Re: [Freesurfer] Repost: Error using LGI script despite making suggested chages to Matlab script.

[prasser]

Hi, Reposting. Thanks.

 On Tue, 27 Sep 2016 16:53:21 -0700 prasserpras...@zoho.com wrote 
 

Hi,

I'm looking to please get some help with -lgi.

I'm using matlab R2015b and FS5.3 with 
recon-all -s subj_id -lgi 
on os x 10.11.

Looking at the output, the first error occurs about here:

preparing pial mesh structure ...
...searching for mesh edges...done (206.94 sec).
... creating path file for vertex 1 / 65274
area file for outer ROIs saved at 1
In an assignment  A(:) = B, the number of elements in A and B must be the same.

Error in dsearchn (line 79)
[d(i),t(i)] = min(sum((x-yi).^2,2));

I have changed the script SearchProjectionOnPial.m as suggested on the 
ReleaseNotes page.

Any help would be much appreciated.

Thanks.


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Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared P Zimmerman]

Yeah, I think I misunderstood what was happening with the ico registration.  I 
thought it was using the ico to downsample the subject surface, but I see that 
this is an atlas space and I can do w/e calculations I need I this space and 
then register back to subject space after. 

Thanks for the help, I got it to work by doing mri_vol2surf to register to my 
subject surface and then mri_surf2surf to downsample.

-jared

> On Sep 29, 2016, at 12:34 PM, Douglas N Greve  
> wrote:
> 
> I don't understand what you mean. When you use ico (when it used to 
> work), it always went to fsaverage space. Do you want to decimate the 
> native space surfaces?
> 
> 
> On 09/29/2016 10:15 AM, Jared P Zimmerman wrote:
>> I want to project to the native subject surfaces though, not 
>> fsaverage.  If I use —trgsubject subjID would that work with the 
>> —icoorder flag?  Alternatively I guess I could project to fsaverage 
>> and then use mri_surf2surf to move back to the subject surface, but 
>> that seems like a roundabout way to do it and will probably add some 
>> unnecessary interpolation.
>> 
>> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder 
>> flags and I did successfully get output with 112745 vertices (is this 
>> FS7 space?  I would have expected ~164k vertices, is this with medial 
>> wall masked?) and I could try to resample that with mri_surf2surf.  I 
>> wasn’t able to do this before, but I didn’t use the flag —trgsubject 
>> or —trgicoorder flags, though I suspect I will run into the same 
>> problem trying doing this.  I’m not at my computer now but can try 
>> this later this afternoon though.
>> 
>> Thanks,
>> Jared
>> 
>>> On Sep 29, 2016, at 12:00 AM, Douglas Greve 
>>>  
>>> >> 
>>> wrote:
>>> 
>>> you can actually skip the ico thing and just use --trgsubject fsaverage6
>>> 
>>> 
>>> On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
 Thanks Doug,
 
 This does seem like it will do the right thing, but it’s failing 
 because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to 
 have an ico subject in my subjects_dir
 
 Should this normally be in the subjects_dir?  I don’t recall ever 
 seeing this made when I’ve run recon-all in the past.
 
 Thanks,
 Jared
 
 Here’s the full terminal output when I run the command:
 
 mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg 
 func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o 
 func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 
 --interp trilinear --noreshape --trgsubject ico --icoorder 6 
 --out_type mgh --surf-fwhm 6
 IcoOrder = 6, nIcoVtxs = 40962
 srcvol = /func_test/filtered_func_residuals.nii.gz
 srcreg = func_test/coreg/fs_ep2struct_fsl.dat
 srcregold = 0
 srcwarp unspecified
 surf = white
 hemi = lh
 trgsubject = ico
 surfreg = sphere.reg
 ProjFrac = 0.5
 thickness = thickness
 reshape = 0
 interp = trilinear
 float2int = round
 GetProjMax = 0
 INFO: float2int code = 0
 Done loading volume
 Reading surface /subjdir_test//subID/surf/lh.white
 Done reading source surface
 Reading thickness /subjdir_test//subID/surf/lh.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 = 11345
 Reading source surface registration
 subjdir_test//subID/surf/lh.sphere.reg
 Done loading source registration surface
 Reading icosahedron, order = 6, radius = 100
  Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
 Done loading target registration surface
 Mapping Surfaces (subID -> ico)
 surf2surf_nnfr: building source hash (res=16).
 Surf2Surf: Forward Loop (40962)
 
 surf2surf_nnfr: building target hash (res=16).
 Surf2Surf: Reverse Loop (112745)
 Reverse Loop had 72236 hits
 
> On Sep 28, 2016, at 3:34 PM, Douglas Greve 
>  
> >> 
> wrote:
> 
> You need to specify --trgsubject ico in mri_vol2surf
> 
> 
> On 9/28/16 3:01 PM, Jared Zimmerman wrote:
>> Hi All, forwarding this message along again as I'm still having 
>> some trouble getting this to work.  Basically I would like to 1) 
>> project processed residual time-series from the subject-space 
>> volume to the subject-space surface, 2) smooth on the surface, 3) 
>> down-sample to FS4 space.
>> 
>> To do this is have used bbregister to calculate the registration, 
>> then mri_vol2surf to project to the surface, but I am not sure the 
>> output of mri_vol2surf is what I 

[Freesurfer] Training Tracula to add more pathways

[Kristafor Farrant]

Hi there,

As a complete newbie to the Tracula tool, I have a questions about using
it. Is it possible to train tracula to track additional pathways other than
the 18 thats are already included? I was to track several pathways that are
not included with Tracula.

Best,

Kris
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Re: [Freesurfer] Cortical thickness using qdec (between scanners)

[Harms, Michael]

Hi,
Even if the two sites are the same Siemens model, you are going to have difficultly convincing people that any differences you find might not just be a site effect.  In my opinion, this falls into the “not possible at all” category.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of Martin Juneja 
Reply-To: Freesurfer support list 
Date: Thursday, September 29, 2016 at 1:54 PM
To: Freesurfer support list 
Subject: [Freesurfer] Cortical thickness using qdec (between scanners)





Hello FS experts,


I have a data set of 20 subjects (patients) collected at location-1 with 3T Siemens scanner. Also, I have a set of age-matched 20 subjects (controls) collected at location-2 with 3T Siemens scanner.


I am interested in comparing cortical thickness between controls and patients using FreeSurfer but I am not sure if I can do that since I have both the data sets collected at two different locations.


I would really appreciate any inputs on this.


I tried to find some papers on scanner differences but all I could find was between 1.5 T vs 3T or 3T vs 7T. Is there any special covariates I need to define for this purpose (if so then at which step during analysis?) or is it not possible at all?


Thanks.






 



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[Freesurfer] Cortical thickness using qdec (between scanners)

[Martin Juneja]

Hello FS experts,

I have a data set of 20 subjects (patients) collected at location-1 with 3T
Siemens scanner. Also, I have a set of age-matched 20 subjects (controls)
collected at location-2 with 3T Siemens scanner.

I am interested in comparing cortical thickness between controls and
patients using FreeSurfer but I am not sure if I can do that since I have
both the data sets collected at two different locations.

I would really appreciate any inputs on this.

I tried to find some papers on scanner differences but all I could find was
between 1.5 T vs 3T or 3T vs 7T. Is there any special covariates I need to
define for this purpose (if so then at which step during analysis?) or is
it not possible at all?

Thanks.
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Re: [Freesurfer] Infalted/Label

[Bruce Fischl]

glad it worked out
Bruce
On Thu, 29 Sep 2016, Crawford, Anna wrote:

> i used dmax white. I now can see it on the inflated surface. Thank you for 
> all your help in getting this working. Sorry, it took so long since I'm 
> trying to figure all of this out still. The next step will be to take a 
> volume that already has a selected region defined and projecting that region 
> onto the inflated surface which I'm guessing will be somewhat similar to this.
>
> Thanks again,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 1:14 PM
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford
> Subject: Re: [Freesurfer] Infalted/Label
>
> you can also look at the vertex index of the first entry in the label
> file and type that into the "cursor" field in freeview so it will go to
> that point. My guess is that it does intersect the surface, otherwise the
> label indices would have stayed -1
>
> On Thu, 29 Sep 2016, Douglas N Greve wrote:
>
>> Sounds like it. View the label on the volume while displaying the surfaces in
>> the volume and see if they intersect
>>
>>
>> On 09/29/2016 01:12 PM, Crawford, Anna wrote:
>>> I added the --paint option which seemed to run successfully. I loaded it as
>>> a label on the inflated surface and it did not crash, but I do not see it
>>> anywhere on the surface. Does this just mean that I didn't actually draw it
>>> on the surface? As in, everything was done correct, the location of the
>>> label isn't on the surface though.
>>>
>>> Thank you!
>>> Anna
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 12:45 PM
>>> To: Crawford, Anna; Bruce Fischl
>>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: Infalted/Label
>>>
>>> That is a volume-based label. Try using the --paint option to
>>> mri_label2label to convert it to a surface-based label (assuming it is
>>> actually on the surface). Run mri_label2label with --help to get an example
>>>
>>>
>>> On 09/29/2016 12:38 PM, Crawford, Anna wrote:
 This is the output on label2label. The first colum of the created column
 is -1.

 mri_label2label --srcsubject segfs --srclabel
 /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
 --trgsubject segfs --trglabel Testing1N.label --regmethod volume

 srclabel =
 /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
 srcsubject = segfs
 trgsubject = segfs
 trglabel = Testing1N.label
 regmethod = volume

 usehash = 1
 Use ProjAbs  = 0, 0
 Use ProjFrac = 0, 0
 DoPaint 0

 SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
 FREESURFER_HOME /tools/freesurfer
 Loading source label.
 Found 216 points in source label.
 Starting volumetric mapping 216 points
 Src2TrgVolReg: -
1.000   0.000   0.000   0.000;
0.000   1.000   0.000  -0.000;
0.000  -0.000   1.000  -0.000;
0.000   0.000   0.000   1.000;
 0  -39. 17. 55.-39. 17. 55.
 1  -38. 17. 55.-38. 17. 55.
 2  -40. 18. 55.-40. 18. 55.
 3  -39. 18. 55.-39. 18. 55.
 4  -38. 18. 55.-38. 18. 55.
 Writing label file Testing1N.label 216
 mri_label2label: Done

 Thanks,
 Anna
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, September 29, 2016 12:29 PM
 To: Crawford, Anna
 Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
 Subject: RE: Infalted/Label

 I'll cc the list, which I should have done the first time. No, you
 didn't do anything wrong. This is what mri_label2label should do - sample
 these locations onto the surface you specify and fill in the vertex
 indices. Check the output of label2label and see if it has values >= 0
 cheers
 Bruce

 On Thu, 29 Sep 2016, Crawford, Anna wrote:

> Hi,
>
> I just checked all the labels I created and they all have -1 in the first
> column (the file name ending in 'N' should be the one created from
> mri_label2label). So, I did something wrong when originally creating the
> label I assume. When I created it, under the ROI tab, I created a new one
> and then drew it in the viewer with a volume (I did both white matter and
> brain mask) also loaded. Was this wrong?
>
> Thank you,
> Anna
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, 

Re: [Freesurfer] Warping an ROI from one subject to another

[Joel Bruss]

Ah, I see.  The ROI will be subject-dependent (I want to do this for
multiple subjects) but the majority, if not all, should be cortical.
Any help you'd be willing to provide would be much appreciated.


On 09/29/2016 11:31 AM, Douglas N Greve wrote:
> The way you have it configured now, this is a volume-based ROI, so you
> need to use the volume-based reg method. This will map between the two
> subjects using the affine (12 dof) talairach registration which will not
> be as accurate as the surface-based registration. If this is a cortical
> ROI, I can show you how to redo this using a surface-based label.
>
>
> On 09/29/2016 11:37 AM, Joel Bruss wrote:
>> Another bump.
>>
>> On 09/21/2016 04:18 PM, Joel Bruss wrote:
>>
>>> I have two subjects, subA and subB.  subA has a binary ROI mask, native
>>> space, that I'd like to place in subB's native space. Both subjects have
>>> been run through all stages of recon, edited, etc. Is there a better or
>>> easier way to achieve this than what I've run?:
>>>
>>>
>>> #Resample the native space binary ROI file into "brainmask" space
>>> mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1
>>> ROI.nii.gz /subA/mri/ROI.mgz
>>>
>>> #Convert ROI file into a label
>>> mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label
>>>
>>> #Move label from subA to subB
>>> mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label
>>> --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume
>>>
>>> #Convert warped ROI label to a volume
>>> mri_label2vol --label /subB/mri/ROI_to_subB.label \
>>> --subject subB \
>>> --temp brainmask.mgz \
>>> --regheader brainmask.mgz \
>>> --o /subB/mri/ROI_to_subB.mgz
>>>
>>> #Convert the volume back to native subB space
>>> mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1
>>> /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz
>>>
>>> A few follow-up questions:
>>>
>>> 1) When running mri_label2label, is better to use surface or volume for
>>> the "regmethod"?  Which method will give me a better fit for my output?
>>> 2) The output I'm getting looks striped (there are holes in the binary
>>> mask) and doesn't quite fit the anatomy (the final file is shifted up
>>> and away from where I would expect it to be although in the general
>>> vicinity of what I would expect).  It's almost as if I've chosen a wrong
>>> target or file along the way.  I don't expect the fit to be perfect, but
>>> did I do something wrong?
>>>
>>> Thanks in advance to any and all replies.
>>>
>>>
>>>
>>> 
>>> Notice: This UI Health Care e-mail (including attachments) is covered by 
>>> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is 
>>> intended only for the use of the individual or entity to which it is 
>>> addressed, and may contain information that is privileged, confidential, 
>>> and exempt from disclosure under applicable law. If you are not the 
>>> intended recipient, any dissemination, distribution or copying of this 
>>> communication is strictly prohibited. If you have received this 
>>> communication in error, please notify the sender immediately and delete or 
>>> destroy all copies of the original message and attachments thereto. Email 
>>> sent to or from UI Health Care may be retained as required by law or 
>>> regulation. Thank you.
>>> 
>>>
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
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>>> HelpLine at
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>>> dispose of the e-mail.
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>>
>> 
>> Notice: This UI Health Care e-mail (including attachments) is covered by the 
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>> only for the use of the individual or entity to which it is addressed, and 
>> may contain information that is privileged, confidential, and exempt from 
>> disclosure under applicable law. If you are not the intended recipient, any 
>> dissemination, distribution or copying of this communication is strictly 
>> prohibited. If you have received this communication in error, please notify 
>> the sender immediately and delete or destroy all copies of the original 
>> message and attachments thereto. Email sent to or from UI Health Care may be 
>> retained as required by law or regulation. Thank you.
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Re: [Freesurfer] Infalted/Label

[Crawford, Anna]

i used dmax white. I now can see it on the inflated surface. Thank you for all 
your help in getting this working. Sorry, it took so long since I'm trying to 
figure all of this out still. The next step will be to take a volume that 
already has a selected region defined and projecting that region onto the 
inflated surface which I'm guessing will be somewhat similar to this.

Thanks again,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 1:14 PM
To: Douglas N Greve
Cc: freesurfer@nmr.mgh.harvard.edu; Crawford, Anna; Anna Crawford
Subject: Re: [Freesurfer] Infalted/Label

you can also look at the vertex index of the first entry in the label
file and type that into the "cursor" field in freeview so it will go to
that point. My guess is that it does intersect the surface, otherwise the
label indices would have stayed -1

On Thu, 29 Sep 2016, Douglas N Greve wrote:

> Sounds like it. View the label on the volume while displaying the surfaces in
> the volume and see if they intersect
>
>
> On 09/29/2016 01:12 PM, Crawford, Anna wrote:
>> I added the --paint option which seemed to run successfully. I loaded it as
>> a label on the inflated surface and it did not crash, but I do not see it
>> anywhere on the surface. Does this just mean that I didn't actually draw it
>> on the surface? As in, everything was done correct, the location of the
>> label isn't on the surface though.
>>
>> Thank you!
>> Anna
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:45 PM
>> To: Crawford, Anna; Bruce Fischl
>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: Infalted/Label
>>
>> That is a volume-based label. Try using the --paint option to
>> mri_label2label to convert it to a surface-based label (assuming it is
>> actually on the surface). Run mri_label2label with --help to get an example
>>
>>
>> On 09/29/2016 12:38 PM, Crawford, Anna wrote:
>>> This is the output on label2label. The first colum of the created column
>>> is -1.
>>>
>>> mri_label2label --srcsubject segfs --srclabel
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>> --trgsubject segfs --trglabel Testing1N.label --regmethod volume
>>>
>>> srclabel =
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>> srcsubject = segfs
>>> trgsubject = segfs
>>> trglabel = Testing1N.label
>>> regmethod = volume
>>>
>>> usehash = 1
>>> Use ProjAbs  = 0, 0
>>> Use ProjFrac = 0, 0
>>> DoPaint 0
>>>
>>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
>>> FREESURFER_HOME /tools/freesurfer
>>> Loading source label.
>>> Found 216 points in source label.
>>> Starting volumetric mapping 216 points
>>> Src2TrgVolReg: -
>>>1.000   0.000   0.000   0.000;
>>>0.000   1.000   0.000  -0.000;
>>>0.000  -0.000   1.000  -0.000;
>>>0.000   0.000   0.000   1.000;
>>> 0  -39. 17. 55.-39. 17. 55.
>>> 1  -38. 17. 55.-38. 17. 55.
>>> 2  -40. 18. 55.-40. 18. 55.
>>> 3  -39. 18. 55.-39. 18. 55.
>>> 4  -38. 18. 55.-38. 18. 55.
>>> Writing label file Testing1N.label 216
>>> mri_label2label: Done
>>>
>>> Thanks,
>>> Anna
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 12:29 PM
>>> To: Crawford, Anna
>>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
>>> Subject: RE: Infalted/Label
>>>
>>> I'll cc the list, which I should have done the first time. No, you
>>> didn't do anything wrong. This is what mri_label2label should do - sample
>>> these locations onto the surface you specify and fill in the vertex
>>> indices. Check the output of label2label and see if it has values >= 0
>>> cheers
>>> Bruce
>>>
>>> On Thu, 29 Sep 2016, Crawford, Anna wrote:
>>>
 Hi,

 I just checked all the labels I created and they all have -1 in the first
 column (the file name ending in 'N' should be the one created from
 mri_label2label). So, I did something wrong when originally creating the
 label I assume. When I created it, under the ROI tab, I created a new one
 and then drew it in the viewer with a volume (I did both white matter and
 brain mask) also loaded. Was this wrong?

 Thank you,
 Anna
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, September 29, 2016 12:00 PM
 To: Crawford, Anna
 Cc: Anna Crawford; Douglas N. Greve
 Subject: RE: Infalted/Label

 Hi Anna

 the label you send me hasn't been sampled onto the 

Re: [Freesurfer] Re Re Re Re: Question regarding mri_convert

[Tamara Tavares]

I looked at some structures and the absolute differences range from 8-35
mm^3. They are quite small but I was surprised to see any difference since
they are the same scan.

Thanks,
Tamara


Hi Tamara

can you let us know how big the differences are?

thanks
Bruce
On Wed, 28 Sep 2016,
Douglas Greve wrote:

>
> I don't understand what the problem is. Can you elaborate?
>
>
> On 9/27/16 12:13 PM, Tamara Tavares wrote:
>   The differences have been found in the outputs from the aseg
>   file. Particularly, I am interested in the ventricles and the
>   intracranial volumes. I have loaded both anatomicals in FreeView
>   and toggled between them and have found no differences visually.
>   ?
>
> I have attached the files (Via Google Drive since they are large).
> They are from the same participant.
>
> Thank you again,
> Tamara
>
> ?[icon_10_generic_list.png] ?rawavg_MriConvert.mgz[x_8px.png]
> ??[icon_10_generic_list.png] ?rawavgSlicer4.mgz[x_8px.png]
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Infalted/Label

[Bruce Fischl]

oh, don't use inflated! The sampling uses the surface to look up the 
location for the sampling. Use white most likely. The vertex index will 
allow you to see if on the inflated surface without doing anything else

cheers
Bruce
On 
Thu, 29 Sep 2016, Crawford, Anna wrote:

> It seems as though I did something else wrong. I am guessing it has to do 
> with dmax (I used inflated as my surface) for the --paint option. I had tried 
> 0,1, and dmax as the input to the option. The new label it created only had 1 
> entry of all zeros which is why I cannot find it on the surface or the volume 
> I would imagine.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 1:13 PM
> To: Crawford, Anna; Bruce Fischl
> Cc: freesurfer@nmr.mgh.harvard.edu; Anna Crawford
> Subject: Re: [Freesurfer] Infalted/Label
>
> Sounds like it. View the label on the volume while displaying the
> surfaces in the volume and see if they intersect
>
>
> On 09/29/2016 01:12 PM, Crawford, Anna wrote:
>> I added the --paint option which seemed to run successfully. I loaded it as 
>> a label on the inflated surface and it did not crash, but I do not see it 
>> anywhere on the surface. Does this just mean that I didn't actually draw it 
>> on the surface? As in, everything was done correct, the location of the 
>> label isn't on the surface though.
>>
>> Thank you!
>> Anna
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:45 PM
>> To: Crawford, Anna; Bruce Fischl
>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: Infalted/Label
>>
>> That is a volume-based label. Try using the --paint option to
>> mri_label2label to convert it to a surface-based label (assuming it is
>> actually on the surface). Run mri_label2label with --help to get an example
>>
>>
>> On 09/29/2016 12:38 PM, Crawford, Anna wrote:
>>> This is the output on label2label. The first colum of the created column is 
>>> -1.
>>>
>>> mri_label2label --srcsubject segfs --srclabel 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>>  --trgsubject segfs --trglabel Testing1N.label --regmethod volume
>>>
>>> srclabel = 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>> srcsubject = segfs
>>> trgsubject = segfs
>>> trglabel = Testing1N.label
>>> regmethod = volume
>>>
>>> usehash = 1
>>> Use ProjAbs  = 0, 0
>>> Use ProjFrac = 0, 0
>>> DoPaint 0
>>>
>>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
>>> FREESURFER_HOME /tools/freesurfer
>>> Loading source label.
>>> Found 216 points in source label.
>>> Starting volumetric mapping 216 points
>>> Src2TrgVolReg: -
>>>1.000   0.000   0.000   0.000;
>>>0.000   1.000   0.000  -0.000;
>>>0.000  -0.000   1.000  -0.000;
>>>0.000   0.000   0.000   1.000;
>>> 0  -39. 17. 55.-39. 17. 55.
>>> 1  -38. 17. 55.-38. 17. 55.
>>> 2  -40. 18. 55.-40. 18. 55.
>>> 3  -39. 18. 55.-39. 18. 55.
>>> 4  -38. 18. 55.-38. 18. 55.
>>> Writing label file Testing1N.label 216
>>> mri_label2label: Done
>>>
>>> Thanks,
>>> Anna
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 12:29 PM
>>> To: Crawford, Anna
>>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
>>> Subject: RE: Infalted/Label
>>>
>>> I'll cc the list, which I should have done the first time. No, you
>>> didn't do anything wrong. This is what mri_label2label should do - sample
>>> these locations onto the surface you specify and fill in the vertex
>>> indices. Check the output of label2label and see if it has values >= 0
>>> cheers
>>> Bruce
>>>
>>> On Thu, 29 Sep 2016, Crawford, Anna wrote:
>>>
 Hi,

 I just checked all the labels I created and they all have -1 in the first 
 column (the file name ending in 'N' should be the one created from 
 mri_label2label). So, I did something wrong when originally creating the 
 label I assume. When I created it, under the ROI tab, I created a new one 
 and then drew it in the viewer with a volume (I did both white matter and 
 brain mask) also loaded. Was this wrong?

 Thank you,
 Anna
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, September 29, 2016 12:00 PM
 To: Crawford, Anna
 Cc: Anna Crawford; Douglas N. Greve
 Subject: RE: Infalted/Label

 Hi Anna

 the label you send me hasn't been sampled onto the surface, which is why
 it kills the 

Re: [Freesurfer] Infalted/Label

[Crawford, Anna]

It seems as though I did something else wrong. I am guessing it has to do with 
dmax (I used inflated as my surface) for the --paint option. I had tried 0,1, 
and dmax as the input to the option. The new label it created only had 1 entry 
of all zeros which is why I cannot find it on the surface or the volume I would 
imagine. 

Thanks,
Anna

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 1:13 PM
To: Crawford, Anna; Bruce Fischl
Cc: freesurfer@nmr.mgh.harvard.edu; Anna Crawford
Subject: Re: [Freesurfer] Infalted/Label

Sounds like it. View the label on the volume while displaying the
surfaces in the volume and see if they intersect


On 09/29/2016 01:12 PM, Crawford, Anna wrote:
> I added the --paint option which seemed to run successfully. I loaded it as a 
> label on the inflated surface and it did not crash, but I do not see it 
> anywhere on the surface. Does this just mean that I didn't actually draw it 
> on the surface? As in, everything was done correct, the location of the label 
> isn't on the surface though.
>
> Thank you!
> Anna
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 12:45 PM
> To: Crawford, Anna; Bruce Fischl
> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
> Subject: Re: Infalted/Label
>
> That is a volume-based label. Try using the --paint option to
> mri_label2label to convert it to a surface-based label (assuming it is
> actually on the surface). Run mri_label2label with --help to get an example
>
>
> On 09/29/2016 12:38 PM, Crawford, Anna wrote:
>> This is the output on label2label. The first colum of the created column is 
>> -1.
>>
>> mri_label2label --srcsubject segfs --srclabel 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>  --trgsubject segfs --trglabel Testing1N.label --regmethod volume
>>
>> srclabel = 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>> srcsubject = segfs
>> trgsubject = segfs
>> trglabel = Testing1N.label
>> regmethod = volume
>>
>> usehash = 1
>> Use ProjAbs  = 0, 0
>> Use ProjFrac = 0, 0
>> DoPaint 0
>>
>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
>> FREESURFER_HOME /tools/freesurfer
>> Loading source label.
>> Found 216 points in source label.
>> Starting volumetric mapping 216 points
>> Src2TrgVolReg: -
>>1.000   0.000   0.000   0.000;
>>0.000   1.000   0.000  -0.000;
>>0.000  -0.000   1.000  -0.000;
>>0.000   0.000   0.000   1.000;
>> 0  -39. 17. 55.-39. 17. 55.
>> 1  -38. 17. 55.-38. 17. 55.
>> 2  -40. 18. 55.-40. 18. 55.
>> 3  -39. 18. 55.-39. 18. 55.
>> 4  -38. 18. 55.-38. 18. 55.
>> Writing label file Testing1N.label 216
>> mri_label2label: Done
>>
>> Thanks,
>> Anna
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:29 PM
>> To: Crawford, Anna
>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
>> Subject: RE: Infalted/Label
>>
>> I'll cc the list, which I should have done the first time. No, you
>> didn't do anything wrong. This is what mri_label2label should do - sample
>> these locations onto the surface you specify and fill in the vertex
>> indices. Check the output of label2label and see if it has values >= 0
>> cheers
>> Bruce
>>
>> On Thu, 29 Sep 2016, Crawford, Anna wrote:
>>
>>> Hi,
>>>
>>> I just checked all the labels I created and they all have -1 in the first 
>>> column (the file name ending in 'N' should be the one created from 
>>> mri_label2label). So, I did something wrong when originally creating the 
>>> label I assume. When I created it, under the ROI tab, I created a new one 
>>> and then drew it in the viewer with a volume (I did both white matter and 
>>> brain mask) also loaded. Was this wrong?
>>>
>>> Thank you,
>>> Anna
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 12:00 PM
>>> To: Crawford, Anna
>>> Cc: Anna Crawford; Douglas N. Greve
>>> Subject: RE: Infalted/Label
>>>
>>> Hi Anna
>>>
>>> the label you send me hasn't been sampled onto the surface, which is why
>>> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You
>>> can tell this is the case as the first column has all -1. If it had been
>>> sampled onto the surface these values would be in [0, nvertices].
>>>
>>> Does you newer one have non-zero values in this column?
>>>
>>> cheers
>>> Bruce
>>>
>>> On Thu, 29 Sep 2016,
>>> Crawford, Anna wrote:
>>>
 It is in the left hemisphere.
 

Re: [Freesurfer] Infalted/Label

[Bruce Fischl]

you can also look at the vertex index of the first entry in the label 
file and type that into the "cursor" field in freeview so it will go to 
that point. My guess is that it does intersect the surface, otherwise the 
label indices would have stayed -1

On Thu, 29 Sep 2016, Douglas N Greve wrote:

> Sounds like it. View the label on the volume while displaying the surfaces in 
> the volume and see if they intersect
>
>
> On 09/29/2016 01:12 PM, Crawford, Anna wrote:
>> I added the --paint option which seemed to run successfully. I loaded it as 
>> a label on the inflated surface and it did not crash, but I do not see it 
>> anywhere on the surface. Does this just mean that I didn't actually draw it 
>> on the surface? As in, everything was done correct, the location of the 
>> label isn't on the surface though.
>> 
>> Thank you!
>> Anna
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:45 PM
>> To: Crawford, Anna; Bruce Fischl
>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: Infalted/Label
>> 
>> That is a volume-based label. Try using the --paint option to
>> mri_label2label to convert it to a surface-based label (assuming it is
>> actually on the surface). Run mri_label2label with --help to get an example
>> 
>> 
>> On 09/29/2016 12:38 PM, Crawford, Anna wrote:
>>> This is the output on label2label. The first colum of the created column 
>>> is -1.
>>> 
>>> mri_label2label --srcsubject segfs --srclabel 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>>  
>>> --trgsubject segfs --trglabel Testing1N.label --regmethod volume
>>> 
>>> srclabel = 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>>> srcsubject = segfs
>>> trgsubject = segfs
>>> trglabel = Testing1N.label
>>> regmethod = volume
>>> 
>>> usehash = 1
>>> Use ProjAbs  = 0, 0
>>> Use ProjFrac = 0, 0
>>> DoPaint 0
>>> 
>>> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
>>> FREESURFER_HOME /tools/freesurfer
>>> Loading source label.
>>> Found 216 points in source label.
>>> Starting volumetric mapping 216 points
>>> Src2TrgVolReg: -
>>>1.000   0.000   0.000   0.000;
>>>0.000   1.000   0.000  -0.000;
>>>0.000  -0.000   1.000  -0.000;
>>>0.000   0.000   0.000   1.000;
>>> 0  -39. 17. 55.-39. 17. 55.
>>> 1  -38. 17. 55.-38. 17. 55.
>>> 2  -40. 18. 55.-40. 18. 55.
>>> 3  -39. 18. 55.-39. 18. 55.
>>> 4  -38. 18. 55.-38. 18. 55.
>>> Writing label file Testing1N.label 216
>>> mri_label2label: Done
>>> 
>>> Thanks,
>>> Anna
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 12:29 PM
>>> To: Crawford, Anna
>>> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
>>> Subject: RE: Infalted/Label
>>> 
>>> I'll cc the list, which I should have done the first time. No, you
>>> didn't do anything wrong. This is what mri_label2label should do - sample
>>> these locations onto the surface you specify and fill in the vertex
>>> indices. Check the output of label2label and see if it has values >= 0
>>> cheers
>>> Bruce
>>> 
>>> On Thu, 29 Sep 2016, Crawford, Anna wrote:
>>> 
 Hi,
 
 I just checked all the labels I created and they all have -1 in the first 
 column (the file name ending in 'N' should be the one created from 
 mri_label2label). So, I did something wrong when originally creating the 
 label I assume. When I created it, under the ROI tab, I created a new one 
 and then drew it in the viewer with a volume (I did both white matter and 
 brain mask) also loaded. Was this wrong?
 
 Thank you,
 Anna
 
 From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
 Sent: Thursday, September 29, 2016 12:00 PM
 To: Crawford, Anna
 Cc: Anna Crawford; Douglas N. Greve
 Subject: RE: Infalted/Label
 
 Hi Anna
 
 the label you send me hasn't been sampled onto the surface, which is why
 it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You
 can tell this is the case as the first column has all -1. If it had been
 sampled onto the surface these values would be in [0, nvertices].
 
 Does you newer one have non-zero values in this column?
 
 cheers
 Bruce
 
 On Thu, 29 Sep 2016,
 Crawford, Anna wrote:
 
> It is in the left hemisphere.
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 10:38 AM
> To: Anna Crawford
> Cc: Crawford, Anna; Douglas N. Greve
> Subject: Re: Infalted/Label
> 
> are the 

Re: [Freesurfer] Infalted/Label

[Crawford, Anna]

I added the --paint option which seemed to run successfully. I loaded it as a 
label on the inflated surface and it did not crash, but I do not see it 
anywhere on the surface. Does this just mean that I didn't actually draw it on 
the surface? As in, everything was done correct, the location of the label 
isn't on the surface though.

Thank you!
Anna

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 12:45 PM
To: Crawford, Anna; Bruce Fischl
Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu
Subject: Re: Infalted/Label

That is a volume-based label. Try using the --paint option to
mri_label2label to convert it to a surface-based label (assuming it is
actually on the surface). Run mri_label2label with --help to get an example


On 09/29/2016 12:38 PM, Crawford, Anna wrote:
> This is the output on label2label. The first colum of the created column is 
> -1.
>
> mri_label2label --srcsubject segfs --srclabel 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>  --trgsubject segfs --trglabel Testing1N.label --regmethod volume
>
> srclabel = 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
> srcsubject = segfs
> trgsubject = segfs
> trglabel = Testing1N.label
> regmethod = volume
>
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> FREESURFER_HOME /tools/freesurfer
> Loading source label.
> Found 216 points in source label.
> Starting volumetric mapping 216 points
> Src2TrgVolReg: -
>   1.000   0.000   0.000   0.000;
>   0.000   1.000   0.000  -0.000;
>   0.000  -0.000   1.000  -0.000;
>   0.000   0.000   0.000   1.000;
>0  -39. 17. 55.-39. 17. 55.
>1  -38. 17. 55.-38. 17. 55.
>2  -40. 18. 55.-40. 18. 55.
>3  -39. 18. 55.-39. 18. 55.
>4  -38. 18. 55.-38. 18. 55.
> Writing label file Testing1N.label 216
> mri_label2label: Done
>
> Thanks,
> Anna
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 12:29 PM
> To: Crawford, Anna
> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
> Subject: RE: Infalted/Label
>
> I'll cc the list, which I should have done the first time. No, you
> didn't do anything wrong. This is what mri_label2label should do - sample
> these locations onto the surface you specify and fill in the vertex
> indices. Check the output of label2label and see if it has values >= 0
> cheers
> Bruce
>
> On Thu, 29 Sep 2016, Crawford, Anna wrote:
>
>> Hi,
>>
>> I just checked all the labels I created and they all have -1 in the first 
>> column (the file name ending in 'N' should be the one created from 
>> mri_label2label). So, I did something wrong when originally creating the 
>> label I assume. When I created it, under the ROI tab, I created a new one 
>> and then drew it in the viewer with a volume (I did both white matter and 
>> brain mask) also loaded. Was this wrong?
>>
>> Thank you,
>> Anna
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:00 PM
>> To: Crawford, Anna
>> Cc: Anna Crawford; Douglas N. Greve
>> Subject: RE: Infalted/Label
>>
>> Hi Anna
>>
>> the label you send me hasn't been sampled onto the surface, which is why
>> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You
>> can tell this is the case as the first column has all -1. If it had been
>> sampled onto the surface these values would be in [0, nvertices].
>>
>> Does you newer one have non-zero values in this column?
>>
>> cheers
>> Bruce
>>
>> On Thu, 29 Sep 2016,
>> Crawford, Anna wrote:
>>
>>> It is in the left hemisphere.
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 10:38 AM
>>> To: Anna Crawford
>>> Cc: Crawford, Anna; Douglas N. Greve
>>> Subject: Re: Infalted/Label
>>>
>>> are the labels lh or rh?
>>> On Wed, 28 Sep 2016, Anna Crawford wrote:
>>>
 Hopefully this works better for you. Thank you,

 Anna


>>>
>>> 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.
>>>
>>>
>>> ===
>>>
>>>
>>> Please consider the environment before printing this e-mail
>>>
>>> Cleveland Clinic is 

Re: [Freesurfer] Infalted/Label

[Douglas N Greve]

That is a volume-based label. Try using the --paint option to 
mri_label2label to convert it to a surface-based label (assuming it is 
actually on the surface). Run mri_label2label with --help to get an example


On 09/29/2016 12:38 PM, Crawford, Anna wrote:
> This is the output on label2label. The first colum of the created column is 
> -1.
>
> mri_label2label --srcsubject segfs --srclabel 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
>  --trgsubject segfs --trglabel Testing1N.label --regmethod volume
>
> srclabel = 
> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
> srcsubject = segfs
> trgsubject = segfs
> trglabel = Testing1N.label
> regmethod = volume
>
> usehash = 1
> Use ProjAbs  = 0, 0
> Use ProjFrac = 0, 0
> DoPaint 0
>
> SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
> FREESURFER_HOME /tools/freesurfer
> Loading source label.
> Found 216 points in source label.
> Starting volumetric mapping 216 points
> Src2TrgVolReg: -
>   1.000   0.000   0.000   0.000;
>   0.000   1.000   0.000  -0.000;
>   0.000  -0.000   1.000  -0.000;
>   0.000   0.000   0.000   1.000;
>0  -39. 17. 55.-39. 17. 55.
>1  -38. 17. 55.-38. 17. 55.
>2  -40. 18. 55.-40. 18. 55.
>3  -39. 18. 55.-39. 18. 55.
>4  -38. 18. 55.-38. 18. 55.
> Writing label file Testing1N.label 216
> mri_label2label: Done
>
> Thanks,
> Anna
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 12:29 PM
> To: Crawford, Anna
> Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
> Subject: RE: Infalted/Label
>
> I'll cc the list, which I should have done the first time. No, you
> didn't do anything wrong. This is what mri_label2label should do - sample
> these locations onto the surface you specify and fill in the vertex
> indices. Check the output of label2label and see if it has values >= 0
> cheers
> Bruce
>
> On Thu, 29 Sep 2016, Crawford, Anna wrote:
>
>> Hi,
>>
>> I just checked all the labels I created and they all have -1 in the first 
>> column (the file name ending in 'N' should be the one created from 
>> mri_label2label). So, I did something wrong when originally creating the 
>> label I assume. When I created it, under the ROI tab, I created a new one 
>> and then drew it in the viewer with a volume (I did both white matter and 
>> brain mask) also loaded. Was this wrong?
>>
>> Thank you,
>> Anna
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 12:00 PM
>> To: Crawford, Anna
>> Cc: Anna Crawford; Douglas N. Greve
>> Subject: RE: Infalted/Label
>>
>> Hi Anna
>>
>> the label you send me hasn't been sampled onto the surface, which is why
>> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You
>> can tell this is the case as the first column has all -1. If it had been
>> sampled onto the surface these values would be in [0, nvertices].
>>
>> Does you newer one have non-zero values in this column?
>>
>> cheers
>> Bruce
>>
>> On Thu, 29 Sep 2016,
>> Crawford, Anna wrote:
>>
>>> It is in the left hemisphere.
>>> 
>>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, September 29, 2016 10:38 AM
>>> To: Anna Crawford
>>> Cc: Crawford, Anna; Douglas N. Greve
>>> Subject: Re: Infalted/Label
>>>
>>> are the labels lh or rh?
>>> On Wed, 28 Sep 2016, Anna Crawford wrote:
>>>
 Hopefully this works better for you. Thank you,

 Anna


>>>
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>>> applicable law.  If the reader of this message is not the intended 
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>>> to the 

Re: [Freesurfer] REPOST cluster feature extraction from qdec output

[Douglas N Greve]

1) Sorry, I don't understand what you are trying to do

2) Depends on what you are testing. If you are looking at the slopes of 
the covariates, then demeaning is not important. If you are looking at 
group differences, you should first look for a difference in the slopes. 
If there is no significant differences, then reanalyze using DOSS 
instead of DODS in which case demeaning will not matter.

3) Correct


On 09/29/2016 09:09 AM, Damien MARIE wrote:
> Hi,
>
> Many thanks for your prompt reply Pr. Greve.
>
> I did :
>
> mri_glmfit --y 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh 
> --fsgd 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/qdec.fsgd
>  
> dods --glmdir 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA 
> --surf fsaverage rh --label 
> /home/damien/bin/freesurfer/subjects/fsaverage/label/rh.aparc.label 
> --C 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Avg-Intercept-area.mat
>  
> --C 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-dyslexic-control-Intercept-area.mat
>  
> --C 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-male-female-Intercept-area.mat
>  
> --C 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-X-group-gender-Intercept-area.mat
>  
> --eres-save
>
> mri_segstats --in 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/eres.mgh
>  
> --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf 
> RH_Dys-CT_CSA_AgeGenderWRCSA.dat
>
>
> 1) I don’t get it though. Probably I made a bad description of my 
> goal, perhaps using this terminology of “residuals” also is not very 
> accurate.
>
> I exported the txt file (output of mri_segstats computed on eres.mgh) 
> to a statistical software and ran a mancova per cluster on cluster 
> values with covariatess : age, right hemispheric surface area + gender 
> factor. I find significant effects of the covariates on 7/9 clusters.
>
> I was not expecting such effects. I wanted to extract residuals of 
> surface area in the significant clusters obtain using the Qdec Monte 
> Carlo simulation on the contrast of interest (Dys - Ct) after removing 
> all covariate effects.
>
> My aim was to look at the differences between the two levels of the 
> factor of interest to get a sense of what is happening in this Qdec 
> analysis and this particular contrast of interest. These results are 
> in an opposite direction in comparison with other Qdec analysis 
> without covariates / ROI analysis on surface area residuals after 
> removing effect of gender, age and right hemispheric surface area 
> (Destrieux's labels) / Whole-brain VBM analyses with covariates (not 
> on surface area then...)
>
> Basically I have the feeling there is something wrong with the 
> contrast display in this particular qdec analysis. I don’t know how I 
> could get what I called the CSA residuals in the framework of this 
> analysis.
>
>
> 2) Another question: should I standardize or center my covariates 
> before proceeding to the analysis?
>
>
> 3) A silly question probably but to be 100% sure… If in the 
> qdec.table.dat, order of subjects is first group “ dys “ then second 
> group “ ct “ and that the contrast is called: 
> rh-Diff-dys-dyslexic-control-intercept-area , negative p value means 
> decrease of surface area in the first group (dys) as compared to the 
> second group (ct), right ?
>
>
> Thank you and best,
> *Damien MARIE*
> *
> *
> *
> *
> *
> *
> *
> *
> *
> *
> *Douglas Greve 
> Wed,
>  
> 28 Sep 2016 12:40:51 -0700 
> *
> *
> *
> *Those are not residuals. If you want residuals, you will need to run 
> mri_glmfit from the command line adding --eres-save. You can get the 
> command line from the mri_glmfit.log file in the glmdir*
>
>
>
>
> *
> On 9/28/16 10:58 AM, Damien MARIE wrote:
>
> Dear FreeSurfers,
>
> Sorry for the repost. I’m still trying to extract the residuals of
> cortical surface area from a qdec analysis with two factors (2
> levels) and 2 covariates.
>
> I tried this command line:
>
> mri_segstats --in
> 
> /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh
> --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf
> RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9
> columns (number of clusters) and 69 lines (number of subjects).
> Now I am not 100% sure it’s really the residuals (y.mgh) so I
> would be glad if somebody could tell me please.
>
> Best,
> Damien
> Original post:
> Dear experts,
>
> I would like to know what is the best and simplest way to extract cortical
> surface 

Re: [Freesurfer] Infalted/Label

[Crawford, Anna]

This is the output on label2label. The first colum of the created column is -1.

mri_label2label --srcsubject segfs --srclabel 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label 
--trgsubject segfs --trglabel Testing1N.label --regmethod volume

srclabel = 
/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label/Testing1.label
srcsubject = segfs
trgsubject = segfs
trglabel = Testing1N.label
regmethod = volume

usehash = 1
Use ProjAbs  = 0, 0
Use ProjFrac = 0, 0
DoPaint 0

SUBJECTS_DIR/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/
FREESURFER_HOME /tools/freesurfer
Loading source label.
Found 216 points in source label.
Starting volumetric mapping 216 points
Src2TrgVolReg: -
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000  -0.000;
 0.000  -0.000   1.000  -0.000;
 0.000   0.000   0.000   1.000;
  0  -39. 17. 55.-39. 17. 55.
  1  -38. 17. 55.-38. 17. 55.
  2  -40. 18. 55.-40. 18. 55.
  3  -39. 18. 55.-39. 18. 55.
  4  -38. 18. 55.-38. 18. 55.
Writing label file Testing1N.label 216
mri_label2label: Done

Thanks,
Anna

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 29, 2016 12:29 PM
To: Crawford, Anna
Cc: Anna Crawford; freesurfer@nmr.mgh.harvard.edu; Douglas N. Greve
Subject: RE: Infalted/Label

I'll cc the list, which I should have done the first time. No, you
didn't do anything wrong. This is what mri_label2label should do - sample
these locations onto the surface you specify and fill in the vertex
indices. Check the output of label2label and see if it has values >= 0
cheers
Bruce

On Thu, 29 Sep 2016, Crawford, Anna wrote:

> Hi,
>
> I just checked all the labels I created and they all have -1 in the first 
> column (the file name ending in 'N' should be the one created from 
> mri_label2label). So, I did something wrong when originally creating the 
> label I assume. When I created it, under the ROI tab, I created a new one and 
> then drew it in the viewer with a volume (I did both white matter and brain 
> mask) also loaded. Was this wrong?
>
> Thank you,
> Anna
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 12:00 PM
> To: Crawford, Anna
> Cc: Anna Crawford; Douglas N. Greve
> Subject: RE: Infalted/Label
>
> Hi Anna
>
> the label you send me hasn't been sampled onto the surface, which is why
> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You
> can tell this is the case as the first column has all -1. If it had been
> sampled onto the surface these values would be in [0, nvertices].
>
> Does you newer one have non-zero values in this column?
>
> cheers
> Bruce
>
> On Thu, 29 Sep 2016,
> Crawford, Anna wrote:
>
>> It is in the left hemisphere.
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 10:38 AM
>> To: Anna Crawford
>> Cc: Crawford, Anna; Douglas N. Greve
>> Subject: Re: Infalted/Label
>>
>> are the labels lh or rh?
>> On Wed, 28 Sep 2016, Anna Crawford wrote:
>>
>>> Hopefully this works better for you. Thank you,
>>>
>>> Anna
>>>
>>>
>>
>>
>> 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.
>>
>>
>> ===
>>
>>
>> Please consider the environment before printing this e-mail
>>
>> Cleveland Clinic is ranked as one of the top hospitals in America by 
>> U.S.News & World Report (2015).
>> Visit us online at http://www.clevelandclinic.org for a complete listing of 
>> our services, staff and locations.
>>
>>
>> Confidentiality Note:  This message is intended for use only by the 
>> individual or entity to which it is addressed and may contain information 
>> that is privileged, confidential, and exempt from disclosure under 
>> applicable law.  If the reader of this message is not the intended recipient 
>> or the employee or agent responsible for delivering the message to the 
>> intended recipient, you are hereby notified that any dissemination, 
>> distribution or copying of this communication is strictly prohibited.  If 
>> you have received this communication in error,  please contact the sender 
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>
> Please consider the environment before printing this e-mail
>

Re: [Freesurfer] Demeaning of "group" covariate in LME models

[Douglas N Greve]

sorry, not sure I understand. Are you coding a catagorical variable as a 
continuous covariate? What tutorial are you referring to?


On 09/29/2016 10:39 AM, Valsasina Paola wrote:
>
> Dear all,
>
> I am trying to perform a longitudinal statistic by using the LME mass 
> univariate toolbox. I have two groups of subjects (each acquired 3 or 
> 4 times over the follow-up), and I want to test whether atrophy 
> progresses differently over time in these two groups.
>
> I followed the tutorial on the Website, and I used the following 
> design matrix to test the time x group interaction: X=[ones(length 
> (M),1) M M(:,1).*M(:,2)]
>
> I first tried to code the categorical variable “group” assigning 
> values 1 and 2 for subjects belonging to group 1 and 2, respectively 
> (as it is suggested also in the tutorial). Then, I tried to re-run the 
> same model by using mean-centered values for “group” (i.e., assigning 
> -1 to subjects of group 1, and 1 to subjects of group 2).
>
> When I run the two statistical models, I obtain different results. 
> Therefore, I would like to ask which is the correct way to model the 
> group covariate? Should it be zero-centered or not? How de-meaning is 
> affecting the estimate?
>
> Thank you so much for any suggestion
>
> Kind regards
>
> Paola
>
>
>
> /Rispetta l’ambiente: non stampare questa mail se non è necessario.
> Respect the environment: if it's not necessary, don't print this mail./
>
>
>   IL TUO 5XMILLE AL SAN RAFFAELE DI MILANO
>
> Devolvi il tuo 5 per mille all’Ospedale San Raffaele: perché al centro 
> della Ricerca ci sei TU. CODICE FISCALE: 07636600962, nel riquadro 
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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] Projecting processed 4D functional data to individual surfaces

[Douglas N Greve]

I don't understand what you mean. When you use ico (when it used to 
work), it always went to fsaverage space. Do you want to decimate the 
native space surfaces?


On 09/29/2016 10:15 AM, Jared P Zimmerman wrote:
> I want to project to the native subject surfaces though, not 
> fsaverage.  If I use —trgsubject subjID would that work with the 
> —icoorder flag?  Alternatively I guess I could project to fsaverage 
> and then use mri_surf2surf to move back to the subject surface, but 
> that seems like a roundabout way to do it and will probably add some 
> unnecessary interpolation.
>
> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder 
> flags and I did successfully get output with 112745 vertices (is this 
> FS7 space?  I would have expected ~164k vertices, is this with medial 
> wall masked?) and I could try to resample that with mri_surf2surf.  I 
> wasn’t able to do this before, but I didn’t use the flag —trgsubject 
> or —trgicoorder flags, though I suspect I will run into the same 
> problem trying doing this.  I’m not at my computer now but can try 
> this later this afternoon though.
>
> Thanks,
> Jared
>
>> On Sep 29, 2016, at 12:00 AM, Douglas Greve 
>> > wrote:
>>
>> you can actually skip the ico thing and just use --trgsubject fsaverage6
>>
>>
>> On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
>>> Thanks Doug,
>>>
>>> This does seem like it will do the right thing, but it’s failing 
>>> because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to 
>>> have an ico subject in my subjects_dir
>>>
>>> Should this normally be in the subjects_dir?  I don’t recall ever 
>>> seeing this made when I’ve run recon-all in the past.
>>>
>>> Thanks,
>>> Jared
>>>
>>> Here’s the full terminal output when I run the command:
>>>
>>> mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg 
>>> func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o 
>>> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 
>>> --interp trilinear --noreshape --trgsubject ico --icoorder 6 
>>> --out_type mgh --surf-fwhm 6
>>> IcoOrder = 6, nIcoVtxs = 40962
>>> srcvol = /func_test/filtered_func_residuals.nii.gz
>>> srcreg = func_test/coreg/fs_ep2struct_fsl.dat
>>> srcregold = 0
>>> srcwarp unspecified
>>> surf = white
>>> hemi = lh
>>> trgsubject = ico
>>> surfreg = sphere.reg
>>> ProjFrac = 0.5
>>> thickness = thickness
>>> reshape = 0
>>> interp = trilinear
>>> float2int = round
>>> GetProjMax = 0
>>> INFO: float2int code = 0
>>> Done loading volume
>>> Reading surface /subjdir_test//subID/surf/lh.white
>>> Done reading source surface
>>> Reading thickness /subjdir_test//subID/surf/lh.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 = 11345
>>> Reading source surface registration
>>> subjdir_test//subID/surf/lh.sphere.reg
>>> Done loading source registration surface
>>> Reading icosahedron, order = 6, radius = 100
>>>   Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
>>> Done loading target registration surface
>>> Mapping Surfaces (subID -> ico)
>>> surf2surf_nnfr: building source hash (res=16).
>>> Surf2Surf: Forward Loop (40962)
>>>
>>> surf2surf_nnfr: building target hash (res=16).
>>> Surf2Surf: Reverse Loop (112745)
>>> Reverse Loop had 72236 hits
>>>
 On Sep 28, 2016, at 3:34 PM, Douglas Greve 
 > wrote:

 You need to specify --trgsubject ico in mri_vol2surf


 On 9/28/16 3:01 PM, Jared Zimmerman wrote:
> Hi All, forwarding this message along again as I'm still having 
> some trouble getting this to work.  Basically I would like to 1) 
> project processed residual time-series from the subject-space 
> volume to the subject-space surface, 2) smooth on the surface, 3) 
> down-sample to FS4 space.
>
> To do this is have used bbregister to calculate the registration, 
> then mri_vol2surf to project to the surface, but I am not sure the 
> output of mri_vol2surf is what I should be expecting.  The output 
> file has dimensions 112745 x 1 x 1 x 120 when I'm expecting ~40k 
> vertices for FS6 space and ~3k vertices for FS4 space, but 
> changing the --icoorder flag seems to have no effect on the number 
> of vertices in the output.
>
> I have loaded the output surface functional image into Matlab to 
> se that there is real time-series data in there, but I have no way 
> of knowing if it has mapped the data appropriately.  Additionally, 
> I've tried to use mri_surf2surf to downsample this data but have 
> not ben able to successfully get that to downsample the surface. 
>  The mri_surf2surf call I used is as follows:
>
> mri_surf2surf --srcsubject subjID --srcsurfval 
> 

Re: [Freesurfer] Warping an ROI from one subject to another

[Douglas N Greve]

The way you have it configured now, this is a volume-based ROI, so you 
need to use the volume-based reg method. This will map between the two 
subjects using the affine (12 dof) talairach registration which will not 
be as accurate as the surface-based registration. If this is a cortical 
ROI, I can show you how to redo this using a surface-based label.


On 09/29/2016 11:37 AM, Joel Bruss wrote:
> Another bump.
>
> On 09/21/2016 04:18 PM, Joel Bruss wrote:
>
>> I have two subjects, subA and subB.  subA has a binary ROI mask, native
>> space, that I'd like to place in subB's native space. Both subjects have
>> been run through all stages of recon, edited, etc. Is there a better or
>> easier way to achieve this than what I've run?:
>>
>>
>> #Resample the native space binary ROI file into "brainmask" space
>> mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1
>> ROI.nii.gz /subA/mri/ROI.mgz
>>
>> #Convert ROI file into a label
>> mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label
>>
>> #Move label from subA to subB
>> mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label
>> --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume
>>
>> #Convert warped ROI label to a volume
>> mri_label2vol --label /subB/mri/ROI_to_subB.label \
>> --subject subB \
>> --temp brainmask.mgz \
>> --regheader brainmask.mgz \
>> --o /subB/mri/ROI_to_subB.mgz
>>
>> #Convert the volume back to native subB space
>> mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1
>> /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz
>>
>> A few follow-up questions:
>>
>> 1) When running mri_label2label, is better to use surface or volume for
>> the "regmethod"?  Which method will give me a better fit for my output?
>> 2) The output I'm getting looks striped (there are holes in the binary
>> mask) and doesn't quite fit the anatomy (the final file is shifted up
>> and away from where I would expect it to be although in the general
>> vicinity of what I would expect).  It's almost as if I've chosen a wrong
>> target or file along the way.  I don't expect the fit to be perfect, but
>> did I do something wrong?
>>
>> Thanks in advance to any and all replies.
>>
>>
>>
>> 
>> Notice: This UI Health Care e-mail (including attachments) is covered by the 
>> Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended 
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>> disclosure under applicable law. If you are not the intended recipient, any 
>> dissemination, distribution or copying of this communication is strictly 
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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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Outgoing: 

Re: [Freesurfer] Infalted/Label

[Bruce Fischl]

I'll cc the list, which I should have done the first time. No, you 
didn't do anything wrong. This is what mri_label2label should do - sample 
these locations onto the surface you specify and fill in the vertex 
indices. Check the output of label2label and see if it has values >= 0
cheers
Bruce

On Thu, 29 Sep 2016, Crawford, Anna wrote:

> Hi,
>
> I just checked all the labels I created and they all have -1 in the first 
> column (the file name ending in 'N' should be the one created from 
> mri_label2label). So, I did something wrong when originally creating the 
> label I assume. When I created it, under the ROI tab, I created a new one and 
> then drew it in the viewer with a volume (I did both white matter and brain 
> mask) also loaded. Was this wrong?
>
> Thank you,
> Anna
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, September 29, 2016 12:00 PM
> To: Crawford, Anna
> Cc: Anna Crawford; Douglas N. Greve
> Subject: RE: Infalted/Label
>
> Hi Anna
>
> the label you send me hasn't been sampled onto the surface, which is why
> it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You
> can tell this is the case as the first column has all -1. If it had been
> sampled onto the surface these values would be in [0, nvertices].
>
> Does you newer one have non-zero values in this column?
>
> cheers
> Bruce
>
> On Thu, 29 Sep 2016,
> Crawford, Anna wrote:
>
>> It is in the left hemisphere.
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Thursday, September 29, 2016 10:38 AM
>> To: Anna Crawford
>> Cc: Crawford, Anna; Douglas N. Greve
>> Subject: Re: Infalted/Label
>>
>> are the labels lh or rh?
>> On Wed, 28 Sep 2016, Anna Crawford wrote:
>>
>>> Hopefully this works better for you. Thank you,
>>>
>>> Anna
>>>
>>>
>>
>>
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Re: [Freesurfer] Warping an ROI from one subject to another

[Joel Bruss]

Another bump.

On 09/21/2016 04:18 PM, Joel Bruss wrote:

> I have two subjects, subA and subB.  subA has a binary ROI mask, native
> space, that I'd like to place in subB's native space. Both subjects have
> been run through all stages of recon, edited, etc. Is there a better or
> easier way to achieve this than what I've run?:
>
>
> #Resample the native space binary ROI file into "brainmask" space
> mri_convert -rl /subA/mri/brainmask.mgz -rt nearest --no_scale 1
> ROI.nii.gz /subA/mri/ROI.mgz
>
> #Convert ROI file into a label
> mri_cor2label --id 1 --c /subA/mri --i ROI.mgz --l ROI.label
>
> #Move label from subA to subB
> mri_label2label --srcsubject subA --srclabel /subA/mri/ROI.label
> --trgsubject subB --trglabel /subB/mri/ROI_to_subB.label --regmethod volume
>
> #Convert warped ROI label to a volume
> mri_label2vol --label /subB/mri/ROI_to_subB.label \
> --subject subB \
> --temp brainmask.mgz \
> --regheader brainmask.mgz \
> --o /subB/mri/ROI_to_subB.mgz
>
> #Convert the volume back to native subB space
> mri_convert -rl subB_native.nii.gz -rt nearest --no_scale 1
> /subB/mri/ROI_to_subB.mgz ROI_to_subB_native.nii.gz
>
> A few follow-up questions:
>
> 1) When running mri_label2label, is better to use surface or volume for
> the "regmethod"?  Which method will give me a better fit for my output?
> 2) The output I'm getting looks striped (there are holes in the binary
> mask) and doesn't quite fit the anatomy (the final file is shifted up
> and away from where I would expect it to be although in the general
> vicinity of what I would expect).  It's almost as if I've chosen a wrong
> target or file along the way.  I don't expect the fit to be perfect, but
> did I do something wrong?
>
> Thanks in advance to any and all replies.
>
>
>
> 
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[Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

I would like to register PET image onto T1 anatomical. I used bbregister
with the following command and it failed :
*bbregister  --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg
Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out
Pet2T1.init.register.dof6.dat --o rPET.nii.gz *

Having heard about mri_coreg solving some bbregister fails, I tested it
with the following command :
*mri_coreg --s SUBJID  --mov PET.nii.gz --reg
Pet2T1.register.dof6.mri_coreg.lta --regdat
Pet2T1.register.dof6.mri_coreg.dat*

But it failed in the same way than bbregister. Do you have any advice on
this problem ?

Best regards,
Matthieu
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Re: [Freesurfer] Longitudinal surface analysis of PET data

[Matthieu Vanhoutte]

Dear Freesurfer's experts,

Could you answer me about my last question with no response in the mail
below ?

When using cortical thickness in longitudinal analysis with LME, we used
lh.thickness or rh.thickness from -long subject directories. These data
followed particular processing steps including registrations in order to
use them with more precision in longitudinal studies, didn't they ?

My problem is that I would like to perform longitudinal study on PET data
images with LME. So I wonder if I just have to resample onto -long cortical
subject surface ? Do I need to follow the same steps than cortical
thickness from cross-sectional to -long subject directories ? If this is
the case, which commands should I use to mimic cortical thickness
longitudinal data ?

Many thanks in advance for helping !

Best regards,
Matthieu

2016-09-18 23:02 GMT+02:00 Matthieu Vanhoutte :

> Hi Martin,
>
> Thanks for your answer. However, it seems to me that cortical thickness
> follow a particular process with the recon-all -long process, isn’t it ? Is
> there any resample onto average time subject then other operation following
> ?
>
> Best regards,
> Matthieu
>
> > Le 18 sept. 2016 à 16:26, Martin Reuter  a
> écrit :
> >
> > Hi Matthieu,
> >
> > I never used PET data, but once you manage to resample you pet data onto
> the surface, you will have a file similar to the thickness file for each
> subjects. Instead of thickness it holds you PET information. From that
> point on everything should be identical to the thickness analysis.
> >
> > So this is really more a question how to get your PET data sampled onto
> the surface. If no one else replies, write that into the subject line and
> repost.
> >
> > Best, Martin
> >
> >
> >> On Sep 17, 2016, at 7:37 AM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
> >>
> >> Dear Freesurfer’s experts,
> >>
> >> I would like to use the longitudinal mixed-effects model for surface
> PET analysis. Although I could find all the process to follow the
> longitudinal analysis of cortical thickness, I couldn’t resolve the
> steps/commands to apply successively to coregistered PET data on T1 MRI.
> >>
> >> Could you precise me the process and commands to use for PET
> longitudinal analysis ?
> >>
> >> Many thanks in advance !
> >>
> >> Best regards,
> >> Matthieu
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[Freesurfer] VM box installation error

[Arshad Zaman]

Hi,


I am a new user and trying to install Freesurfer using the virtualbox 
installation instructions (windows 7). I have

created the virtual machine and can view the VB manager with the correct 
specific (general, system, display,  etc) using the freesurfer image 
(freesurfer*.vdi). The FreeSurfer5.3 machine is running however the pop-up box

displays,


error: file not found.

grub rescue>


Any suggestions will be most appreciated (to save me hours of painful trial and 
error attempts!),


Best wishes,


Arshad





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[Freesurfer] Demeaning of "group" covariate in LME models

[Valsasina Paola]

Dear all,

I am trying to perform a longitudinal statistic by using the LME mass 
univariate toolbox. I have two groups of subjects (each acquired 3 or 4 times 
over the follow-up), and I want to test whether atrophy progresses differently 
over time in these two groups.

I followed the tutorial on the Website, and I used the following design matrix 
to test the time x group interaction: X=[ones(length (M),1) M M(:,1).*M(:,2)]

I first tried to code the categorical variable "group" assigning values 1 and 2 
for subjects belonging to group 1 and 2, respectively (as it is suggested also 
in the tutorial). Then, I tried to re-run the same model by using mean-centered 
values for "group" (i.e., assigning -1 to subjects of group 1, and 1 to 
subjects of group 2).

When I run the two statistical models, I obtain different results. Therefore, I 
would like to ask which is the correct way to model the group covariate? Should 
it be zero-centered or not? How de-meaning is affecting the estimate?

Thank you so much for any suggestion
Kind regards
Paola




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Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared P Zimmerman]

Ahh, thanks Bruce.  Is there a way to downsample the subject meshes?

-jared

> On Sep 29, 2016, at 10:18 AM, Bruce Fischl  wrote:
> 
> Hi Jared
> 
> the icosahedra are only used to represent average space surface 
> (fsaverage[4-7]), not individual subjects.
> 
> cheers
> Bruce
> On Thu, 29 Sep 2016, Jared P Zimmerman wrote:
> 
>> I want to project to the native subject surfaces though, not fsaverage.  If
>> I use —trgsubject subjID would that work with the —icoorder flag?
>>  Alternatively I guess I could project to fsaverage and then use
>> mri_surf2surf to move back to the subject surface, but that seems like a
>> roundabout way to do it and will probably add some unnecessary
>> interpolation.
>> Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and
>> I did successfully get output with 112745 vertices (is this FS7 space?  I
>> would have expected ~164k vertices, is this with medial wall masked?) and I
>> could try to resample that with mri_surf2surf.  I wasn’t able to do this
>> before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though
>> I suspect I will run into the same problem trying doing this.  I’m not at my
>> computer now but can try this later this afternoon though.
>> Thanks,
>> Jared
>> 
>>  On Sep 29, 2016, at 12:00 AM, Douglas Greve
>>   wrote:
>> you can actually skip the ico thing and just use --trgsubject
>> fsaverage6
>> On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
>>  Thanks Doug,
>> This does seem like it will do the right thing, but it’s failing
>> because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to
>> have an ico subject in my subjects_dir
>> Should this normally be in the subjects_dir?  I don’t recall
>> ever seeing this made when I’ve run recon-all in the past.
>> Thanks,
>> Jared
>> Here’s the full terminal output when I run the command:
>> mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz
>> --reg func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o
>> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac
>> 0.5 --interp trilinear --noreshape --trgsubject ico --icoorder 6
>> --out_type mgh --surf-fwhm 6
>> IcoOrder = 6, nIcoVtxs = 40962
>> srcvol = /func_test/filtered_func_residuals.nii.gz
>> srcreg = func_test/coreg/fs_ep2struct_fsl.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> trgsubject = ico
>> surfreg = sphere.reg
>> ProjFrac = 0.5
>> thickness = thickness
>> reshape = 0
>> interp = trilinear
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Reading surface /subjdir_test//subID/surf/lh.white
>> Done reading source surface
>> Reading thickness /subjdir_test//subID/surf/lh.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 = 11345
>> Reading source surface registration
>> subjdir_test//subID/surf/lh.sphere.reg
>> Done loading source registration surface
>> Reading icosahedron, order = 6, radius = 100
>>   Reading icosahedron
>> /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
>> Done loading target registration surface
>> Mapping Surfaces (subID -> ico)
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (40962)
>> surf2surf_nnfr: building target hash (res=16).
>> Surf2Surf: Reverse Loop (112745)
>> Reverse Loop had 72236 hits 
>> 
>>  On Sep 28, 2016, at 3:34 PM, Douglas Greve
>>   wrote:
>> You need to specify --trgsubject ico in mri_vol2surf
>> On 9/28/16 3:01 PM, Jared Zimmerman wrote:
>>  Hi All, forwarding this message along again as
>>  I'm still having some trouble getting this to
>>  work.  Basically I would like to 1) project
>>  processed residual time-series from the
>>  subject-space volume to the subject-space
>>  surface, 2) smooth on the surface, 3)
>>  down-sample to FS4 space.
>> 
>>  To do this is have used bbregister to
>>  calculate the registration, then mri_vol2surf
>>  to project to the surface, but I am not sure
>>  the output of mri_vol2surf is what I should be
>>  expecting.  The output file has dimensions
>>  112745 x 1 x 1 x 120 when I'm expecting ~40k
>>  vertices for FS6 space and ~3k vertices for
>>  FS4 space, but changing the --icoorder flag
>>  seems to have no effect on the number of
>>  vertices in the output.
>> 
>>  I have loaded the output surface functional
>>  image into Matlab to se that there is real
>>  time-series data in there, but I have no way
>>  of knowing if it has mapped the data
>>  appropriately.  Additionally, I've tried to
>>  use mri_surf2surf to downsample this data but
>>  have not ben able to successfully get that to
>>  downsample the surface.  The mri_surf2surf
>>  call I used is as follows:
>> 
>>  mri_surf2surf --srcsubject 

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Bruce Fischl]

Hi Jared

the icosahedra are only used to represent average space surface 
(fsaverage[4-7]), not individual subjects.


cheers
Bruce
On Thu, 29 Sep 2016, Jared P 
Zimmerman wrote:



I want to project to the native subject surfaces though, not fsaverage.  If
I use —trgsubject subjID would that work with the —icoorder flag?
 Alternatively I guess I could project to fsaverage and then use
mri_surf2surf to move back to the subject surface, but that seems like a
roundabout way to do it and will probably add some unnecessary
interpolation.
Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and
I did successfully get output with 112745 vertices (is this FS7 space?  I
would have expected ~164k vertices, is this with medial wall masked?) and I
could try to resample that with mri_surf2surf.  I wasn’t able to do this
before, but I didn’t use the flag —trgsubject or —trgicoorder flags, though
I suspect I will run into the same problem trying doing this.  I’m not at my
computer now but can try this later this afternoon though.

Thanks,
Jared

  On Sep 29, 2016, at 12:00 AM, Douglas Greve
   wrote:

you can actually skip the ico thing and just use --trgsubject
fsaverage6


On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
  Thanks Doug,
This does seem like it will do the right thing, but it’s failing
because it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to
have an ico subject in my subjects_dir

Should this normally be in the subjects_dir?  I don’t recall
ever seeing this made when I’ve run recon-all in the past.

Thanks,
Jared

Here’s the full terminal output when I run the command:

mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz
--reg func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o
func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac
0.5 --interp trilinear --noreshape --trgsubject ico --icoorder 6
--out_type mgh --surf-fwhm 6
IcoOrder = 6, nIcoVtxs = 40962
srcvol = /func_test/filtered_func_residuals.nii.gz
srcreg = func_test/coreg/fs_ep2struct_fsl.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = ico
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilinear
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Reading surface /subjdir_test//subID/surf/lh.white
Done reading source surface
Reading thickness /subjdir_test//subID/surf/lh.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 = 11345
Reading source surface registration
subjdir_test//subID/surf/lh.sphere.reg
Done loading source registration surface
Reading icosahedron, order = 6, radius = 100
  Reading icosahedron
/share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
Done loading target registration surface
Mapping Surfaces (subID -> ico)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (40962)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (112745)
Reverse Loop had 72236 hits 

  On Sep 28, 2016, at 3:34 PM, Douglas Greve
   wrote:

You need to specify --trgsubject ico in mri_vol2surf


On 9/28/16 3:01 PM, Jared Zimmerman wrote:
  Hi All, forwarding this message along again as
  I'm still having some trouble getting this to
  work.  Basically I would like to 1) project
  processed residual time-series from the
  subject-space volume to the subject-space
  surface, 2) smooth on the surface, 3)
  down-sample to FS4 space.

  To do this is have used bbregister to
  calculate the registration, then mri_vol2surf
  to project to the surface, but I am not sure
  the output of mri_vol2surf is what I should be
  expecting.  The output file has dimensions
  112745 x 1 x 1 x 120 when I'm expecting ~40k
  vertices for FS6 space and ~3k vertices for
  FS4 space, but changing the --icoorder flag
  seems to have no effect on the number of
  vertices in the output.

  I have loaded the output surface functional
  image into Matlab to se that there is real
  time-series data in there, but I have no way
  of knowing if it has mapped the data
  appropriately.  Additionally, I've tried to
  use mri_surf2surf to downsample this data but
  have not ben able to successfully get that to
  downsample the surface.  The mri_surf2surf
  call I used is as follows:

  mri_surf2surf --srcsubject subjID --srcsurfval
  /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh
  --trgsubject subjID --trgsurfval
  /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh
  --hemi lh --trgicoorder 4

  Any advice on how to achieve my goal of
  projecting to subject surfaces, smoothing and
  downsampling to FS4, as well as
  recommendations on how to visualize the
  surface functional data and confirm that the
  

Re: [Freesurfer] Projecting processed 4D functional data to individual surfaces

[Jared P Zimmerman]

I want to project to the native subject surfaces though, not fsaverage.  If I 
use —trgsubject subjID would that work with the —icoorder flag?  Alternatively 
I guess I could project to fsaverage and then use mri_surf2surf to move back to 
the subject surface, but that seems like a roundabout way to do it and will 
probably add some unnecessary interpolation.

Also, I’ve used mri_vol2surf without the —trgsubject or —icoorder flags and I 
did successfully get output with 112745 vertices (is this FS7 space?  I would 
have expected ~164k vertices, is this with medial wall masked?) and I could try 
to resample that with mri_surf2surf.  I wasn’t able to do this before, but I 
didn’t use the flag —trgsubject or —trgicoorder flags, though I suspect I will 
run into the same problem trying doing this.  I’m not at my computer now but 
can try this later this afternoon though.

Thanks,
Jared

> On Sep 29, 2016, at 12:00 AM, Douglas Greve  wrote:
> 
> you can actually skip the ico thing and just use --trgsubject fsaverage6
> 
> On 9/28/16 7:06 PM, Jared P Zimmerman wrote:
>> Thanks Doug,
>> 
>> This does seem like it will do the right thing, but it’s failing because 
>> it’s looking for /SUBJECTS_DIR/ico/ and I do not seem to have an ico subject 
>> in my subjects_dir
>> 
>> Should this normally be in the subjects_dir?  I don’t recall ever seeing 
>> this made when I’ve run recon-all in the past.
>> 
>> Thanks,
>> Jared
>> 
>> Here’s the full terminal output when I run the command:
>> 
>>  mri_vol2surf --mov /func_test/filtered_func_residuals.nii.gz --reg 
>> func_test/coreg/fs_ep2struct_fsl.dat --hemi lh --o 
>> func_test/surface/lh_surf_filtered_func_residuals.mgh --projfrac 0.5 
>> --interp trilinear --noreshape --trgsubject ico --icoorder 6 --out_type mgh 
>> --surf-fwhm 6
>> IcoOrder = 6, nIcoVtxs = 40962
>> srcvol = /func_test/filtered_func_residuals.nii.gz
>> srcreg = func_test/coreg/fs_ep2struct_fsl.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> trgsubject = ico
>> surfreg = sphere.reg
>> ProjFrac = 0.5
>> thickness = thickness
>> reshape = 0
>> interp = trilinear
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> Reading surface /subjdir_test//subID/surf/lh.white
>> Done reading source surface
>> Reading thickness /subjdir_test//subID/surf/lh.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 = 11345
>> Reading source surface registration 
>>  subjdir_test//subID/surf/lh.sphere.reg
>> Done loading source registration surface
>> Reading icosahedron, order = 6, radius = 100
>>Reading icosahedron /share/apps/freesurfer/5.3.0/lib/bem/ic6.tri
>> Done loading target registration surface
>> Mapping Surfaces (subID -> ico)
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (40962)
>> 
>> surf2surf_nnfr: building target hash (res=16).
>> Surf2Surf: Reverse Loop (112745)
>>  Reverse Loop had 72236 hits 
>> 
>>> On Sep 28, 2016, at 3:34 PM, Douglas Greve >> > wrote:
>>> 
>>> You need to specify --trgsubject ico in mri_vol2surf
>>> 
>>> 
>>> On 9/28/16 3:01 PM, Jared Zimmerman wrote:
 Hi All, forwarding this message along again as I'm still having some 
 trouble getting this to work.  Basically I would like to 1) project 
 processed residual time-series from the subject-space volume to the 
 subject-space surface, 2) smooth on the surface, 3) down-sample to FS4 
 space.
 
 To do this is have used bbregister to calculate the registration, then 
 mri_vol2surf to project to the surface, but I am not sure the output of 
 mri_vol2surf is what I should be expecting.  The output file has 
 dimensions 112745 x 1 x 1 x 120 when I'm expecting ~40k vertices for FS6 
 space and ~3k vertices for FS4 space, but changing the --icoorder flag 
 seems to have no effect on the number of vertices in the output.
 
 I have loaded the output surface functional image into Matlab to se that 
 there is real time-series data in there, but I have no way of knowing if 
 it has mapped the data appropriately.  Additionally, I've tried to use 
 mri_surf2surf to downsample this data but have not ben able to 
 successfully get that to downsample the surface.  The mri_surf2surf call I 
 used is as follows:
 
 mri_surf2surf --srcsubject subjID --srcsurfval 
 /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh --trgsubject 
 subjID --trgsurfval 
 /mov_dir/filtered_func_residuals_fs4_lh_6mm_noreshape.mgh --hemi lh 
 --trgicoorder 4
 
 Any advice on how to achieve my goal of projecting to subject surfaces, 
 smoothing and downsampling to FS4, as well as recommendations on how to 
 visualize the surface functional data and confirm that 

Re: [Freesurfer] tksurfer viewing issues

[Bruce Fischl]

Hi Paige

we have stopped development and most support of tksurfer. Can you use 
freeview instead or is there still some functionality that you need that 
is unique to tksurfer?

cheers
Bruce
On Thu, 29 Sep 2016, Paige Scalf wrote:

> Hello,
> 
> I too am having trouble with tksurfer displaying the surfaces upside down
> and back to front, but believing that they are correctly oriented (i.e.
> Talairach coordinates change in the wrong direction wrt to the surface but
> in the correct direction wrt the display window). I"m also running a CentOs
> flavor. Did anyone manage to solve this issue?
> 
> All the best,
> Paige
> 
>
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[Freesurfer] Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall

[GAJENDRA KATUWAL (RIT Student)]

Hello FreeSurfer experts,

I am considering using Freesurfer recon-all for segmentation of T1 brain
MRIs of young subjects (1-4 years). I am planning to use a Freesurfer
compliant pediatric template to maximize the segmentation accuracy.

In the publication titled *A FreeSurfer-compliant consistent manual
segmentation of infant brains spanning the 0–2 year age range (*
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/) by *Katyucia de
Macedo Rodrigues, Emma Ben-Avi, Danielle D. Sliva, Myong-sun Choe, Marie
Drottar, Ruopeng Wang, Bruce Fischl, Patricia E. Grant,and Lilla Zöllei, * it
has been mentioned that "Furthermore, we are also planning on making an
atlas generated from our training data sets available to the scientific
community (as part of the FreeSurfer package), which can serve as a
template in structural and functional studies and as a teaching tool for
trainees."

Has the pediatric template been released yet? Is there anyway
the pediatric template can be accessed if it has been released? Is it
available in the dev version or upcoming Freesurfer 6?

Regards,
Gajendra Jung Katuwal
PhD Candidate in Imaging Science
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Re: [Freesurfer] REPOST cluster feature extraction from qdec output

[Damien MARIE]

Hi,

Many thanks for your prompt reply Pr. Greve.

I did :

mri_glmfit --y 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh 
--fsgd 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/qdec.fsgd
 dods --glmdir 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA --surf 
fsaverage rh --label 
/home/damien/bin/freesurfer/subjects/fsaverage/label/rh.aparc.label --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Avg-Intercept-area.mat
 --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-dyslexic-control-Intercept-area.mat
 --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-male-female-Intercept-area.mat
 --C 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-X-group-gender-Intercept-area.mat
 --eres-save

mri_segstats --in 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/eres.mgh 
--sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf 
RH_Dys-CT_CSA_AgeGenderWRCSA.dat


1) I don’t get it though. Probably I made a bad description of my goal, perhaps 
using this terminology of “residuals” also is not very accurate.

I exported the txt file (output of mri_segstats computed on eres.mgh) to a 
statistical software and ran a mancova per cluster on cluster values with 
covariatess : age, right hemispheric surface area + gender factor. I find 
significant effects of the covariates on 7/9 clusters.

I was not expecting such effects. I wanted to extract residuals of surface area 
in the significant clusters obtain using the Qdec Monte Carlo simulation on the 
contrast of interest (Dys - Ct) after removing all covariate effects.

My aim was to look at the differences between the two levels of the factor of 
interest to get a sense of what is happening in this Qdec analysis and this 
particular contrast of interest. These results are in an opposite direction in 
comparison with other Qdec analysis without covariates / ROI analysis on 
surface area residuals after removing effect of gender, age and right 
hemispheric surface area (Destrieux's labels) / Whole-brain VBM analyses with 
covariates (not on surface area then...)

Basically I have the feeling there is something wrong with the contrast display 
in this particular qdec analysis. I don’t know how I could get what I called 
the CSA residuals in the framework of this analysis.


2) Another question: should I standardize or center my covariates before 
proceeding to the analysis?


3) A silly question probably but to be 100% sure… If in the qdec.table.dat, 
order of subjects is first group “ dys “ then second group “ ct “ and that the 
contrast is called: rh-Diff-dys-dyslexic-control-intercept-area , negative p 
value means decrease of surface area in the first group (dys) as compared to 
the second group (ct), right ?


Thank you and best,
Damien MARIE





Douglas Greve 

 Wed, 28 Sep 2016 12:40:51 -0700 


Those are not residuals. If you want residuals, you will need to run mri_glmfit 
from the command line adding --eres-save. You can get the command line from the 
mri_glmfit.log file in the glmdir





On 9/28/16 10:58 AM, Damien MARIE wrote:
Dear FreeSurfers,
Sorry for the repost. I’m still trying to extract the residuals of cortical 
surface area from a qdec analysis with two factors (2 levels) and 2 covariates.
I tried this command line:
mri_segstats --in 
/home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh 
--sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf 
RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9 columns (number of 
clusters) and 69 lines (number of subjects). Now I am not 100% sure it’s really 
the residuals (y.mgh) so I would be glad if somebody could tell me please.
Best,
Damien
Original post:
Dear experts,

I would like to know what is the best and simplest way to extract cortical
surface area and thickness from clusters obtained after a Monte Carlo
correction. This is a group comparison I did with qdec including gender as
discrete variable + age and mean thickness or whole hemispheric surface area as
nuisance factors, so I would like to get the feature residuals after the
removal of the covariate effects.
I am sorry, I saw several posts about that but for me it’s not completely clear
what command line I should use to get tables for this…

Thank you and best,
Damien




*Damien MARIE*

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Re: [Freesurfer] mgz file format

[Douglas Greve]

No, no PHI gets transferred into the mgz file.


On 9/29/16 1:08 AM, prasser wrote:

Hi,

When using mri_convert to create 001.mgz from dicom that have *not* 
been anonymized does any patient, institution, study description etc 
information get transferred into the 001.mgz?


Thanks.




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[Freesurfer] tksurfer viewing issues

[Paige Scalf]

Hello,

I too am having trouble with tksurfer displaying the surfaces upside down
and back to front, but believing that they are correctly oriented (i.e.
Talairach coordinates change in the wrong direction wrt to the surface but
in the correct direction wrt the display window). I"m also running a CentOs
flavor. Did anyone manage to solve this issue?

All the best,
Paige
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[Freesurfer] hello experts

[A-reum Min]

Hello experts.

I have some question to you.

I used SurfStat statistical tool to analyze the two group(control, patient)

When i click the surf in fsaverage folder and then show up lh.pial and
lh.pial_avg.

What is the differences between lh.pial and lh.pial_avg ?

lh.pial_avg means that real subjects's average pial?

plz reply.
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Re: [Freesurfer] trac-all -path Segmentation fault

[Knut J Bjuland]

Hei

Er det id 2 og 3 du har problemer med? Det ser ut som at du ikke har kjørt 
bedpostx på disse to idene og jeg ser at du ikke har kjørt trac-all -prep 
utifra logfilen
.
[/work/projects/nn9208k/subjects/LMR/dtitracula/2]: ls
dlabel  dmri  dpath  scripts

[/work/projects/nn9208k/subjects/LMR/dtitracula/3]: ls
dlabel  dmri  dpath  scripts

Hilsen

Knut Jørgen


On 21 Sep 2016, at 11:14, Lars M. Rimol 
> wrote:

trac-paths exited with ERRORS

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