Re: [Freesurfer] recon-all Process Flow

[Rujing Zha]

Dear Bruce,
Thanks for your precious promt.
All the best.
2013-11-22



Rujing Zha



发件人：Bruce Fischl 
发送时间：2013-11-21 22:42
主题：Re: [Freesurfer] recon-all Process Flow
收件人："Rujing Zha"
抄送："freesurfer"

Hi Rujing 

sure, you can run them individually if you want. Just make sure it is in  
the right order and you don't skip any or they will fail 

cheers 
Bruce 
On Thu, 21 Nov 2013, Rujing  
Zha wrote: 

> Dear all, 
> As we know, recon-all is a integrated code. I have read this code process 
> flow in the website 
> http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. Can I run the a 
> series of command which are presented in command line step by step to 
> realize all the function of recon-all? 
> All the best. 
>   
> 2013-11-21 
>  
>  
> Rujing Zha 
>  
>  
> "Rujing Zha" 
> ?2013-11-21 22:30 
> ???Re:[Freesurfer] recon-all -s subjects -all unexpected termination 
> "freesurfer" 
> ??? 
>   
> Dear professor Bruce, 
> Thanks for your precious prompt. I will try it. 
> All the best. 
> Rujing Zha 
>   
>  
>  
> Bruce Fischl  
> ?2013-11-21 21:39 
> ???Re:[Freesurfer] recon-all -s subjects -all unexpected termination 
> "Rujing Zha" 
> ???"freesurfer" 
>   
> Hi Rujing  
>   
> run:  
>   
> recon-all -s  -make all  
>   
> that will figure out what needs to be rerun and do so.  
>   
> cheers  
> Bruce  
> On Thu, 21 Nov 2013,   
> Rujing Zha wrote:  
>   
> > Dear all,  
> > I have run recon-all for some subjects,but this code is unexpected  
> > terminated before it normally end. Can I run the code agian directly with 
> out  
> > deleting some outputs obtained from recon-all? That is to say, part of  
> > recon-all outputs do exist(as I have run recon-all previously), then  
> > recon-all new output will overwrite the existing files when I run recon-a 
> ll  
> > again?  
> > All the best.  
> >
> > 2013-11-21  
> >   
> > _ 
> ___  
> > Rujing Zha  
> >   
> >  
> ___  
> 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 i 
> s  
> addressed. If you believe this e-mail was sent to you in error and the e-ma 
> il  
> contains patient information, please contact the Partners Compliance HelpLi 
> ne at  
> http://www.partners.org/complianceline . If the e-mail was sent to you in e 
> rror  
> but does not contain patient information, please contact the sender and pro 
> perly  
> 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 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] comparing left and right cortical thickness

[Jacobs H (NP)]

Dear FreeSurfers,

Is it possible to compare left and right cortical thickness patterns, 
vertex-wise?

Thanks
Heidi



Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092

___
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] comparing left and right cortical thickness

[Shantanu Ghosh]

Maybe do an interhemispheric comparison?

On Fri, November 22, 2013 8:24 am, Jacobs H (NP) wrote:
> Dear FreeSurfers,
>
> Is it possible to compare left and right cortical thickness patterns,
> vertex-wise?
>
> Thanks
> Heidi
>
>
> 
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> h.jac...@maastrichtuniversity.nl
> www.maastrichtuniversity.nl
> www.heidijacobs.nl
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


-- 
Shantanu Ghosh, Ph.D.
Harvard Medical School & Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
Not only is the universe stranger than we think, it is stranger than we
can think. -Werner Heisenberg

___
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] help with save_nifti

[Leila Reddy]

Hi Doug,

Thanks for your reply. I have the problem even if I use MRIread and MRIwrite. 
But I have done a little more digging following your suggestions. Basically, 
there are differences in the output of mri_vol2surf (that I should have spotted 
earlier), as well as differences in the header information. I highlight the 
differences below, and I have put the detailed outputs of mri_vol2surf at the 
end in case you still need to look at it. 

I think the clearest way of explaining the different outcomes is as follows.:

1) mri_vol2surf performed on a nifti volume generated by Nibabel. Nothing done 
in Matlab.
mri_vol2surf ouput:
"Number of source voxels hit = 22587".
"niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm"
Results looks fine in tksurfer (i.e., I have a distribution of voxel values in 
the Configure Overlay window).
If I look at the nifti header, hdr.volres= [2.e+10 2.e+10 2.e+10] 
and several other fields (e.g., vox2ras etc) also have the same magnitude. In 
addition, hdr.niftihdr.dim'=[3    76    76    93 1 1 1 1]

2) The Nibabel nifti is opened in matlab with MRIread and immediately saved 
with MRIwrite. Nothing else is done to the data in Matlab.
Output of MRIread=WARNING: xyz units code 0 is unrecognized
Rescaling NIFTI: slope = 1, intercept = 0
mri_vol2surf output:
"Number of source voxels hit = 1".
Nothing about NIFTI_UNITS (note the header is the same as in 1 above). Rest of 
mri_vol2surf output is exactly as for #1 above.
The header values are as above except hdr.niftihdr.dim'=[4    76    76    93
 1 1 1 1]

3) The Nibabel nifti is opened in matlab with MRIread. The 3d volume is saved 
with MRIwrite but with the header information from a FSFAST created nifti.
mri_vol2surf says "Number of source voxels hit = 22587".
hdr.volres=[2 2 2] and other fields have values of the same order. 
hdr.niftihdr.dim'=[4    76    76    93 1 1 1 1]

I don't know if I have focused on the relevant header information here so I 
also attach the headers from steps 1-3 above.

Thanks a lot for your help and time on this. I will often have to go back and 
forth between python functions and Matlab/FS-FAST scripts so this will be very 
useful.

Leila

Detailed output of mri_vol2surf with fsfast header (#3 above):
mri_vol2surf --src fs_hdr.nii --hemi rh --out_type mgh --float2int round --o 
fshdr-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage
srcvol = fs_hdr.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /APPLICATIONS/freesurfer/subjects/fsaverage/mri/orig.mgz as target 
reference.
Reading surface /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.white
Done reading source surface
Reading thickness /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 22587
Writing to fshdr-rh.mgh
Dim: 163842 1 1

Detailed output of mri_vol2surf with nibabel header (after opening and saving 
in matlab) (#2 above):
 mri_vol2surf --src test.nii --hemi rh --out_type mgh --float2int round --o 
test-rh.mgh --projfrac 0.5 --trgsubject fsaverage --regheader fsaverage
srcvol = test.nii
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /APPLICATIONS/freesurfer/subjects/fsaverage/mri/orig.mgz as target 
reference.
Reading surface /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.white
Done reading source surface
Reading thickness /APPLICATIONS/freesurfer/subjects/fsaverage/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 1
Writing to test-rh.mgh
Dim: 163842 1 1

hdrs.mat
Description: application/matlab-workspace
___
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] re-running complete recon-all after manual edits

[Thomas Fink]

Dear Experts,

When re-running the complete recon-all stream after numeral manual edits
almost all the files in the mri folder are overwritten (apart from the
brain.finalsurfs.manedit.mgz,
brainmask.gcuts.mgz and mdi_nu_correct.mni.log.bak). The control points and
the changes of the brainmask are thus taken into account while the white
matter manual changes are disregarded (new wm.mgz).
Is this normal? Is there a trick to be able and keep the wm changes?

Thank you very much in advance,
Thomas
___
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] Order of edits for longitudinal data

[Martin Reuter]

Hi Rongxiang,

looks good. You seemed to need a lot of different types of edits though, 
usually you don't really need to edit much.
Surfaces in the base should be as accurate as possible, so you should 
fix topological defects there.


Best, Martin

On 11/14/2013 11:24 PM, Rongxiang Tang wrote:

Dear All,

I was would like to double check the order of edits for longitudinal 
data. I did edits for my cross-sectional data, and for my base data, I 
did the following:
1. skull strips edits (if necessary) 2. control points edits 3. white 
matter edits 4. pial edits 5.brain final surfs edits.
I was also wondering if correction for topological defects is needed 
for the base data.


Thanks,
Rongxiang




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

___
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] longitudinal 5.3 used with baseline fs 5.1 recon-all

[Martin Reuter]

Hi Knut,

yes you can. Make sure that you create all base (subject templates) and 
long runs with 5.3 and don't mix that with 5.1.


Best, Martin


On 11/19/2013 09:19 AM, Knut J Bjuland wrote:

Hi,
we have finished cross sectional scanworkups in Freesurfer 5.1 and 
gone through qa. Can we use these scanworkups for further processing 
in the longitudinal stream in Freesurfer 5.3?


Knut J


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

___
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] scale bar question

[Cesar Echavarria]

Hi freesurfers,

Anyone know what the scale bar in TkSurfer represents? From past threads I
gathered that it represent 1 cm on the human brain. However, the size of
the bar displayed gets smaller as I scale the brain up which does not make
sense if the bar is supposed to represent a constant length.

Cesar
___
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] scale bar question

[Douglas N Greve]

I think it is 1cm. I noticed that it gets smaller on the first zoom, but 
then it gets bigger after that. When I zoom in 3 or 4 times, I can 
measure the distance from end to end by looking at the xyz of the 
vertices at the ends, and it comes out to 10mm

doug

On 11/22/2013 12:10 PM, Cesar Echavarria wrote:
> Hi freesurfers,
>
> Anyone know what the scale bar in TkSurfer represents? >From past 
> threads I gathered that it represent 1 cm on the human brain. However, 
> the size of the bar displayed gets smaller as I scale the brain up 
> which does not make sense if the bar is supposed to represent a 
> constant length.
>
> Cesar
>
>
> ___
> 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] scale bar question

[Bruce Fischl]

Hi Cesar

what do you mean by "scale the brain up"?

Bruce
On Fri, 22 Nov 2013, Cesar 
Echavarria wrote:

> Hi freesurfers,
> Anyone know what the scale bar in TkSurfer represents? >From past threads I
> gathered that it represent 1 cm on the human brain. However, the size of the
> bar displayed gets smaller as I scale the brain up which does not make sense
> if the bar is supposed to represent a constant length.
> 
> Cesar
> 
>
___
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] scale bar question

[Cesar Echavarria]

I meant zoom in on the brain. I guess I'll take Doug's approach and
estimate the scale of the bar with the xyz coordinates.

Cesar


On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl
wrote:

> Hi Cesar
>
> what do you mean by "scale the brain up"?
>
> Bruce
>
> On Fri, 22 Nov 2013, Cesar Echavarria wrote:
>
>  Hi freesurfers,
>> Anyone know what the scale bar in TkSurfer represents? >From past threads
>> I
>> gathered that it represent 1 cm on the human brain. However, the size of
>> the
>> bar displayed gets smaller as I scale the brain up which does not make
>> sense
>> if the bar is supposed to represent a constant length.
>>
>> Cesar
>>
>>
>>
>
> 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.
>
>


-- 
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012
___
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] scale bar question

[Cesar Echavarria]

Actually, Doug can you tell me how to get the xyz coordinates on Tksurfer
so I can figure out the length of the bar as you did?

Thanks

Cesar


On Fri, Nov 22, 2013 at 12:19 PM, Cesar Echavarria
wrote:

> I meant zoom in on the brain. I guess I'll take Doug's approach and
> estimate the scale of the bar with the xyz coordinates.
>
> Cesar
>
>
> On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl  > wrote:
>
>> Hi Cesar
>>
>> what do you mean by "scale the brain up"?
>>
>> Bruce
>>
>> On Fri, 22 Nov 2013, Cesar Echavarria wrote:
>>
>>  Hi freesurfers,
>>> Anyone know what the scale bar in TkSurfer represents? >From past
>>> threads I
>>> gathered that it represent 1 cm on the human brain. However, the size of
>>> the
>>> bar displayed gets smaller as I scale the brain up which does not make
>>> sense
>>> if the bar is supposed to represent a constant length.
>>>
>>> Cesar
>>>
>>>
>>>
>>
>> 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.
>>
>>
>
>
> --
> Cesar Echavarria
> Research Assistant
> Martinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences | MIT 2012
>



-- 
Cesar Echavarria
Research Assistant
Martinos Center for Biomedical Imaging, Harvard-MGH
Brain & Cognitive Sciences | MIT 2012
___
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] scale bar question

[Douglas N Greve]

Just click on a point and look at the vertex RAS. At zoom=1, you have to 
translate the surface over to the scale bar. At zoom=1 I got about 10mm, 
but it did seem to change when I zoomed in.

doug


On 11/22/2013 12:23 PM, Cesar Echavarria wrote:
> Actually, Doug can you tell me how to get the xyz coordinates on 
> Tksurfer so I can figure out the length of the bar as you did?
>
> Thanks
>
> Cesar
>
>
> On Fri, Nov 22, 2013 at 12:19 PM, Cesar Echavarria 
> mailto:cechavarri...@gmail.com>> wrote:
>
> I meant zoom in on the brain. I guess I'll take Doug's approach
> and estimate the scale of the bar with the xyz coordinates.
>
> Cesar
>
>
> On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>
> wrote:
>
> Hi Cesar
>
> what do you mean by "scale the brain up"?
>
> Bruce
>
> On Fri, 22 Nov 2013, Cesar Echavarria wrote:
>
> Hi freesurfers,
> Anyone know what the scale bar in TkSurfer represents?
> >From past threads I
> gathered that it represent 1 cm on the human brain.
> However, the size of the
> bar displayed gets smaller as I scale the brain up which
> does not make sense
> if the bar is supposed to represent a constant length.
>
> Cesar
>
>
>
>
> 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.
>
>
>
>
> -- 
> Cesar Echavarria
> Research Assistant
> Martinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences | MIT 2012
>
>
>
>
> -- 
> Cesar Echavarria
> Research Assistant
> Martinos Center for Biomedical Imaging, Harvard-MGH
> Brain & Cognitive Sciences | MIT 2012

-- 
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] Moving already processed subjects from 5.1 to 5.3

[Soules, Mary]

Hi All-

We have a longitudinal study that is ongoing and we have already processed most 
of our scans to date with Freesurfer 5.1. We would like to upgrade our software 
to 5.3. Is there a way to bring the already reconstructed scans forward to 
Freesurfer 5.3 without starting over from scratch? Or, am I going to have to 
continue reconstructing my data in 5.1?

Thanks for your time,

Mary Soules

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 
___
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] affine registration with mri_robust_register

[Nathaniel Reynolds]

Hi all,

I can't find any explanation of how to perform an affine registration with 
mdi_robust_register. Could someone please explain?

Thanks,
Nathaniel
___
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] affine registration with mri_robust_register

[Lilla Zollei]

mri_robust_register --help

You would need to use the "--affine" flag.

Lilla


On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:

> Hi all,
>
> I can't find any explanation of how to perform an affine registration with 
> mdi_robust_register. Could someone please explain?
>
> Thanks,
> Nathaniel
> ___
> 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] TRACULA exists uncompleted

[Knut J Bjuland]

Hi

You should do cat -n 
$RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bvec 
and cat -n set bvalfile = 
$RAW_DATA/Bled_Jean_Jacques/TENSEUR_50_directions_ASSET_10/20121113_141004COMA201210s010a1001.bval 
to look for empty lines. Trac-all -prep -c runscript crashed because 
bvecs and bvals don't have the same number of entries.



Knut J


On 11/22/2013 10:34 PM, Emad Ahmadi wrote:

Hello,

I'm using TRACULA for analyzing a number of cases, and I've made a file to
successively run the three stages of pre-processing, model fitting, and
pathways reconstruction which is attached (ter1.tcsh). I've also attached
the configuration file I'm using (dmrircTer1.cshell).

The problem is that TRACULA exists uncompleted. I've attached the log
files. I'd really appreciate it if you let me know where I'm making some
sort of a mistake.

All the best,
Emad


___
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] mri_mi

[Nathaniel Reynolds]

Hi again,

Does anybody know about a function called "mri_mi"?

I have someone else's script that seems to utilize it, but I can't seem to 
access it myself.

Thanks,
Nathaniel
___
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_mi

[Lilla Zollei]

It is not checked in as of now to the FS distribution. I can send it to 
you.

On Fri, 22 Nov 2013, Nathaniel Reynolds wrote:

> Hi again,
>
> Does anybody know about a function called "mri_mi"?
>
> I have someone else's script that seems to utilize it, but I can't seem to 
> access it myself.
>
> Thanks,
> Nathaniel
> ___
> 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] Fixed-Effects Analysis carried out by mri_glmfit

[Clark Fisher]

Hi Freesurfers,

I am working with fsfast, and interested in doing a 2nd-level fixed effects 
analysis over a number of subjects.  However, the volumes I'm using aren't in a 
standard freesurfer space (native, talraich, etc.).  They are nx1x1 volumes 
containing results from n ROIs.  While I got first level analysis in fs-fast 
working, I don't think I'll get mri_glmfit to work in this space.

What is the math that mri_glmfit carries out to do the fixed-effects analysis?  
Based on the inputs, it seems to rely upon the variance and degrees of freedom 
from each individual subject, and I can't find a formula in the general MRI 
literature (or in the freesurfer group analysis presentation) that uses both of 
these in a fixed-effects analysis.

Thanks,
Clark
___
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] LONG stream question {Disarmed}

[Kirov, Ivan]

Dear FreeSurfer group/Dr. Reuter,

My questions are in regards to the LONG stream.

My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

1) Error message
During the creation of the BASE, I get the following error in the beginning of 
the recon:
>>>WARNING: Image geometries differ across time, maybe due to aquisition 
>>>changes?
 This can potentially bias a longitudinal study! Will continue in 
10s.
What should I be aware of in regards to this error?

The images were all acquired using the same MPRAGE protocol.
All timepoints were fed MPRAGEs reconstructed in the axial orientation, but 
some may have been reconstructed at an angle. I was assured that this is not an 
issue for FreeSurfer, but could this be the reason for the error?


2) Conversion of LONG run aseg.mgz segmentations to native anatomical space

Executing the commands for converting aseg.mgz to native space 
(http://freesurfer.net/fswiki/FsAnat-to-NativeAnat)
 in the folder of a long run (me1.long.me_base) does not convert.

It seems to me that (unlike the cross runs) the long runs are all in the same 
space (in the template/ base space?) and their rawavg.mgz does not match that 
of the corresponding cross run. Some insight on this would be appreciated.

The question is how to convert an individual long run's aseg.mgz into native 
anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run?

Thank you very much!
Ivan

--
Ivan Kirov, PhD
Postdoctoral fellow
New York University School of Medicine
Center for Biomedical Imaging
660 1st Ave, 4th floor, New York, NY 10016
Tel: 212-263-3337
Fax: 212-263-7541

This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain information that is proprietary, 
confidential, and exempt from disclosure under applicable law. Any unauthorized 
review, use, disclosure, or distribution is prohibited. If you have received 
this email in error please notify the sender by return email and delete the 
original message. Please note, the recipient should check this email and any 
attachments for the presence of viruses. The organization accepts no liability 
for any damage caused by any virus transmitted by this email.
=
___
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] LONG stream questions

[Kirov, Ivan]

Dear FreeSurfer group/Dr. Reuter,

My questions are in regards to the LONG stream.

My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

1) Error message
During the creation of the BASE, I get the following error in the beginning of 
the recon:
>>>WARNING: Image geometries differ across time, maybe due to aquisition 
>>>changes?
 This can potentially bias a longitudinal study! Will continue in 
10s.
What should I be aware of in regards to this error?

The images were all acquired using the same MPRAGE protocol.
All timepoints were fed MPRAGEs reconstructed in the axial orientation, but 
some may have been reconstructed at an angle. I was assured that this is not an 
issue for FreeSurfer, but could this be the reason for the error?


2) Conversion of LONG run aseg.mgz segmentations to native anatomical space

Executing the commands for converting aseg.mgz to native space (as noted in the 
FsAnat-to-NativeAnat wiki entry) in the folder of a long run (me1.long.me_base) 
does not convert.

It seems to me that (unlike the cross runs) the long runs are all in the same 
space (in the template/ base space?) and their rawavg.mgz does not match that 
of the corresponding cross run. Some insight on this would be appreciated.

The question is how to convert an individual long run's aseg.mgz into native 
anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run?

Thank you very much!
Ivan

--
Ivan Kirov, PhD
Postdoctoral fellow
New York University School of Medicine
Center for Biomedical Imaging
660 1st Ave, 4th floor, New York, NY 10016
Tel: 212-263-3337
Fax: 212-263-7541

This email message, including any attachments, is for the sole use of the 
intended recipient(s) and may contain information that is proprietary, 
confidential, and exempt from disclosure under applicable law. Any unauthorized 
review, use, disclosure, or distribution is prohibited. If you have received 
this email in error please notify the sender by return email and delete the 
original message. Please note, the recipient should check this email and any 
attachments for the presence of viruses. The organization accepts no liability 
for any damage caused by any virus transmitted by this email.
=
___
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.