Re: [Freesurfer] segmentation help

[Dilip Puri]

In this regard I've decided to change the dataset. We're going for ADNI
Dataset  where I can find data in various
format(nifti, mnc).

Is there any other dataset I can find labeled dataset for Hippocampus
segmentation.

Thank you for helping me!

Dilip

On Mon, Apr 10, 2017 at 6:31 PM, Bruce Fischl 
wrote:

> you can also just give them to recon-all directly. Analyze is a dangerous
> format to use however as it doesn't allow you to determine left from right.
> Hopefully you have some type of fiducial marker in the image (e.g. a
> vitamin E tablet)
>
> cheers
> Bruce
> On Mon, 10 Apr 2017, Nina Jacobsen wrote:
>
> Hi Dilip,
>> Try the mri_convert function to convert your images, so recon-all can read
>> them:
>> https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert
>> .help.xml.html
>>
>> 
>> 
>> Fra: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri
>> [dilippurip...@gmail.com]
>> Sendt: 10. april 2017 10:02
>> Til: Freesurfer support list
>> Emne: Re: [Freesurfer] segmentation help
>>
>> Hi all,
>>
>> Actually I've images in Analyze7.5 format(.img/.hdr).
>> Can anyone help me to reconstruct('recon-all') for this format.
>>
>> Thanks
>> Dilip
>>
>> On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen 
>> wrote:
>>   Hi Dilip.
>> You have to place your files where the subject-directory points. If
>> you dont change the directory yourself, this is under
>> freesurfer/subjects.
>>
>> For more info about recon all,see https://surfer.nmr.mgh
>> .harvard.edu/fswiki/recon-allhttps://surfer.nmr.m
>> gh.harvard.edu/fswiki/recon-all
>>
>> Nina.
>>
>> 
>> 
>>
>> Fra: freesurfer-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri
>> [dilippurip...@gmail.com]
>> Sendt: 10. april 2017 07:46
>> Til: Freesurfer support list
>> Emne: Re: [Freesurfer] segmentation help
>>
>> Hi,
>>
>> To-do "recon-all" where should I keep all the files. I mean in which
>> directory. What are the command lines?
>>
>>
>> Hope for response.
>>
>>
>> Thanks
>> Dilip
>>
>> On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl
>>  wrote:
>>   Hi Dilip
>>
>>   you need to run your image through recon-all.
>>
>>   cheers
>>   Bruce
>>
>>   On Sun, 9 Apr 2017, Dilip Puri
>>   wrote:
>>
>>   > Hi all,
>>   >
>>   > I've 200 analyze7.5 format images(OASIS Dataset) and I
>>   want to segment
>>   > HippoCampus.
>>   >
>>   > My input file xyz.img and output file will be like
>>   xyz_seg.img which
>>   > contains only hippocampus image it like Grond Truth
>>   image for my original
>>   > input image.
>>   >
>>   > Here is sample files including original and segmented
>>   mask link.
>>   >
>>   > Even I am very new to FREESURFER so I don't know the
>>   procedure to
>>   > reconstruct the images.
>>   >
>>   >
>>   > Kindly help me.
>>   >
>>   >
>> ___
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>>
>>
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>> dispose of the e-mail.
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>>
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>>
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Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

[Bruce Fischl]

sorry, not easily. I guess you could recon them in the newer version then 
try using mri_label2label to transport them to the older one, but it isn't 
trivial since the fsaverage coordinate system has changed


Bruce

On Mon, 10 Apr 2017, Taylor, Johnmark wrote:


(the reason I did this was because the new Freesurfer version outputs labels
for perirhinal cortex as part of the reconstruction process, and we were
interested in using this ROI in our analyses; as an additional question, is
there a way of producing these anatomical labels without reconstructing the
surface from scratch?)

On Mon, Apr 10, 2017 at 5:46 PM, Taylor, Johnmark
 wrote:
  Hello,
Recently, I re-ran recon-all with Freesurfer version 5 on some
subjects whose surfaces had previously been reconstructed with
Freesurfer version 4. As a result, it appears that their surface
reconstructions have subtly changed, such that the labels that were
specified in the old reconstruction are all messed up in the new
reconstruction (since the surfaces that they were once associated with
have changed). Did recon-all change between Freesurfer versions, and
if so, is there a way to go back to the old algorithm short of simply
switching back to Freesurfer version 4? It is possible that I have
accidentally changed something else and that's why the surface files
are different, but I wanted to see if there were any changes in the
reconstruction algorithm between versions that might have caused this.

Thank you very much,

JohnMark Taylor 



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Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

[Taylor, Johnmark]

(the reason I did this was because the new Freesurfer version outputs
labels for perirhinal cortex as part of the reconstruction process, and we
were interested in using this ROI in our analyses; as an additional
question, is there a way of producing these anatomical labels without
reconstructing the surface from scratch?)

On Mon, Apr 10, 2017 at 5:46 PM, Taylor, Johnmark <
johnmarktay...@g.harvard.edu> wrote:

> Hello,
>
> Recently, I re-ran recon-all with Freesurfer version 5 on some subjects
> whose surfaces had previously been reconstructed with Freesurfer version 4.
> As a result, it appears that their surface reconstructions have subtly
> changed, such that the labels that were specified in the old reconstruction
> are all messed up in the new reconstruction (since the surfaces that they
> were once associated with have changed). Did recon-all change between
> Freesurfer versions, and if so, is there a way to go back to the old
> algorithm short of simply switching back to Freesurfer version 4? It is
> possible that I have accidentally changed something else and that's why the
> surface files are different, but I wanted to see if there were any changes
> in the reconstruction algorithm between versions that might have caused
> this.
>
> Thank you very much,
>
> JohnMark Taylor
>
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Re: [Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

[Bruce Fischl]

Hi JohnMark

lots of things change between versions and it is not possible to go back 
unless you just run the old version


cheers
Bruce
On Mon, 10 Apr 2017, Taylor, Johnmark 
wrote:



Hello,
Recently, I re-ran recon-all with Freesurfer version 5 on some subjects
whose surfaces had previously been reconstructed with Freesurfer version 4.
As a result, it appears that their surface reconstructions have subtly
changed, such that the labels that were specified in the old reconstruction
are all messed up in the new reconstruction (since the surfaces that they
were once associated with have changed). Did recon-all change between
Freesurfer versions, and if so, is there a way to go back to the old
algorithm short of simply switching back to Freesurfer version 4? It is
possible that I have accidentally changed something else and that's why the
surface files are different, but I wanted to see if there were any changes
in the reconstruction algorithm between versions that might have caused
this.

Thank you very much,

JohnMark Taylor 

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[Freesurfer] Difference in Recon-All Output Between Freesurfer Versions?

[Taylor, Johnmark]

Hello,

Recently, I re-ran recon-all with Freesurfer version 5 on some subjects
whose surfaces had previously been reconstructed with Freesurfer version 4.
As a result, it appears that their surface reconstructions have subtly
changed, such that the labels that were specified in the old reconstruction
are all messed up in the new reconstruction (since the surfaces that they
were once associated with have changed). Did recon-all change between
Freesurfer versions, and if so, is there a way to go back to the old
algorithm short of simply switching back to Freesurfer version 4? It is
possible that I have accidentally changed something else and that's why the
surface files are different, but I wanted to see if there were any changes
in the reconstruction algorithm between versions that might have caused
this.

Thank you very much,

JohnMark Taylor
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Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

[Douglas N Greve]

They are being run but do not need to be. It does not change the 
results, but it is not needed and wastes cycles.


On 04/10/2017 04:24 PM, Antonin Skoch wrote:
> Dear Doug,
>
> do you think that it is necessary/useful to rerun
>
> -normalization2
> -maskbfs
> -segmentation
>
> steps after wm.mgz have been edited (that is what the -autorecon2-wm is used 
> for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
>
> In contrast, it seems to me that the documentation is more close to the 
> optimum (the three steps: normalization, mask and segmentation steps are run 
> only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
>
> Antonin
>
>
> I think the stages in the command line help are out of date
> On 04/08/2017 05:58 PM, Antonin Skoch wrote:
> > Dear experts,
> >
> > I noticed inconsistency between recon-all -help and actual code of
> > recon-all in -autorecon2-wm option.
> > According to the recon-all --help the -autorecon2-wm processes stages
> > 15-23 (fill through make white surfaces) and -autorecon2-cp processes
> > stages 12-23 (normalization2 throuhgh make white surfaces). But, in
> > the code both -autorecon2-wm and -autorecon2-cp are equivalently
> > processing stages 12-23.
> >
> > It seems to me that the stages 12-14 are not needed to process again
> > in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
> >
> > Could you please comment on?
> >
> > Regards,
> >
> > Antonin Skoch
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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Re: [Freesurfer] Surface down sample by taking cortical vertices only

[dg wakeman]

Hi Dorothy,

That would be extreme under sampling. I don't expect it to be very meaningful.

hth
d

On Mon, Apr 10, 2017 at 2:42 PM, Dorothy Sincasto  wrote:
> Hi
>
> I want to do an MEG analysis and first I want to downsample the surface to
> around 100 vertices per hemisphere.  I tried the command mris_downsample,
> but when i plot the surface I see that the vertices go deep into the white
> matter.
>
> Is there an option to extract for example 100 equidistant vertices from a
> fsaverage?  Maybe knowing  how the vertices are organized when saved would
> help, so for example, when I load a surface in matlab the vertices are shown
> as a vector, is there a way to know the spatial order?
>
> Thanks
> Dorothy
>
>
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>
>
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> HelpLine at
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Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

[Douglas N Greve]

oops, sorry, I thought you were asking about your other question...


On 04/10/2017 04:45 PM, Douglas N Greve wrote:
> I'm not sure. The problem is in the segmentation. There are several
> steps in the segmentation, and it actually gets it right in the early
> ones but then undoes it later on. There are some parameters that can be
> played with (eg, -prior 0.5), I just have not had the chance to dig into
> it.
>
>
> On 04/10/2017 04:24 PM, Antonin Skoch wrote:
>> Dear Doug,
>>
>> do you think that it is necessary/useful to rerun
>>
>> -normalization2
>> -maskbfs
>> -segmentation
>>
>> steps after wm.mgz have been edited (that is what the -autorecon2-wm is used 
>> for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
>>
>> In contrast, it seems to me that the documentation is more close to the 
>> optimum (the three steps: normalization, mask and segmentation steps are run 
>> only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
>>
>> Antonin
>>
>>
>> I think the stages in the command line help are out of date
>> On 04/08/2017 05:58 PM, Antonin Skoch wrote:
>>> Dear experts,
>>>
>>> I noticed inconsistency between recon-all -help and actual code of
>>> recon-all in -autorecon2-wm option.
>>> According to the recon-all --help the -autorecon2-wm processes stages
>>> 15-23 (fill through make white surfaces) and -autorecon2-cp processes
>>> stages 12-23 (normalization2 throuhgh make white surfaces). But, in
>>> the code both -autorecon2-wm and -autorecon2-cp are equivalently
>>> processing stages 12-23.
>>>
>>> It seems to me that the stages 12-14 are not needed to process again
>>> in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
>>>
>>> Could you please comment on?
>>>
>>> Regards,
>>>
>>> Antonin Skoch
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

[Douglas N Greve]

I'm not sure. The problem is in the segmentation. There are several 
steps in the segmentation, and it actually gets it right in the early 
ones but then undoes it later on. There are some parameters that can be 
played with (eg, -prior 0.5), I just have not had the chance to dig into 
it.


On 04/10/2017 04:24 PM, Antonin Skoch wrote:
> Dear Doug,
>
> do you think that it is necessary/useful to rerun
>
> -normalization2
> -maskbfs
> -segmentation
>
> steps after wm.mgz have been edited (that is what the -autorecon2-wm is used 
> for I suppose)? The wm.mgz is not used in this steps as far as I can tell.
>
> In contrast, it seems to me that the documentation is more close to the 
> optimum (the three steps: normalization, mask and segmentation steps are run 
> only when it is needed - in -autorecon2-cp, not in -autorecon2-wm).
>
> Antonin
>
>
> I think the stages in the command line help are out of date
> On 04/08/2017 05:58 PM, Antonin Skoch wrote:
> > Dear experts,
> >
> > I noticed inconsistency between recon-all -help and actual code of
> > recon-all in -autorecon2-wm option.
> > According to the recon-all --help the -autorecon2-wm processes stages
> > 15-23 (fill through make white surfaces) and -autorecon2-cp processes
> > stages 12-23 (normalization2 throuhgh make white surfaces). But, in
> > the code both -autorecon2-wm and -autorecon2-cp are equivalently
> > processing stages 12-23.
> >
> > It seems to me that the stages 12-14 are not needed to process again
> > in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
> >
> > Could you please comment on?
> >
> > Regards,
> >
> > Antonin Skoch
>
>
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-- 
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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
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Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

[Antonin Skoch]

Dear Doug,

do you think that it is necessary/useful to rerun

-normalization2
-maskbfs
-segmentation

steps after wm.mgz have been edited (that is what the -autorecon2-wm is used 
for I suppose)? The wm.mgz is not used in this steps as far as I can tell. 

In contrast, it seems to me that the documentation is more close to the optimum 
(the three steps: normalization, mask and segmentation steps are run only when 
it is needed - in -autorecon2-cp, not in -autorecon2-wm).

Antonin


I think the stages in the command line help are out of date
On 04/08/2017 05:58 PM, Antonin Skoch wrote:
> Dear experts,
>
> I noticed inconsistency between recon-all -help and actual code of 
> recon-all in -autorecon2-wm option.
> According to the recon-all --help the -autorecon2-wm processes stages 
> 15-23 (fill through make white surfaces) and -autorecon2-cp processes 
> stages 12-23 (normalization2 throuhgh make white surfaces). But, in 
> the code both -autorecon2-wm and -autorecon2-cp are equivalently 
> processing stages 12-23.
>
> It seems to me that the stages 12-14 are not needed to process again 
> in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
>
> Could you please comment on?
>
> Regards,
>
> Antonin Skoch___
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Re: [Freesurfer] Mri_convert defaults to trilinear interpolation if "--like" option is used, regardless of "-rt nearest"

[Douglas N Greve]

I don't know if this is fixed or not, but you can use mri_vol2vol with 
the --regheader option and specify the interpolation method with --interp


On 03/29/2017 06:25 PM, Harris Hoke wrote:
>
> I’m currently running freesurfer 6.0.0, and I’ve run into the same 
> problem described in this thread on the archives 
>  
> . Does anyone know if a fix exists?
>
> ~Harris
>
> ​
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] calculating geodesic distances between vertices

[Douglas N Greve]

Mukund Balasubramanian did something with barycentric coordinates to 
solve this problem, but I don't know whether he ended up publishing it 
or not.


On 03/30/2017 06:19 PM, Burke Rosen wrote:
> I am interested in finding the distance between two vertices along the 
> cortical surface.
>
> So far I have used two methods:
>
> (1) Compute the shortest path with a variant of Dijkstra's algorithm 
> on the white surface.
>
> (2) Compute the great circle distance on the sphere surface.
> (as done by Risk et.al . 2016 Neuroimage)
>
> Method (1) is slow and will tend to overestimate distances as the path 
> only goes along mesh edges.
>
> Method (2) is very fast and gives a true geodesic but gives a scaled 
> result because the radius of  sphere surface is arbitrary; also this 
> method is subject to distortions introduced by the inflation algorithm.
>
> My current strategy is to perform a linear regression between the 
> triangle face areas of the sphere and white surfaces. And then apply 
> the coefficients to the sphere surface diameter before calculating 
> geodesic distances. This yields a distance matrix with a similar 
> pattern to the Method (1) at about 62% scale. That scale seems like it 
> might be reasonable. However, the regression only explains ~58% of the 
> variance. My hunch is that the rest is due to inflation distortions.
>
> Is there a better way of scaling the sphere surface? Or a way to 
> inflate in such a way that inter-vertex distances are preserved? Or, 
> more generally, what is a good method of computing geodesic distances 
> on freesurfer surfaces.
>
> Thank you,
>
> Burke Rosen
>
>
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Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Douglas N Greve]

It estimates the FWHM from the residuals of the analysis (it does not 
use whatever value you smoothed it with). For some reason this estimate 
is not-a-number (NaN). Are you using a mask? Can you send the terminal 
output from running mri_glmfit?


On 03/31/2017 03:29 AM, Clara Kühn wrote:
> ah, ok. I used the proper glmdir now with this command:
>   mri_glmfit-sim --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ 
> --cache-dir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
> --cache 3.0 abs --cwp 0.05 --2spaces
>
> And this is the terminal output:
>
> cmdline mri_glmfit --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>  --fsgd 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>  doss --C 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>
> WARNING: unrecognized mri_glmfit cmd option doss
>
> log file is 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//cache.mri_glmfit-sim.log
>
> cd /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2
> /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/mri_glmfit-sim
> --glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ 
> --cache-dir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
> --cache 3.0 abs --cwp 0.05 --2spaces
>
> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> Fri Mar 31 09:17:53 CEST 2017
> Linux etsch 4.4.0-66-generic #87-Ubuntu SMP Fri Mar 3 15:29:05 UTC 2017 
> x86_64 x86_64 x86_64 GNU/Linux
> ckuehn
> setenv SUBJECTS_DIR /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/
> FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64
>
> Original mri_glmfit command line:
> cmdline mri_glmfit --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>  --fsgd 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>  doss --C 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = doss
> fwhm = -nan
> ERROR: cannot find 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-corcortex/fwhmNaN/abs/th30/mc-z.csd
>
>
>
> For some reason it doesn't recognize that I smoothed the data with --fwhm 10 
> during mris_surf2surf. And the other thing is, that it doesn't find the 
> correct path for the mc-z.csd. It should be in 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/81kids_template/lh/cortex/fwhm10/abs/mc-z.csd
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 30. März 2017 19:13:43
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> you are not giving it the proper glmdir dir. the glmdir is
>
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova
>
>
> On 03/30/2017 01:12 PM, Clara Kühn wrote:
>> I tried this command:
>>
>> mri_glmfit-sim --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post
>>  --cache-dir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
>> --cache 3.0 abs --cwp 0.05 --2spaces
>>
>> and got this error:
>> ERROR: cannot find 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mri_glmfit.log
>>
>> then I copied the .log file into the contrast directory C-pre-vs-post and 
>> tried the same command again and got this error:
>>
>> ERROR: could not determine file for 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mask
>>
>> Ususally I would run the MC on the lh-Diff-1-3-Intercept-long.area-spc 
>> folder but with the rmanova I get these two folders: 
>> 40kids-lh.thickness10-rmanova and C-pre-vs-post
>>
>> Cheers
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Donnerstag, 30. März 2017 18:57:36
>> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
>> columns
>>
>> what do you mean that it did not seem to work?
>>
>>
>> On 03/30/2017 11:25 AM, Clara Kühn wrote:
>>> Thank you! I completely didn't see that. It worked.
>>>
>>> I was wondering how to proceed next. The tutorial ends with running the 
>>> glmfit command. I've tried correcting for multiple comparisons with Monte 
>>> Carlo but that doesn't seem to 

Re: [Freesurfer] FreeSurfer : About ROI analysis

[Douglas N Greve]

Yes, that is fine


On 03/31/2017 05:42 AM, Lisa Delalande wrote:
> Hello Doug,
>
> Yes this mail was quite difficult to write, so I resume :
> First, I did a thickness analysis on Freesurfer
> Then, with the clusters found, I draw  ROIs and extracted the 
> statistical values (command : creation of .label and 
> mris_anatomical_stats-l..label-t rh.thickness-b-f 
> .../stats/...stats rh). Finally, I made correlations and multiple 
> regressions (with the values for thickness but also surface area, 
> volume, meancurv obtained via the command above) on the software "R". 
> I only found a significant correlation with the surface.
> My question is: can I correlate a behavioral score with SURFACE values 
> when I found these values thanks to a THICKNESS analysis?
>
> I hope it's clearer,
> If not do not hesitate to ask me again,
> Thanks in advance.
>
> Marine
> 
>
>
>
> 
> *De :* freesurfer-boun...@nmr.mgh.harvard.edu 
>  de la part de Douglas Greve 
> 
> *Envoyé :* mardi 28 mars 2017 16:58
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* Re: [Freesurfer] FreeSurfer : About ROI analysis
>
> Hi Marine, I'm having a hard time following what you are trying to do. 
> It sounds like you have done a thickenss analysis where you have found 
> some clusters, but after that I'm not sure what you are asking. Please 
> elaborate.
>
> doug
>
>
> On 3/28/17 6:07 AM, Lisa Delalande wrote:
>>
>> Hello,
>>
>> As a PhD student, I often use Freesurfer software and more precisely 
>> QDEC. A great question arises in connection with my last work. After 
>> drawing ROIs, I extricated values thanks to a " .levels" and a 
>> creation of a "stat" folder for each participant (aparcstat2table).
>>
>> My question is : can I make a correlation between a behavioral score 
>> and the value of "average SURFACE" obtained for each participant 
>> thanks to the command above-mentioned considering that my ROI has 
>> been drawn from clusters detected with a correlational analysis 
>> between THICKNESS (and not surface) and a behavioral score on QDEC ?
>>
>> Many thanks in advance for your assistance, and I am looking forward 
>> to hearing from you.
>>
>> Marine
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
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Re: [Freesurfer] -autorecon2-wm: Inconsistency between recon-all code and documentation

[Douglas N Greve]

I think the stages in the command line help are out of date


On 04/08/2017 05:58 PM, Antonin Skoch wrote:
> Dear experts,
>
> I noticed inconsistency between recon-all -help and actual code of 
> recon-all in -autorecon2-wm option.
> According to the recon-all --help the -autorecon2-wm processes stages 
> 15-23 (fill through make white surfaces) and -autorecon2-cp processes 
> stages 12-23 (normalization2 throuhgh make white surfaces). But, in 
> the code both -autorecon2-wm and -autorecon2-cp are equivalently 
> processing stages 12-23.
>
> It seems to me that the stages 12-14 are not needed to process again 
> in -autorecon2-wm (which is used for re-processing after editing wm.mgz).
>
> Could you please comment on?
>
> Regards,
>
> Antonin Skoch
>
>
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Re: [Freesurfer] correlation coefficient R

[Douglas N Greve]

Try something like

mri_segstats --i pcc.mgh --seg cluster.ocn.mgh --excludeid 0 --sum 
cluster.pcc.dat


On 04/07/2017 08:35 PM, tom parker wrote:
> Hi Doug,
>
> Thank you for your answer!
>
> It would be great if you could send me some instructions.
>
> Thanks for the help!
>
> Douglas N Greve 
> 
>  
> Thu, 06 Apr 2017 13:32:07 -0700 
> 
>  
>
>
> I guess you could average it over space (eg, over a cluster). Let me
> know if you want instructions. Otherwise, I'm not sure what to say.
>
>
> 2017-04-04 11:49 GMT+01:00 tom parker  >:
>
> Hi Doug,
>
> Thanks! I realize now I didn't explain myself properly.
>
> I need one single R value for the correlation analysis I made,
> similarly to when I correlate two variables with Pearson's R in a
> statistical package. I have a referee asking me to put it on a
> table with the freesurfer results. Is there a way to get a single
> average R value from the pcc.mgh file?
>
> Thank you so much!
>
> Douglas Greve
> 
> 
> Mon, 03 Apr 2017 18:46:46 -0700
> 
> 
>
>
> Each vertex is a correlation value.
>
>
> 2017-04-04 1:09 GMT+01:00 tom parker  >:
>
> Thanks Doug!
>
> I have version 6 and got a pcc.mgh file.
>
> How can I get a correlation R value from this file?
>
> Thanks again
>
> Douglas N Greve
> 
> 
> Mon, 03 Apr 2017 09:41:41 -0700
> 
> 
>
>
> if you are using version 6, then it should have produced a file called
> pcc.mgh. This the partial pearson correlation coef.
>
>
>
> 2017-04-03 15:40 GMT+01:00 tom parker  >:
>
> Dear Freesurfers,
>
> I made some correlations between cortical thickness and
> age in qdec.
>
> Is it possible to get the correlation coefficient value of
> this analysis?
>
> I just need to put it in a table with the significant results.
>
> Thank you so much!
>
>
>
>
>
>
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Re: [Freesurfer] create mask from cluster number?

[Douglas N Greve]

mri_binarize --i HC.43.rh/v1.slope/results.ocn.mgh --match 1 --o 
cluster1mask.mgh

You can concatenate all your subjects together in fsaverage space 
(mris_preprpoc), optionally smooth it, then

mri_segstats ---i yourstackallsubjects.mgh --excludeid 0 --seg 
HC.43.rh/v1.slope/results.ocn.mgh --avgwf ocn.avgwf.dat

ocn.avgwf.dat will be a text file with number of rows = number of 
subjects in the stack, and number of columns equal to the number of clusters


On 04/09/2017 12:01 PM, lindsay hanford wrote:
> Hello Freesurfer Developers,
>
> The main point of my post is to determine whether its possible to 
> create a mask from a cluster ID run using a subset of the sample, and 
> then use that mask to extract cortical thickness values from a model 
> run with the full sample.
>
> I am running a pretty basic cortical thickness- behavioural 
> correlation analysis with two groups using fsgd. Because I have a 
> relatively small sample size (just over 40 participants in each group) 
> I wanted to restrict my analysis to only regions that showed a 
> relationship within the HC group. I ran the model using mri_glmfit:
>
> mri_glmfit --y HC.43.rh.10.mgh --fsgd Behav.fsgd --C v1.slope.mtx 
> --surf fsaverage rh --cortex --glmdir MCCB.HC.43.rh
>
> Behav.fsgd setup:
> GroupDescriptorFile 1
> Title MaineffectofGroup
> Class HC
> Variables BehavMC
> Input 128 HC -5
> Input 132 HC 8
> Input 192 HC -10
> Input 193 HC -6
> ...
>
> v1.slope.mtx:
> 0 1
>
> *quick side question - in the past I was curious to see if this could 
> test positive and negative relationships. I tried two different 
> contrasts: 0 1 and 0 -1 to test the positive and negative 
> relationships, respectively, however the results were the direct 
> inverse of each other... it didn't show negative slope relationships. 
> I am curious if its possible to test for negative relationships in 
> freesurfer? How would you set up that contrast?
>
> next, I used mri_surfcluster to generate image and table files:
> mri_surfcluster --in HC.43.rh/v1.slope/sig.mgh --subject fsaverage 
> --hemi rh --surf pial --annot aparc --thmin 2 --ocn 
> HC.43.rh/v1.slope/results.ocn.mgh --sum HC.43.rh/v1.slope/results.sum.txt
>
> my results.sum.txt file shows a number of clusters
> ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs Annot
>13.719  163035270.33 57.7  -34.6  -21.5   234 
>  inferiortemporal
>23.499   22608217.35 33.2  -48.2  -15.1   230  fusiform
>33.1702804 93.01 42.1   22.1 23.9   132 
>  rostralmiddlefrontal
>
> Would it be possible to create a mask defined by say "ClusterNo 1"?
>
> Once the mask is created, I want to use it to extract the cortical 
> thickness values for all participants (including those that weren't 
> used to create the mask).. Is this possible? Can that be done using 
> mri_segstats?
>
> Let me know if you require any other details.
> Freesurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
>
>
> Thank you in advance,
>
>
> Lindsay
>
>
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Re: [Freesurfer] Volume vs cortical thickness

[Douglas N Greve]

The thickness is an average of two numbers. One is the distance from a 
white surface vertex to the pial surface along the normal to the white. 
The other is the distance from the pial to the white along the normal to 
the pial.

Volume (in v6) is computed as the volume of a truncated tetrahedron. 
Prior to v6 it was surface area times thickness


On 04/10/2017 12:24 PM, John Anderson wrote:
> Dear Freesurfer experts,
> I highly appreciate if anybody clarify how Freesurfer calculate 
> cortical thickness and gray matter volume.
> If the cortical thickness of e.g. precentral gurus is measured as the 
> closest distance from the gray-white boundary to the gray-CSF boundray 
> at each vertex on the tessellated surface (Fischl and Dale. 2000).
> How the gray matter volume for the precentral gyrus was measured?
>
> Thank you for any clarification!
>
> John
>
>
>
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Re: [Freesurfer] dimension mismatch between source and mask

[Douglas N Greve]

You should only need those first two commands (+ the mri_mask). Use 
--interp nearest with the ribbon


On 04/10/2017 12:27 PM, Maria Hakonen wrote:
>
> Hi Bruce,
>
>
> Thank you for the reply! I have now tried:
>
>
> mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh 
> --tal --talres 2
>
> mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh 
> --tal --talres 2
>
> mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz
>
> mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz
>
> mri_convert masked_fmri.mgz masked_fmri.nii
>
>
> I got:
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from masked_fmri.mgz...
>
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, 0, -1)
>
> k_ras = (0, 1, 0)
>
> writing to masked_fmri.nii...
>
>
> However, when I opened the masked_fmri.nii in fslview, the masked_fmri 
> seems to be empty (intensity is zero and no brain is shown).
>
> I would need to get a matrix containing voxels in the grey matter at 
> all time points. Could you please let me know what I am doing wrong 
> above? Or is there some better way to do this? I am new with 
> Freesurfer, so sorry if my questions are trivial.
>
>
> Best,
>
> Maria
>
>
> 2017-04-10 17:28 GMT+03:00 Bruce Fischl  >:
>
> Hi Maria
>
> are they in register? If so you can do:
>
> mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
> mri_mask fmri_data.mgh mask.mgz  masked_fmri.mgz
>
> cheers
> Bruce
>
>
>
> On Mon, 10 Apr 2017, Maria Hakonen wrote:
>
> Dear Freesurfer experts,
> I have tried to mask fMRI data with grey matter mask as follows:
> mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
>
> However, I am getting an error " dimension mismatch between
> source and mask".
>
> Could someone please let me know how to solve this problem?
>
> Best,
> Maria
>
>
> ___
> 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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-- 
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
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Re: [Freesurfer] Ventricle-to-Brain Ratio

[Gullickson, James]

Doug,

Thank you very much! That helps clear things up for me.

Best,

James

On Mon, Apr 10, 2017 at 2:21 PM, Douglas N Greve 
wrote:

> sorry, I would use these two
>
> TVV = left lateral ventricle + left inf lateral ventricle + right
> lateral ventricle + right inf lateral ventricle + 3rd ventricle
>+ 4th   ventricle + 5th ventricle + choroid plexus
>
> TBV = BrainSegVolNotVent
>
> On 04/10/2017 09:43 AM, Gullickson, James wrote:
> > Hi Doug,
> >
> > To clarify: to calculate VBR, I need two things: a measure of TBV
> > /and/ and measure of TVV. I'm just wondering what the best way to
> > derive each of these is.
> >
> > Thanks,
> >
> > James
> >
> > On Fri, Apr 7, 2017 at 11:24 AM, Douglas N Greve
> > > wrote:
> >
> > I would use the TVV
> >
> >
> > On 04/06/2017 06:28 PM, Gullickson, James wrote:
> > > Doug,
> > >
> > > Thanks for your reply.
> > >
> > > Difference between the two TVV methods ranges between 1-6%
> > > Difference between the two TBV methods ranges between 2-4%
> > >
> > > Basically, my question is two-fold:
> > >
> > > a) what is the most accurate representation of total ventricular
> > volume
> > > b) what is the most accurate representation of total brain
> > volume (all
> > > parenchyma)
> > >
> > > Best,
> > >
> > > James
> > >
> > > On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve
> > > 
> >  > >> wrote:
> > >
> > > that looks right. how different are the values?
> > >
> > >
> > > On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > > > Hello all,
> > > >
> > > > I want to calculate a Ventricle-to-Brain ratio (VBR) as a
> > measure of
> > > > parenchymal atrophy using Freesurfer version 5.3.0. I have
> > tried
> > > to go
> > > > about this using the aseg.stats output (using
> > asegstats2table),
> > > but am
> > > > running into inconsistencies.
> > > >
> > > > The basic calculation for VBR is:
> > > >
> > > > (Total Ventricular Volume/Total Brain Volume) * 100
> > > >
> > > > i.e. Bigler, E. D. (2013). Traumatic brain injury,
> > neuroimaging, and
> > > > neurodegeneration. /Frontiers in human neuroscience/, /7/,
> > 395.
> > > >
> > > >
> > > > What is the best way to get Total Ventricular Volume (TVV)
> > and Total
> > > > Brain Volume (TBV) for this calculation? I have tried
> > several ways,
> > > > which lead to different values:
> > > >
> > > > TVV = left lateral ventricle + left inf lateral ventricle
> > + right
> > > > lateral ventricle + right inf lateral ventricle + 3rd
> > ventricle
> > > + 4th
> > > > ventricle + 5th ventricle + choroid plexus
> > > >
> > > > which gives me a different result than
> > > >
> > > > TVV = BrainSegVol - BrainSegVolNotVent
> > > >
> > > >
> > > > and for TBV
> > > >
> > > > TBV = TotalGrayVol + CorticalWhiteMatterVol
> > > >
> > > > which differs from
> > > >
> > > > TBV = BrainSegVolNotVent
> > > >
> > > >
> > > > Thank you for your help,
> > > >
> > > > James Gullickson
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > ___
> > > > 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
> > 

Re: [Freesurfer] dimension mismatch between source and mask

[Douglas N Greve]

Probably you'll want to use mri_vol2vol so that you can incorporate your 
registration between the fMRI and the anatomical


On 04/10/2017 10:28 AM, Bruce Fischl wrote:
> Hi Maria
>
> are they in register? If so you can do:
>
> mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
> mri_mask fmri_data.mgh mask.mgz  masked_fmri.mgz
>
> cheers
> Bruce
>
>
> On Mon, 10 Apr 2017, Maria Hakonen wrote:
>
>> Dear Freesurfer experts,
>> I have tried to mask fMRI data with grey matter mask as follows:
>> mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
>>
>> However, I am getting an error " dimension mismatch between source 
>> and mask".
>>
>> Could someone please let me know how to solve this problem?
>>
>> Best,
>> Maria
>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Ventricle-to-Brain Ratio

[Douglas N Greve]

sorry, I would use these two

TVV = left lateral ventricle + left inf lateral ventricle + right
lateral ventricle + right inf lateral ventricle + 3rd ventricle
   + 4th   ventricle + 5th ventricle + choroid plexus

TBV = BrainSegVolNotVent

On 04/10/2017 09:43 AM, Gullickson, James wrote:
> Hi Doug,
>
> To clarify: to calculate VBR, I need two things: a measure of TBV 
> /and/ and measure of TVV. I'm just wondering what the best way to 
> derive each of these is.
>
> Thanks,
>
> James
>
> On Fri, Apr 7, 2017 at 11:24 AM, Douglas N Greve 
> > wrote:
>
> I would use the TVV
>
>
> On 04/06/2017 06:28 PM, Gullickson, James wrote:
> > Doug,
> >
> > Thanks for your reply.
> >
> > Difference between the two TVV methods ranges between 1-6%
> > Difference between the two TBV methods ranges between 2-4%
> >
> > Basically, my question is two-fold:
> >
> > a) what is the most accurate representation of total ventricular
> volume
> > b) what is the most accurate representation of total brain
> volume (all
> > parenchyma)
> >
> > Best,
> >
> > James
> >
> > On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> > that looks right. how different are the values?
> >
> >
> > On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > > Hello all,
> > >
> > > I want to calculate a Ventricle-to-Brain ratio (VBR) as a
> measure of
> > > parenchymal atrophy using Freesurfer version 5.3.0. I have
> tried
> > to go
> > > about this using the aseg.stats output (using
> asegstats2table),
> > but am
> > > running into inconsistencies.
> > >
> > > The basic calculation for VBR is:
> > >
> > > (Total Ventricular Volume/Total Brain Volume) * 100
> > >
> > > i.e. Bigler, E. D. (2013). Traumatic brain injury,
> neuroimaging, and
> > > neurodegeneration. /Frontiers in human neuroscience/, /7/,
> 395.
> > >
> > >
> > > What is the best way to get Total Ventricular Volume (TVV)
> and Total
> > > Brain Volume (TBV) for this calculation? I have tried
> several ways,
> > > which lead to different values:
> > >
> > > TVV = left lateral ventricle + left inf lateral ventricle
> + right
> > > lateral ventricle + right inf lateral ventricle + 3rd
> ventricle
> > + 4th
> > > ventricle + 5th ventricle + choroid plexus
> > >
> > > which gives me a different result than
> > >
> > > TVV = BrainSegVol - BrainSegVolNotVent
> > >
> > >
> > > and for TBV
> > >
> > > TBV = TotalGrayVol + CorticalWhiteMatterVol
> > >
> > > which differs from
> > >
> > > TBV = BrainSegVolNotVent
> > >
> > >
> > > Thank you for your help,
> > >
> > > James Gullickson
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > 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
> 
> >  >
> > 

[Freesurfer] Surface down sample by taking cortical vertices only

[Dorothy Sincasto]

Hi

I want to do an MEG analysis and first I want to downsample the surface to
around 100 vertices per hemisphere.  I tried the command mris_downsample,
but when i plot the surface I see that the vertices go deep into the white
matter.

Is there an option to extract for example 100 equidistant vertices from a
fsaverage?  Maybe knowing  how the vertices are organized when saved would
help, so for example, when I load a surface in matlab the vertices are
shown as a vector, is there a way to know the spatial order?

Thanks
Dorothy
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Re: [Freesurfer] dimension mismatch between source and mask

[Maria Hakonen]

Hi Bruce,


Thank you for the reply! I have now tried:


mri_vol2vol --mov mri_data.mgh --reg register.dat --o mri_data-tal.mgh
--tal --talres 2

mri_vol2vol --mov ribbon.mgz --reg register.dat --o ribbon-tal.mgh --tal
--talres 2

mri_convert -rl mri_data-tal.mgh ribbon-tal.mgz mask.mgz

mri_mask mri_data-tal.mgh mask.mgz masked_fmri.mgz

mri_convert masked_fmri.mgz masked_fmri.nii


I got:

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from masked_fmri.mgz...

TR=0.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 0, -1)

k_ras = (0, 1, 0)

writing to masked_fmri.nii...


However, when I opened the masked_fmri.nii in fslview, the masked_fmri
seems to be empty (intensity is zero and no brain is shown).

I would need to get a matrix containing voxels in the grey matter at all
time points. Could you please let me know what I am doing wrong above? Or
is there some better way to do this? I am new with Freesurfer, so sorry if
my questions are trivial.


Best,

Maria

2017-04-10 17:28 GMT+03:00 Bruce Fischl :

> Hi Maria
>
> are they in register? If so you can do:
>
> mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
> mri_mask fmri_data.mgh mask.mgz  masked_fmri.mgz
>
> cheers
> Bruce
>
>
>
> On Mon, 10 Apr 2017, Maria Hakonen wrote:
>
> Dear Freesurfer experts,
>> I have tried to mask fMRI data with grey matter mask as follows:
>> mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz
>>
>> However, I am getting an error " dimension mismatch between source and
>> mask".
>>
>> Could someone please let me know how to solve this problem?
>>
>> Best,
>> Maria
>>
>>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] Volume vs cortical thickness

[John Anderson]

Dear Freesurfer experts,
I highly appreciate if anybody clarify how Freesurfer calculate cortical 
thickness and gray matter volume.
If the cortical thickness of e.g. precentral gurus is measured as the closest 
distance from the gray-white boundary to the gray-CSF boundray at each vertex 
on the tessellated surface (Fischl and Dale. 2000).
How the gray matter volume for the precentral gyrus was measured?

Thank you for any clarification!

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Re: [Freesurfer] white matter edits not incorporated.

[Octavian Lie]

Dear All,

I wanted to know if there is any take on the issue of white matter edits
(specifically deleting unwanted voxels from wm.mgz). I sent a subject a
week ago for your review. It seems this is a problem that I had with
several scans, and by the message list, I am not the only one.
Recent users having the same issues have raised the possibility of editing
orig.mgz by replacing wm intensity with gm intensity in the troubled areas
as workaround to the wm.mgz issue.

Please let me know,

Thank you,

octavian




Dear Bruce,

I just transferred subject r02.tar.gz.

Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated
on reruns using any of the
recon-all -autorecon-wm -aitorecon3
recon-all -autorecon2 -autorecon3
recon-all -make all

FOr example, the complete command line for  a rerun is

recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02
-parallel > output.txt &


Here are some of the edited voxels which are not excluded from the wm on
rerun:


-40.14, -2.67, 116.29 coronal slice 132
12.73, -23.67, 126.16 coronal slice 171
14.05, 12.33, 11.61 coronal slice 147


I mention this is not the only subject where I have this problem.
Thank you for your help.
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Re: [Freesurfer] QDEC and ROI drawing

[Douglas N Greve]

Sorry, I don't know what is going on with qdec. Why do you need to do 
this in qdec? If it is to draw labels, then you can also use tksurfer.


On 04/10/2017 11:34 AM, Arnaud Boré wrote:
> Hi Douglas,
> What more can I do to help you figure out what's wrong ?
> Thank you in advance
> Arnaud
>
> 2017-04-07 16:50 GMT-04:00 Arnaud Boré  >:
>
> There is no shift in freeview.
>
> 2017-04-07 16:35 GMT-04:00 Douglas N Greve
> >:
>
> Not yet. Did you try to load it into freeview? If so, do you
> still see the shift?
>
>
> On 04/07/2017 04:14 PM, Arnaud Boré wrote:
>
> Do you want me to attach/upload a screenshot of the shift ?
>
> 2017-04-07 13:10 GMT-04:00 Arnaud Boré
> 
>  >>:
>
> I try to view it on O_Nap_04MB.
>
> I've tried these two command lines:
> qdec --table qdec.all_subjs.table.dat --surface
> O_Nap_04MB/surf/rh.pial --label
> O_Nap_04MB/label/rh.M1_v4.label
> qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB
> --surface O_Nap_04MB/surf/rh.pial --label
> O_Nap_04MB/label/rh.M1_v4.label
>
> I get the same results.
>
>
> 2017-04-07 12:03 GMT-04:00 Douglas N Greve
>  
>  >>:
>
> when you view it in qdec, are you viewing it on
> fsaverage or
> on O_Nap_04MB ?
>
>
> On 04/07/2017 11:47 AM, Arnaud Boré wrote:
>
> I used this command line: mri_label2label
> --srclabel
> rh.M1_v4.label --srcsubject fsaverage --trgsubject
> O_Nap_04MB --trglabel rh.M1_v4.label
> --regmethod surface
> --hemi rh
> The output label overlaps the surface using
> freeview but
> using qdec it is shifted.
> Thank you for your help.
> Arnaud
>
> 2017-04-07 10:23 GMT-04:00 basile pinsard
>  
>  >
>  
>  
>
> -- Forwarded message --
> From: *Douglas N Greve*
> 
>  >
>  
>   Date: Thu, Apr 6, 2017 at 4:53 PM
> Subject: Re: [Freesurfer] QDEC and ROI drawing
> To: freesurfer@nmr.mgh.harvard.edu
> 
>  >
>  
>  >>
>
>
> what is your label2label command line?
>
>
>
> On 04/06/2017 04:52 PM, Arnaud Boré wrote:
> > Dear Freesurfer's experts,
> > I draw a specific region on fsaverage
> using QDEC,
> then I mapped this
> > label on each subject using
> mri_label2label. I
> looked at these
> > registered labels using freeview. Most
> of them are
> perfect but for
> > some of them I would like to correct the
> segmentation. I would
> like to
> > modify it 

Re: [Freesurfer] TR: FreeSurfer : About ROI analysis

[Douglas N Greve]

Yes you can do that correlation. Is that your only question?


On 04/10/2017 09:59 AM, Lisa Delalande wrote:
> Hello Doug,
>
> Yes this mail was quite difficult to write, so I resume :
> First, I did a thickness analysis on Freesurfer
> Then, with the clusters found, I draw  ROIs and extracted the 
> statistical values (command : creation of .label and 
> mris_anatomical_stats-l..label-t rh.thickness-b-f 
> .../stats/...stats rh). Finally, I made correlations and multiple 
> regressions (with the values for thickness but also surface area, 
> volume, meancurv obtained via the command above) on the software "R". 
> I only found a significant correlation with the surface.
> My question is: can I correlate a behavioral score with SURFACE values 
> when I found these values thanks to a THICKNESS analysis?
>
> I hope it's clearer,
> If not do not hesitate to ask me again,
> Thanks in advance.
>
> Marine
> 
> *De :* Lisa Delalande 
> *Envoyé :* vendredi 31 mars 2017 11:42
> *À :* Freesurfer support list
> *Objet :* RE: [Freesurfer] FreeSurfer : About ROI analysis
> Hello Doug,
>
> Yes this mail was quite difficult to write, so I resume :
> First, I did a thickness analysis on Freesurfer
> Then, with the clusters found, I draw  ROIs and extracted the 
> statistical values (command : creation of .label and 
> mris_anatomical_stats-l..label-t rh.thickness-b-f 
> .../stats/...stats rh). Finally, I made correlations and multiple 
> regressions (with the values for thickness but also surface area, 
> volume, meancurv obtained via the command above) on the software "R". 
> I only found a significant correlation with the surface.
> My question is: can I correlate a behavioral score with SURFACE values 
> when I found these values thanks to a THICKNESS analysis?
>
> I hope it's clearer,
> If not do not hesitate to ask me again,
> Thanks in advance.
>
> Marine
> 
>
>
>
> 
> *De :* freesurfer-boun...@nmr.mgh.harvard.edu 
>  de la part de Douglas Greve 
> 
> *Envoyé :* mardi 28 mars 2017 16:58
> *À :* freesurfer@nmr.mgh.harvard.edu
> *Objet :* Re: [Freesurfer] FreeSurfer : About ROI analysis
>
> Hi Marine, I'm having a hard time following what you are trying to do. 
> It sounds like you have done a thickenss analysis where you have found 
> some clusters, but after that I'm not sure what you are asking. Please 
> elaborate.
>
> doug
>
>
> On 3/28/17 6:07 AM, Lisa Delalande wrote:
>>
>> Hello,
>>
>> As a PhD student, I often use Freesurfer software and more precisely 
>> QDEC. A great question arises in connection with my last work. After 
>> drawing ROIs, I extricated values thanks to a " .levels" and a 
>> creation of a "stat" folder for each participant (aparcstat2table).
>>
>> My question is : can I make a correlation between a behavioral score 
>> and the value of "average SURFACE" obtained for each participant 
>> thanks to the command above-mentioned considering that my ROI has 
>> been drawn from clusters detected with a correlational analysis 
>> between THICKNESS (and not surface) and a behavioral score on QDEC ?
>>
>> Many thanks in advance for your assistance, and I am looking forward 
>> to hearing from you.
>>
>> Marine
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] QDEC and ROI drawing

[Arnaud Boré]

Hi Douglas,
What more can I do to help you figure out what's wrong ?
Thank you in advance
Arnaud

2017-04-07 16:50 GMT-04:00 Arnaud Boré :

> There is no shift in freeview.
>
> 2017-04-07 16:35 GMT-04:00 Douglas N Greve :
>
>> Not yet. Did you try to load it into freeview? If so, do you still see
>> the shift?
>>
>>
>> On 04/07/2017 04:14 PM, Arnaud Boré wrote:
>>
>>> Do you want me to attach/upload a screenshot of the shift ?
>>>
>>> 2017-04-07 13:10 GMT-04:00 Arnaud Boré > arnaud.b...@gmail.com>>:
>>>
>>> I try to view it on O_Nap_04MB.
>>>
>>> I've tried these two command lines:
>>> qdec --table qdec.all_subjs.table.dat --surface
>>> O_Nap_04MB/surf/rh.pial --label O_Nap_04MB/label/rh.M1_v4.label
>>> qdec --table qdec.all_subjs.table.dat --average O_Nap_04MB
>>> --surface O_Nap_04MB/surf/rh.pial --label
>>> O_Nap_04MB/label/rh.M1_v4.label
>>>
>>> I get the same results.
>>>
>>>
>>> 2017-04-07 12:03 GMT-04:00 Douglas N Greve
>>> >:
>>>
>>> when you view it in qdec, are you viewing it on fsaverage or
>>> on O_Nap_04MB ?
>>>
>>>
>>> On 04/07/2017 11:47 AM, Arnaud Boré wrote:
>>>
>>> I used this command line: mri_label2label --srclabel
>>> rh.M1_v4.label --srcsubject fsaverage --trgsubject
>>> O_Nap_04MB --trglabel rh.M1_v4.label --regmethod surface
>>> --hemi rh
>>> The output label overlaps the surface using freeview but
>>> using qdec it is shifted.
>>> Thank you for your help.
>>> Arnaud
>>>
>>> 2017-04-07 10:23 GMT-04:00 basile pinsard
>>> >> 
>>> >> >>:
>>>
>>>
>>> -- Forwarded message --
>>> From: *Douglas N Greve* >> 
>>> >> >>
>>> Date: Thu, Apr 6, 2017 at 4:53 PM
>>> Subject: Re: [Freesurfer] QDEC and ROI drawing
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> 
>>> >> >
>>>
>>>
>>> what is your label2label command line?
>>>
>>>
>>>
>>> On 04/06/2017 04:52 PM, Arnaud Boré wrote:
>>> > Dear Freesurfer's experts,
>>> > I draw a specific region on fsaverage using QDEC,
>>> then I mapped this
>>> > label on each subject using mri_label2label. I
>>> looked at these
>>> > registered labels using freeview. Most of them are
>>> perfect but for
>>> > some of them I would like to correct the
>>> segmentation. I would
>>> like to
>>> > modify it using QDEC but when I overlay this label
>>> on the surface of
>>> > my subject it has been shifted. I think this shift
>>> is because
>>> QDEC is
>>> > using fsaverage as the standard space. I try opening
>>> QDEC using the
>>> > "average" option and use the subject I want but I
>>> still get this
>>> > shift. am I missing something ?
>>> > Thank you in advance for your help.
>>> > Arnaud Bore
>>> >
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> >> >
>>> >
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >> r>
>>>>> .edu/mailman/listinfo/freesurfer
>>> >> r>>
>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> 
>>> >> >
>>> Phone Number: 617-724-2358 
>>> >
>>> Fax: 

Re: [Freesurfer] dimension mismatch between source and mask

[Bruce Fischl]

Hi Maria

are they in register? If so you can do:

mri_convert -rl fmri_data.mgh ribbon.mgz mask.mgz
mri_mask fmri_data.mgh mask.mgz  masked_fmri.mgz

cheers
Bruce


On Mon, 10 Apr 2017, Maria Hakonen 
wrote:



Dear Freesurfer experts,
I have tried to mask fMRI data with grey matter mask as follows:
mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz

However, I am getting an error " dimension mismatch between source and mask".

Could someone please let me know how to solve this problem?

Best,
Maria

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[Freesurfer] dimension mismatch between source and mask

[Maria Hakonen]

Dear Freesurfer experts,

I have tried to mask fMRI data with grey matter mask as follows:
mri_mask fmri_data.mgh ribbon.mgz masked_fmri.mgz

However, I am getting an error " dimension mismatch between source and
mask".

Could someone please let me know how to solve this problem?

Best,
Maria
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[Freesurfer] TR: FreeSurfer : About ROI analysis

[Lisa Delalande]

Hello Doug,

Yes this mail was quite difficult to write, so I resume :
First, I did a thickness analysis on Freesurfer
Then, with the clusters found, I draw  ROIs and extracted the statistical 
values (command : creation of .label and mris_anatomical_stats-l..label-t 
rh.thickness-b-f .../stats/...stats rh). Finally, I made correlations and 
multiple regressions (with the values for thickness but also surface area, 
volume, meancurv obtained via the command above) on the software "R". I only 
found a significant correlation with the surface.

My question is: can I correlate a behavioral score with SURFACE values when I 
found these values thanks to a THICKNESS analysis?

I hope it's clearer,
If not do not hesitate to ask me again,
Thanks in advance.

Marine


De : Lisa Delalande 
Envoyé : vendredi 31 mars 2017 11:42
À : Freesurfer support list
Objet : RE: [Freesurfer] FreeSurfer : About ROI analysis


Hello Doug,

Yes this mail was quite difficult to write, so I resume :
First, I did a thickness analysis on Freesurfer
Then, with the clusters found, I draw  ROIs and extracted the statistical 
values (command : creation of .label and mris_anatomical_stats-l..label-t 
rh.thickness-b-f .../stats/...stats rh). Finally, I made correlations and 
multiple regressions (with the values for thickness but also surface area, 
volume, meancurv obtained via the command above) on the software "R". I only 
found a significant correlation with the surface.

My question is: can I correlate a behavioral score with SURFACE values when I 
found these values thanks to a THICKNESS analysis?

I hope it's clearer,
If not do not hesitate to ask me again,
Thanks in advance.

Marine





De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Douglas Greve 

Envoyé : mardi 28 mars 2017 16:58
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] FreeSurfer : About ROI analysis


Hi Marine, I'm having a hard time following what you are trying to do. It 
sounds like you have done a thickenss analysis where you have found some 
clusters, but after that I'm not sure what you are asking. Please elaborate.

doug

On 3/28/17 6:07 AM, Lisa Delalande wrote:

Hello,

As a PhD student, I often use Freesurfer software and more precisely QDEC. A 
great question arises in connection with my last work. After drawing ROIs, I 
extricated values thanks to a " .levels" and a creation of a "stat" folder for 
each participant (aparcstat2table).

My question is : can I make a correlation between a behavioral score and the 
value of "average SURFACE" obtained for each participant thanks to the command 
above-mentioned considering that my ROI has been drawn from clusters detected 
with a correlational analysis between THICKNESS (and not surface) and a 
behavioral score on QDEC ?



Many thanks in advance for your assistance, and I am looking forward to hearing 
from you.



Marine



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Re: [Freesurfer] Ventricle-to-Brain Ratio

[Gullickson, James]

Hi Doug,

To clarify: to calculate VBR, I need two things: a measure of TBV *and* and
measure of TVV. I'm just wondering what the best way to derive each of
these is.

Thanks,

James

On Fri, Apr 7, 2017 at 11:24 AM, Douglas N Greve 
wrote:

> I would use the TVV
>
>
> On 04/06/2017 06:28 PM, Gullickson, James wrote:
> > Doug,
> >
> > Thanks for your reply.
> >
> > Difference between the two TVV methods ranges between 1-6%
> > Difference between the two TBV methods ranges between 2-4%
> >
> > Basically, my question is two-fold:
> >
> > a) what is the most accurate representation of total ventricular volume
> > b) what is the most accurate representation of total brain volume (all
> > parenchyma)
> >
> > Best,
> >
> > James
> >
> > On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve
> > > wrote:
> >
> > that looks right. how different are the values?
> >
> >
> > On 04/05/2017 10:58 AM, Gullickson, James wrote:
> > > Hello all,
> > >
> > > I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure
> of
> > > parenchymal atrophy using Freesurfer version 5.3.0. I have tried
> > to go
> > > about this using the aseg.stats output (using asegstats2table),
> > but am
> > > running into inconsistencies.
> > >
> > > The basic calculation for VBR is:
> > >
> > > (Total Ventricular Volume/Total Brain Volume) * 100
> > >
> > > i.e. Bigler, E. D. (2013). Traumatic brain injury, neuroimaging,
> and
> > > neurodegeneration. /Frontiers in human neuroscience/, /7/, 395.
> > >
> > >
> > > What is the best way to get Total Ventricular Volume (TVV) and
> Total
> > > Brain Volume (TBV) for this calculation? I have tried several ways,
> > > which lead to different values:
> > >
> > > TVV = left lateral ventricle + left inf lateral ventricle + right
> > > lateral ventricle + right inf lateral ventricle + 3rd ventricle
> > + 4th
> > > ventricle + 5th ventricle + choroid plexus
> > >
> > > which gives me a different result than
> > >
> > > TVV = BrainSegVol - BrainSegVolNotVent
> > >
> > >
> > > and for TBV
> > >
> > > TBV = TotalGrayVol + CorticalWhiteMatterVol
> > >
> > > which differs from
> > >
> > > TBV = BrainSegVolNotVent
> > >
> > >
> > > Thank you for your help,
> > >
> > > James Gullickson
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > 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  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: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 

Re: [Freesurfer] segmentation help

[Bruce Fischl]

you can also just give them to recon-all directly. Analyze is a dangerous 
format to use however as it doesn't allow you to determine left from 
right. Hopefully you have some type of fiducial marker in the image (e.g. 
a vitamin E tablet)


cheers
Bruce
On Mon, 10 Apr 2017, Nina Jacobsen wrote:


Hi Dilip,
Try the mri_convert function to convert your images, so recon-all can read
them:
https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html


Fra: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri
[dilippurip...@gmail.com]
Sendt: 10. april 2017 10:02
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi all,

Actually I've images in Analyze7.5 format(.img/.hdr).
Can anyone help me to reconstruct('recon-all') for this format.

Thanks
Dilip

On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen 
wrote:
  Hi Dilip.
You have to place your files where the subject-directory points. If
you dont change the directory yourself, this is under
freesurfer/subjects.

For more info about recon all,see 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.m
gh.harvard.edu/fswiki/recon-all

Nina.


Fra: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri
[dilippurip...@gmail.com]
Sendt: 10. april 2017 07:46
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which
directory. What are the command lines?


Hope for response.


Thanks
Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl
 wrote:
  Hi Dilip

  you need to run your image through recon-all.

  cheers
  Bruce

  On Sun, 9 Apr 2017, Dilip Puri
  wrote:

  > Hi all,
  >
  > I've 200 analyze7.5 format images(OASIS Dataset) and I
  want to segment
  > HippoCampus.
  >
  > My input file xyz.img and output file will be like
  xyz_seg.img which
  > contains only hippocampus image it like Grond Truth
  image for my original
  > input image.
  >
  > Here is sample files including original and segmented
  mask link.
  >
  > Even I am very new to FREESURFER so I don't know the
  procedure to
  > reconstruct the images.
  >
  >
  > Kindly help me.
  >
  >
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Re: [Freesurfer] segmentation help

[Bruce Fischl]

Hi Dilip

you should go through our online tutorials. They explain all of this in 
detail.

cheers
Bruce
On Mon, 10 Apr 2017, Dilip Puri wrote:

> Hi,
> 
> To-do "recon-all" where should I keep all the files. I mean in which
> directory. What are the command lines?
> 
> 
> Hope for response.
> 
> 
> Thanks
> Dilip
> 
> On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl 
> wrote:
>   Hi Dilip
>
>   you need to run your image through recon-all.
>
>   cheers
>   Bruce
>
>   On Sun, 9 Apr 2017, Dilip Puri
>   wrote:
>
>   > Hi all,
>   >
>   > I've 200 analyze7.5 format images(OASIS Dataset) and I want to
>   segment
>   > HippoCampus.
>   >
>   > My input file xyz.img and output file will be like xyz_seg.img
>   which
>   > contains only hippocampus image it like Grond Truth image for
>   my original
>   > input image.
>   >
>   > Here is sample files including original and segmented mask
>   link.
>   >
>   > Even I am very new to FREESURFER so I don't know the procedure
>   to
>   > reconstruct the images.
>   >
>   >
>   > Kindly help me.
>   >
>   >
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> 
> 
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> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
> 
> 
> 
>
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Re: [Freesurfer] segmentation help

[Nina Jacobsen]

Hi Dilip,

Try the mri_convert function to convert your images, so recon-all can read them:
https://surfer.nmr.mgh.harvard.edu/pub/docs/html/mri_convert.help.xml.html

Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri 
[dilippurip...@gmail.com]
Sendt: 10. april 2017 10:02
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi all,

Actually I've images in Analyze7.5 format(.img/.hdr).
Can anyone help me to reconstruct('recon-all') for this format.

Thanks
Dilip

On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen 
> wrote:
Hi Dilip.

You have to place your files where the subject-directory points. If you dont 
change the directory yourself, this is under freesurfer/subjects.

For more info about recon all, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Nina.

Fra: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 på vegne af Dilip Puri 
[dilippurip...@gmail.com]
Sendt: 10. april 2017 07:46
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which directory. 
What are the command lines?


Hope for response.


Thanks
Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl 
> wrote:
Hi Dilip

you need to run your image through recon-all.

cheers
Bruce

On Sun, 9 Apr 2017, Dilip Puri
wrote:

> Hi all,
>
> I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment
> HippoCampus.
>
> My input file xyz.img and output file will be like xyz_seg.img which
> contains only hippocampus image it like Grond Truth image for my original
> input image.
>
> Here is sample files including original and segmented mask link.
>
> Even I am very new to FREESURFER so I don't know the procedure to
> reconstruct the images.
>
>
> Kindly help me.
>
>
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Re: [Freesurfer] segmentation help

[Dilip Puri]

Hi all,

Actually I've images in Analyze7.5 format(.img/.hdr).
Can anyone help me to reconstruct('recon-all') for this format.

Thanks
Dilip

On Mon, Apr 10, 2017 at 12:14 PM, Nina Jacobsen 
wrote:

> Hi Dilip.
>
> You have to place your files where the subject-directory points. If you
> dont change the directory yourself, this is under freesurfer/subjects.
>
> For more info about recon all, see https://surfer.nmr.mgh.
> harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.harvard.
> edu/fswiki/recon-all
>
> Nina.
> --
> *Fra:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.
> harvard.edu] på vegne af Dilip Puri [dilippurip...@gmail.com]
> *Sendt:* 10. april 2017 07:46
> *Til:* Freesurfer support list
> *Emne:* Re: [Freesurfer] segmentation help
>
> Hi,
>
> To-do "recon-all" where should I keep all the files. I mean in which
> directory. What are the command lines?
>
>
> Hope for response.
>
>
> Thanks
> Dilip
>
> On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl 
> wrote:
>
>> Hi Dilip
>>
>> you need to run your image through recon-all.
>>
>> cheers
>> Bruce
>>
>> On Sun, 9 Apr 2017, Dilip Puri
>> wrote:
>>
>> > Hi all,
>> >
>> > I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment
>> > HippoCampus.
>> >
>> > My input file xyz.img and output file will be like xyz_seg.img which
>> > contains only hippocampus image it like Grond Truth image for my
>> original
>> > input image.
>> >
>> > Here is sample files including original and segmented mask link.
>> >
>> > Even I am very new to FREESURFER so I don't know the procedure to
>> > reconstruct the images.
>> >
>> >
>> > Kindly help me.
>> >
>> >
>> ___
>> 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.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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] segmentation help

[Nina Jacobsen]

Hi Dilip.

You have to place your files where the subject-directory points. If you dont 
change the directory yourself, this is under freesurfer/subjects.

For more info about recon all, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-allhttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Nina.

Fra: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] på vegne af Dilip Puri 
[dilippurip...@gmail.com]
Sendt: 10. april 2017 07:46
Til: Freesurfer support list
Emne: Re: [Freesurfer] segmentation help

Hi,

To-do "recon-all" where should I keep all the files. I mean in which directory. 
What are the command lines?


Hope for response.


Thanks
Dilip

On Sun, Apr 9, 2017 at 7:18 PM, Bruce Fischl 
> wrote:
Hi Dilip

you need to run your image through recon-all.

cheers
Bruce

On Sun, 9 Apr 2017, Dilip Puri
wrote:

> Hi all,
>
> I've 200 analyze7.5 format images(OASIS Dataset) and I want to segment
> HippoCampus.
>
> My input file xyz.img and output file will be like xyz_seg.img which
> contains only hippocampus image it like Grond Truth image for my original
> input image.
>
> Here is sample files including original and segmented mask link.
>
> Even I am very new to FREESURFER so I don't know the procedure to
> reconstruct the images.
>
>
> Kindly help me.
>
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


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The information in this e-mail is intended only for the person to whom it is
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