out of disk
>> space?
>>
>> Bruce
>
>> On Mon, 9 Nov 2015, Nicole Zurcher wrote:
>>
>>> Dear all,
>>>
>>> One of my freesurfer recons is failing and I am not sure how to
>>> troubleshoot.
>>>
>>> This is the error message that I get at the end of the recon-all log
>>> file:
>>>
>>> mris_calc -o lh.area.mid lh.area add lh.area.pial
>>> WARNING: # of slices=-106 in header - assuming 124...
>>> read_signa([path]/surf/I.001): could not open file
>>> No such file or directory
>>> mris_calc: could not establish read access to 'lh.area'.
>>> No such file or directory
>>>
>>> and this is the command that appears in the recon-all.error
>>> CMD mris_calc -o lh.area.mid lh.area add lh.area.pial
>>>
>>> See attachment for entire recon-all log file. Any help is greatly
>>> appreciated.
>>>
>>> Thanks a lot
>>> Nicole
>>>
>>
>
___
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] Trackvis/ Diffusion Toolkit

[Ruopeng Wang]

Hi Alan,

The tracks look weird. Why are they so straight?

Ruopeng

> On Nov 12, 2015, at 2:14 PM, Alan Francis  wrote:
> 
> Hi Anastasia:
> 
> It was great to meet you at the connectivity course at Martinos. I have been 
> using Trackvis to examine the white matter tracks between the anterior insula 
> and the Dorsal ACC. In line with your instruction, I created ROIS at each of 
> these regions. However, the WM tracks generated do not appear to connect. I 
> have attached a screenshot.
> 
> What is the command that one would use to connect the ROIs? 
> 
> thanks so much,
> 
> best regards,
> 
> Alan
> 
> -- 
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> 
> Alan N. Francis PhD
> NIDA T32  Fellow in Computational Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu  
> afran...@mclean.harvard.edu 
>   
>  
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
> ___
> 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] recon_checker missing output files

[Lauren Bystrom]

Dear Experts,

I am trying to run recon_checker on a set of subjects with brain tumors.
Since FreeSurfer cannot deal with this, I am using recon_checker -s SUBJID
-ignore lh. to try and ignore the processes on the hemisphere with the
tumor, but it keeps checking for those files anyway.

Also, it gives me an html file that is supposed to display my snapshot but
the images aren't appearing where the code says they should be. Could this
be caused by the absence of specific files that were missing in the
recon_all, on both hemispheres, and if so is there a way to get my snapshot
images without these files?
Lauren Bystrom
___
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] R: Re: R: Re: R: Re: R: Re: error MRS voxel as seed in FS-FAST

[stdp82]

Thanks.
But the MRS_mask should be in Tal, MNI or native?
Now I'm using a masks that overlaps orig.nii.gz.
Second, if I would like to create a sphere and use it as seed, there 
is a specific command line?


Stefano


>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 9-nov-2015 23.24
>A: 
>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: error MRS voxel as seed in 
FS-FAST
>
>So that mask has 22926 non-zero voxels? The only other thing I can 
think 
>of is that the registration is off. Have you checked that?
>
>On 11/06/2015 07:16 AM, std...@virgilio.it wrote:
>> I hope that this information are fine
>>
>> fslinfo $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz
>> data_type  FLOAT32
>> dim1   256
>> dim2   256
>> dim3   256
>> dim4   1
>> datatype   16
>> pixdim11.00
>> pixdim21.00
>> pixdim31.00
>> pixdim40.00
>> cal_max0.
>> cal_min0.
>> file_type  NIFTI-1+
>>
>>
>> fslstats $SUBJECTS_DIR/Control22/MRS_MASK.nii.gz -V
>> 22926 22926.00
>>
>> Thanks,
>>
>>
>> Stefano
>>
>>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 5-nov-2015 23.43
>>> A: 
>>> Ogg: Re: [Freesurfer] R: Re: R: Re: error MRS voxel as seed in FS-
>> FAST
>>> How many non-zero voxels are in MRS_MASK.mgz? Is MRS_MASK.mgz 
256^3,
>> 1mm3 ?
>>> On 11/05/2015 04:47 PM, std...@virgilio.it wrote:
 Please see the file attached.
 Thanks

 Stefanofile

  Messaggio originale
  Da: gr...@nmr.mgh.harvard.edu
  Data: 5-nov-2015 15.43
  A: 
  Ogg: Re: [Freesurfer] R: Re: error MRS voxel as seed in FS-
FAST

  sorry, should have been

  fcseed-sess -debug -s Control22_FS -cfg MRS_MASK.config |& 
tee
>> doug.log


  On 11/4/15 6:05 PM, std...@virgilio.it wrote:
>  Hi Dough,
>  in summary:
>  I have the MRS_MASK.mgz within $SUBJECTS_DIR/Control22/mri
>  thus, I have copy this file in fMRI directory
>> (fMRI/Control22_FS) the
>  MRS_MASK.mgz
>  and run:
>  fcseed-config -segid 1 -seg Control22_FS/MRS_MASK.mgz -fsd
>> rest -mean -
>  cfg MRS_MASK.config
>  fcseed-sess -s Control22_FS -cfg MRS_MASK.config
>
>  ...Writing to
>  
>> /Applications/freesurfer/subjects/fMRI/Control22_FS/rest/001/tmp.
>> fcseed-
>  sess.12305/avgwf.mgh
>  Segmentation fault
>
>  Therefore, according with your suggestion, I have now run:
>  fcseed-sess -debug -s -cfg MRS_MASK.config | & tee doug.log
>  ERROR: cound not find session -cfg
>
>  The doug.log is attached.
>
>  Thanks,
>
>
>  Stefano
>
>
>
>
>>  Messaggio originale
>>  Da:gr...@nmr.mgh.harvard.edu
>>  Data: 4-nov-2015 16.58
>>  A:
>>  Ogg: Re: [Freesurfer] error MRS voxel as seed in FS-FAST
>>
>>  First, when running fcseed-config, don't give it the full
>> path, just
>  the
>>  path relative to subject/mri (in this case only MRS_MASK.
mgz)
>>
>>  However, I don't think that is the  problem. Please run
>>
>>  fcseed-sess -debug -s -cfg MRS_MASK.config |& tee doug.log
>>
>>  and send  me doug.log
>>
>>
>>
>>
>>
>>  On 11/04/2015 04:14 AM,std...@virgilio.it  wrote:
>>>  Hi list, this error is still occurring:
>>>
>>>  mri_convert $SUBJECTS_DIR/subj/mri/MRS_MASK.nii.gz
>>>  $SUBJECTS_DIR//subj/mri/MRS_MASK.mgz
>>>  fcseed-config -segid 1 -seg 
$SUBJECTS_DIR//subj/mri/MRS_MASK.
>> mgz -
>  fsd
>>>  rest -mean -cfg MRS_MASK.config
>>>  fcseed-sess -s -cfg MRS_MASK.config
>>>
>>>  During
>>>
>>>  fcseed-sess -s subj -cfg MRS_MASK.config
>>>
>>>  Voxel Volume is 64.5752 mm^3
>>>  Generating list of segmentation ids
>>>  Found   1 segmentations
>>>  Computing statistics for each segmentation
>>>  0 1  0
>> 0.000
>>>  MRIalloc(0, 1, 1): bad parm
>>>  Reporting on   0 segmentations
>>>  Computing spatial average of each frame
>>>
>>>  Writing to
>> /Applications/freesurfer/subjects/fMRI/sub/rest/001/tmp.
>>>  fcseed-sess.97908/avgwf.mgh
>>>  Segmentation fault
>>>
>>>  I have read your previous message and you can check the 
MRS
>> voxel
>>>  features.
>>>  MRS voxel mask is in subj directory where I have run 
recon
>> all -
>  all.
>>>  data_type  FLOAT32
>>>  dim1   256
>>>  dim2   256
>>>  dim3   256
>>>  dim4   1
>>>  datatype   16
>>>  pixdim11.00
>>>  pixdim21.00