Re: [Freesurfer] PVE correction tool on Freesurfer 6

[Douglas Greve]

the response is in the body f the mail


On 7/18/16 9:27 PM, Lee Subin Kristine wrote:


Hi Doug,

It seems that the email reply you just sent to me was empty. Could you 
please check your email message again?



Thank you as always,

Subin



*보낸 사람:* Douglas N Greve  대신 
freesurfer-boun...@nmr.mgh.harvard.edu 


*보낸 날짜:* 2016년 7월 19일 화요일 오전 1:59:46
*받는 사람:* freesurfer@nmr.mgh.harvard.edu
*제목:* Re: [Freesurfer] PVE correction tool on Freesurfer 6


On 07/12/2016 11:03 PM, Lee Subin Kristine wrote:
>
> Hi Doug,
>
>
> Thanks a lot for the page! It was very helpful.
>
>
> I have a few questions about one of the commands and a question for
> one of the output files.
>
>
> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the
> point-spread function of the scanner or would a default value of 6
> work for all? I am using PET images from multiple centers and thus
> each image are from different scanners, and I'm not sure how I would
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change
depending upon recon method and parameters and even the ligand used. If
you get it about right, probably it will be close enough.
>
> (b) For the mgx flag, is the GM threshold .01 an optimal threshold
> referring to the p-value?(am new to PVEcorrection and asking out of
> curiosity) What is the difference if I enter .01 versus I don't 
enter it?

>
You must enter a threshold. When Muller-Gartner is implemented, there
are two stages: (1) orthogonalization (subtracting out non-GM) and (2)
rescaling. In the rescaling step, each voxel is divided by the fraction
of GM in that voxel. If that fraction is 0, then you will get an error.
If it is close to 0, you can get extreme noise amplification in that
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be
rescaled, otherwise the voxel is set to 0.
>
>
> 2) From the *gtm.stats.dat *output file, the 5th column(number of PET
> voxels in the ROI) of, for example, the ctx-lh-precuneus and
> ctx-rh-precuneus are 1744 and 1805 respectively. However, in the
> *?h.aparc.stats* files from recon-all, the 4th column(gray matter
> volume) of lh-precuneus and rh-precuneus are 5928 and 6125
> respectively. I am confused because I thought the number of PET voxels
> should be equal to the number of GM voxels in the ROI?
>
You need to scale by the size of the PET voxel.
>
> Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what
> programs can I open them with? It doesn't seem it is openned with
> mricron or gedit.
>
They are nifti files, though you probably don't want to use a nifit
viewer. You can load them into matlab with MRIread('file.nii.gz')

>
> Thank you again in adavnce for your help.
>
>
> Best,
>
> Subin
>
> 
> *보낸 사람:* Douglas N Greve  대신
> freesurfer-boun...@nmr.mgh.harvard.edu
> 
> *보낸 날짜:* 2016년 7월 8일 금요일 오전 2:53:31
> *받는 사람:* freesurfer@nmr.mgh.harvard.edu
> *제목:* Re: [Freesurfer] PVE correction tool on Freesurfer 6
> Hi Subin, I just created this page this morning
> http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
> do you want to take a look and see if it answers your questions. As for
> #2, yes you still need to run gtmseg.
>
> On 06/26/2016 07:45 AM, Lee Subin Kristine wrote:
> >
> > Hello,
> >
> > I am trying to use PVE correction on preprocessed PET data downloaded
> > from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database.
> > I have a couple of questions:
> >
> >
> > 1) I am using the co-registered, averaged image of the dynamic images,
> > and it seems from your answers here
> >
> 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html) 


>
> >
> 
that 


>
> > for static PET images, #3~5 will be different. Could you explain how I
> > would need to enter the command differently?
> >
> > 2) I already have segmentations of my MRI images obtained via
> > FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do
> > procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg
> > because it seemed from the help command that in my case where I
> > already have some FS segmentations that I should use this one:
> >
> > /You can use your own segmentation or a modified FS segmentation. //
> > //It will be easiest if you modify apas+head.mgz to insert your//
> > //segmentations. apas+head.mgz is created by gtmseg but you can//
> > //create it with //
> > /
> > /xcerebralseg --s $subject --o 
$SUBJECTS_DIR/$subject/mri/apas+head.mgz/

> >
> > However 

Re: [Freesurfer] PVE correction tool on Freesurfer 6

[Lee Subin Kristine]

Hi Doug,

It seems that the email reply you just sent to me was empty. Could you please 
check your email message again?


Thank you as always,

Subin



보낸 사람: Douglas N Greve  대신 
freesurfer-boun...@nmr.mgh.harvard.edu 
보낸 날짜: 2016년 7월 19일 화요일 오전 1:59:46
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: Re: [Freesurfer] PVE correction tool on Freesurfer 6



On 07/12/2016 11:03 PM, Lee Subin Kristine wrote:
>
> Hi Doug,
>
>
> Thanks a lot for the page! It was very helpful.
>
>
> I have a few questions about one of the commands and a question for
> one of the output files.
>
>
> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the
> point-spread function of the scanner or would a default value of 6
> work for all? I am using PET images from multiple centers and thus
> each image are from different scanners, and I'm not sure how I would
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change
depending upon recon method and parameters and even the ligand used. If
you get it about right, probably it will be close enough.
>
> (b) For the mgx flag, is the GM threshold .01 an optimal threshold
> referring to the p-value?(am new to PVEcorrection and asking out of
> curiosity) What is the difference if I enter .01 versus I don't enter it?
>
You must enter a threshold. When Muller-Gartner is implemented, there
are two stages: (1) orthogonalization (subtracting out non-GM) and (2)
rescaling. In the rescaling step, each voxel is divided by the fraction
of GM in that voxel. If that fraction is 0, then you will get an error.
If it is close to 0, you can get extreme noise amplification in that
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be
rescaled, otherwise the voxel is set to 0.
>
>
> 2) From the *gtm.stats.dat *output file, the 5th column(number of PET
> voxels in the ROI) of, for example, the ctx-lh-precuneus and
> ctx-rh-precuneus are 1744 and 1805 respectively. However, in the
> *?h.aparc.stats* files from recon-all, the 4th column(gray matter
> volume) of lh-precuneus and rh-precuneus are 5928 and 6125
> respectively. I am confused because I thought the number of PET voxels
> should be equal to the number of GM voxels in the ROI?
>
You need to scale by the size of the PET voxel.
>
> Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what
> programs can I open them with? It doesn't seem it is openned with
> mricron or gedit.
>
They are nifti files, though you probably don't want to use a nifit
viewer. You can load them into matlab with MRIread('file.nii.gz')

>
> Thank you again in adavnce for your help.
>
>
> Best,
>
> Subin
>
> 
> *보낸 사람:* Douglas N Greve  대신
> freesurfer-boun...@nmr.mgh.harvard.edu
> 
> *보낸 날짜:* 2016년 7월 8일 금요일 오전 2:53:31
> *받는 사람:* freesurfer@nmr.mgh.harvard.edu
> *제목:* Re: [Freesurfer] PVE correction tool on Freesurfer 6
> Hi Subin, I just created this page this morning
> http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
> do you want to take a look and see if it answers your questions. As for
> #2, yes you still need to run gtmseg.
>
> On 06/26/2016 07:45 AM, Lee Subin Kristine wrote:
> >
> > Hello,
> >
> > I am trying to use PVE correction on preprocessed PET data downloaded
> > from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database.
> > I have a couple of questions:
> >
> >
> > 1) I am using the co-registered, averaged image of the dynamic images,
> > and it seems from your answers here
> >
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html)
>
> >
> that
>
> > for static PET images, #3~5 will be different. Could you explain how I
> > would need to enter the command differently?
> >
> > 2) I already have segmentations of my MRI images obtained via
> > FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do
> > procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg
> > because it seemed from the help command that in my case where I
> > already have some FS segmentations that I should use this one:
> >
> > /You can use your own segmentation or a modified FS segmentation. //
> > //It will be easiest if you modify apas+head.mgz to insert your//
> > //segmentations. apas+head.mgz is created by gtmseg but you can//
> > //create it with //
> > /
> > /xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz/
> >
> > However when I do try I got the following error:
> >
> > /ERROR: could not open
> >
> 

Re: [Freesurfer] vtk to mgz file

[Bruce Fischl]

What segmentation do you mean? Where are you getting vtk files? We write the 
segmentation into .mgz volumes such as aseg.mgz


Cheers
Bruce


> On Jul 18, 2016, at 1:19 PM, Abbie McNulty  wrote:
> 
> So we were able to figure out how to segment the different parts of the brain 
> using the bert sample, but have run into another problem. 
> I would like to save each segmentation so that I can import it into matlab 
> and create a matrix in order to create a mesh. The volume segment saves a as 
> a .vtk file, which I don't know how to read into matlab. How can I save it as 
> or convert it to a .mgz file so that I can import it into matlab?
> 
> Thanks!
> ___
> 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
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] T2 vs. T2-FLAIR update

[Matt Glasser]

And I would say if you want to do T1w/T2w myelin mapping the T2w scan will
give you more contrast for that, as the fluid inversion does seem to
reduce your contrast for myelin some (though it may increase your contrast
for CSF).  FLAIR can be useful for other things (like seeing some kinds of
brain lesions more easily) so your choice might depend on what else you
want to do with the images.

Peace,

Matt.

On 7/18/16, 6:59 PM, "Bruce Fischl"
 wrote:

>Hi Michelle
>
>that's a tough question. We don't have a ton of experience with it one
>way or the other, but if I had to pick one I would pick FLAIR as long as
>you are getting a 3D FLAIR with around 1mm voxels
>
>cheers
>Bruce
>On Mon, 18 Jul 2016,
>Michelle T Kassel wrote:
>
>> 
>> Hello, 
>> 
>> 
>> I am beginning a new study and would like to determine the
>> optimal T2 acquisition parameters for improved pial surface
>> results from FreeSurfer. I am wondering if there is a difference in
>>using a
>> T2 or T2-FLAIR. I have found a discussion post from 2014 which provided
>> useful 
>>information(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-J
>>uly/039580.ht
>> ml), however, it seems from reading the post that newer developments
>>were
>> underway, and I was wondering if I could get an updated answer to the
>> question:
>> 
>> 
>> is there any difference from freesurfer's perspective of using T2-space
>>or
>> T2-space-flair?
>> 
>> 
>> Thank you for your help!
>> 
>> 
>> Michelle
>> 
>> 
>>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>The information in this e-mail is intended only for the person to whom it
>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to you in
>error
>but does not contain patient information, please contact the sender and
>properly
>dispose of the e-mail.


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Re: [Freesurfer] mri_segstats

[Douglas Greve]

Register the suvr to the anatomical (mri_coreg) then use mri_vol2vol


On 7/18/16 6:58 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug,
> Kindly how can I make the suvr and the anatomical images in the same slice?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, July 18, 2016 6:56 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> Your suvr is axially sliced whereas the anatomical is corronally sliced.
> They must be in exact pixel-for-pixel alignment for mri_segstats to work.
>
> On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote:
>> Thank you Doug!
>>
>> Attached is a report for one of the subjects showing how the cerebellum 
>> structures have zeros for the mean, SD , ...etc  ( red circles) Also if we 
>> scroll down ( not included), all the cerebellum parcellates ( white and 
>> cortex) are zeros.
>>I have this issue with 70 % of the subjects.
>> I applied the first command on all the subjects.
>> I never tried the second command, but I was inquiring because I
>> thought that maybe the first command is missing some flags so
>> "mri-segstats" is unable to read the cerebellum parcellates
>>
>> For the subjects who have zeros for the cerebellum parcellates. I checked 
>> the functional images one by one ( the registration is perfect) and the 
>> images are fine.
>>
>> I can't explain why this is happening so thank you for any suggestion.
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Monday, July 18, 2016 5:45 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats
>>
>> What do you mean you got 0s only for the cblum segs? Did all other segs have 
>> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?
>>
>> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
>>> Thank you very much Doug for your answer.
>>> Kindly I have one more question:
>>> Although the registration between my functional data and "wmparc.mgz" is 
>>> perfect. When I run the first command bellow, I get zeros ( in the report  
>>> wmparc.stats) only for the cerebellum parcellates, and this was prominent 
>>> in many of my subjects.
>>> Is this issue related to a missing  flags in my "mri_segstats" command line?
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
>>> N Greve
>>> Sent: Thursday, July 7, 2016 12:17 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_segstats
>>>
>>> The first one
>>>
>>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
 Dear FS experts,

 I have PET image "pet.anat.mgz" in subject space. I want to
 calculate the mean PET signal for every parcellate and segment in
 the atlas "wmparc.mgz".

 _Which one of the following commands is more accurate? _

 __

 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab
 $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum
 PET.wmparc.stats

 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
 mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/
 PET.anat.mgz--in-intensity-name norm --in-intensity-units MR
 --subject ${subj} --surf-wm-vol --ctab
 /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv

 Best,

 Mohamad



 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> 

Re: [Freesurfer] Checking segmentations with aseg.mgz

[Bruce Fischl]

Hi Reema

you should visualize it over the norm.mgz. The brainmask and brain will 
wash out many low contrast borders (e.g. thalamus, pallidum)


cheers
Bruce
On Mon, 18 Jul 
2016, Reema Jayakar wrote:



Hello FS Listserv members,
With regard to checking amygdala segmentation, is it appropriate to overlay
the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz
on norm.mgz? I am aware of the general rule of thumb that editing the
subcortical segmentations generally is not recommended. 

Also, where can I find documentation on the Freeview options "Resample to
standard RAS space" and

"Apply registration file". I am trying to understand whether or not it is ne
cessary for me to use any of these options for what I am doing with the subc
ortical segmentations.

Thanks in advance for your help!

Reema


--
Reema Jayakar, M.A.Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu


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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] T2 vs. T2-FLAIR update

[Bruce Fischl]

Hi Michelle

that's a tough question. We don't have a ton of experience with it one 
way or the other, but if I had to pick one I would pick FLAIR as long as 
you are getting a 3D FLAIR with around 1mm voxels


cheers
Bruce
On Mon, 18 Jul 2016, 
Michelle T Kassel wrote:




Hello, 


I am beginning a new study and would like to determine the
optimal T2 acquisition parameters for improved pial surface
results from FreeSurfer. I am wondering if there is a difference in using a
T2 or T2-FLAIR. I have found a discussion post from 2014 which provided
useful 
information(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039580.ht
ml), however, it seems from reading the post that newer developments were
underway, and I was wondering if I could get an updated answer to the
question:


is there any difference from freesurfer's perspective of using T2-space or
T2-space-flair?


Thank you for your help!


Michelle


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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_segstats

[Alshikho, Mohamad J.]

Thank you Doug,
I used the command fslswapdim 



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alshikho, Mohamad 
J.
Sent: Monday, July 18, 2016 6:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

Thank you Doug,
Kindly how can I make the suvr and the anatomical images in the same slice?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 6:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

Your suvr is axially sliced whereas the anatomical is corronally sliced. 
They must be in exact pixel-for-pixel alignment for mri_segstats to work.

On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is a report for one of the subjects showing how the cerebellum 
> structures have zeros for the mean, SD , ...etc  ( red circles) Also if we 
> scroll down ( not included), all the cerebellum parcellates ( white and 
> cortex) are zeros.
>   I have this issue with 70 % of the subjects.
> I applied the first command on all the subjects.
> I never tried the second command, but I was inquiring because I 
> thought that maybe the first command is missing some flags so 
> "mri-segstats" is unable to read the cerebellum parcellates
>
> For the subjects who have zeros for the cerebellum parcellates. I checked the 
> functional images one by one ( the registration is perfect) and the images 
> are fine.
>
> I can't explain why this is happening so thank you for any suggestion.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have 
> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?
>
> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
>> Thank you very much Doug for your answer.
>> Kindly I have one more question:
>> Although the registration between my functional data and "wmparc.mgz" is 
>> perfect. When I run the first command bellow, I get zeros ( in the report  
>> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
>> many of my subjects.
>> Is this issue related to a missing  flags in my "mri_segstats" command line?
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: Thursday, July 7, 2016 12:17 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats
>>
>> The first one
>>
>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>>> Dear FS experts,
>>>
>>> I have PET image "pet.anat.mgz" in subject space. I want to 
>>> calculate the mean PET signal for every parcellate and segment in 
>>> the atlas "wmparc.mgz".
>>>
>>> _Which one of the following commands is more accurate? _
>>>
>>> __
>>>
>>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
>>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum 
>>> PET.wmparc.stats
>>>
>>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
>>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
>>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR 
>>> --subject ${subj} --surf-wm-vol --ctab 
>>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> 

Re: [Freesurfer] mri_segstats

[Alshikho, Mohamad J.]

Thank you Doug,
Kindly how can I make the suvr and the anatomical images in the same slice?

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 6:56 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

Your suvr is axially sliced whereas the anatomical is corronally sliced. 
They must be in exact pixel-for-pixel alignment for mri_segstats to work.

On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is a report for one of the subjects showing how the cerebellum 
> structures have zeros for the mean, SD , ...etc  ( red circles) Also if we 
> scroll down ( not included), all the cerebellum parcellates ( white and 
> cortex) are zeros.
>   I have this issue with 70 % of the subjects.
> I applied the first command on all the subjects.
> I never tried the second command, but I was inquiring because I 
> thought that maybe the first command is missing some flags so 
> "mri-segstats" is unable to read the cerebellum parcellates
>
> For the subjects who have zeros for the cerebellum parcellates. I checked the 
> functional images one by one ( the registration is perfect) and the images 
> are fine.
>
> I can't explain why this is happening so thank you for any suggestion.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have 
> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?
>
> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
>> Thank you very much Doug for your answer.
>> Kindly I have one more question:
>> Although the registration between my functional data and "wmparc.mgz" is 
>> perfect. When I run the first command bellow, I get zeros ( in the report  
>> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
>> many of my subjects.
>> Is this issue related to a missing  flags in my "mri_segstats" command line?
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: Thursday, July 7, 2016 12:17 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats
>>
>> The first one
>>
>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>>> Dear FS experts,
>>>
>>> I have PET image "pet.anat.mgz" in subject space. I want to 
>>> calculate the mean PET signal for every parcellate and segment in 
>>> the atlas "wmparc.mgz".
>>>
>>> _Which one of the following commands is more accurate? _
>>>
>>> __
>>>
>>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
>>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum 
>>> PET.wmparc.stats
>>>
>>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
>>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
>>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR 
>>> --subject ${subj} --surf-wm-vol --ctab 
>>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> 

Re: [Freesurfer] mri_segstats

[Douglas N Greve]

Your suvr is axially sliced whereas the anatomical is corronally sliced. 
They must be in exact pixel-for-pixel alignment for mri_segstats to work.

On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is a report for one of the subjects showing how the cerebellum 
> structures have zeros for the mean, SD , ...etc  ( red circles) Also if we 
> scroll down ( not included), all the cerebellum parcellates ( white and 
> cortex) are zeros.
>   I have this issue with 70 % of the subjects.
> I applied the first command on all the subjects.
> I never tried the second command, but I was inquiring because I thought that 
> maybe the first command is missing some flags so "mri-segstats" is unable to 
> read the cerebellum parcellates
>
> For the subjects who have zeros for the cerebellum parcellates. I checked the 
> functional images one by one ( the registration is perfect) and the images 
> are fine.
>
> I can't explain why this is happening so thank you for any suggestion.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have 
> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?
>
> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
>> Thank you very much Doug for your answer.
>> Kindly I have one more question:
>> Although the registration between my functional data and "wmparc.mgz" is 
>> perfect. When I run the first command bellow, I get zeros ( in the report  
>> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
>> many of my subjects.
>> Is this issue related to a missing  flags in my "mri_segstats" command line?
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Thursday, July 7, 2016 12:17 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats
>>
>> The first one
>>
>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>>> Dear FS experts,
>>>
>>> I have PET image "pet.anat.mgz" in subject space. I want to calculate
>>> the mean PET signal for every parcellate and segment in the atlas
>>> "wmparc.mgz".
>>>
>>> _Which one of the following commands is more accurate? _
>>>
>>> __
>>>
>>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab
>>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum
>>> PET.wmparc.stats
>>>
>>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
>>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/
>>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR
>>> --subject ${subj} --surf-wm-vol --ctab
>>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

Re: [Freesurfer] mri_segstats

[Alshikho, Mohamad J.]

I sent the files (wmparc.mgz and the functional image)


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

I'm at a loss as to why that is the case. Can you send the PET.anat.mgz and 
wmparc.mgz to our filedrop?

On 07/18/2016 06:14 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is a report for one of the subjects showing how the 
> cerebellum structures have zeros for the mean, SD , ...etc  ( red circles) 
> Also if we scroll down ( not included), all the cerebellum parcellates ( 
> white and cortex) are zeros.
>   I have this issue with 70 % of the subjects.
> I applied the first command on all the subjects.
> I never tried the second command, but I was inquiring because I 
> thought that maybe the first command is missing some flags so 
> "mri-segstats" is unable to read the cerebellum parcellates
>
> For the subjects who have zeros for the cerebellum parcellates. I checked the 
> functional images one by one ( the registration is perfect) and the images 
> are fine.
>
> I can't explain why this is happening so thank you for any suggestion.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have 
> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?
>
> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
>> Thank you very much Doug for your answer.
>> Kindly I have one more question:
>> Although the registration between my functional data and "wmparc.mgz" is 
>> perfect. When I run the first command bellow, I get zeros ( in the report  
>> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
>> many of my subjects.
>> Is this issue related to a missing  flags in my "mri_segstats" command line?
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas 
>> N Greve
>> Sent: Thursday, July 7, 2016 12:17 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats
>>
>> The first one
>>
>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>>> Dear FS experts,
>>>
>>> I have PET image "pet.anat.mgz" in subject space. I want to 
>>> calculate the mean PET signal for every parcellate and segment in 
>>> the atlas "wmparc.mgz".
>>>
>>> _Which one of the following commands is more accurate? _
>>>
>>> __
>>>
>>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
>>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum 
>>> PET.wmparc.stats
>>>
>>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
>>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
>>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR 
>>> --subject ${subj} --surf-wm-vol --ctab 
>>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 

Re: [Freesurfer] mri_segstats

[Douglas N Greve]

I'm at a loss as to why that is the case. Can you send the PET.anat.mgz 
and wmparc.mgz to our filedrop?

On 07/18/2016 06:14 PM, Alshikho, Mohamad J. wrote:
> Thank you Doug!
>
> Attached is a report for one of the subjects showing how the cerebellum 
> structures have zeros for the mean, SD , ...etc  ( red circles)
> Also if we scroll down ( not included), all the cerebellum parcellates ( 
> white and cortex) are zeros.
>   I have this issue with 70 % of the subjects.
> I applied the first command on all the subjects.
> I never tried the second command, but I was inquiring because I thought that 
> maybe the first command is missing some flags so "mri-segstats" is unable to 
> read the cerebellum parcellates
>
> For the subjects who have zeros for the cerebellum parcellates. I checked the 
> functional images one by one ( the registration is perfect) and the images 
> are fine.
>
> I can't explain why this is happening so thank you for any suggestion.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Monday, July 18, 2016 5:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> What do you mean you got 0s only for the cblum segs? Did all other segs have 
> non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?
>
> On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
>> Thank you very much Doug for your answer.
>> Kindly I have one more question:
>> Although the registration between my functional data and "wmparc.mgz" is 
>> perfect. When I run the first command bellow, I get zeros ( in the report  
>> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
>> many of my subjects.
>> Is this issue related to a missing  flags in my "mri_segstats" command line?
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>> Greve
>> Sent: Thursday, July 7, 2016 12:17 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_segstats
>>
>> The first one
>>
>> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>>> Dear FS experts,
>>>
>>> I have PET image "pet.anat.mgz" in subject space. I want to calculate
>>> the mean PET signal for every parcellate and segment in the atlas
>>> "wmparc.mgz".
>>>
>>> _Which one of the following commands is more accurate? _
>>>
>>> __
>>>
>>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab
>>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum
>>> PET.wmparc.stats
>>>
>>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
>>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/
>>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR
>>> --subject ${subj} --surf-wm-vol --ctab
>>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>>
>>> Best,
>>>
>>> Mohamad
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

Re: [Freesurfer] mri_segstats

[Alshikho, Mohamad J.]

Thank you Doug!

Attached is a report for one of the subjects showing how the cerebellum 
structures have zeros for the mean, SD , ...etc  ( red circles) Also if we 
scroll down ( not included), all the cerebellum parcellates ( white and cortex) 
are zeros.
 I have this issue with 70 % of the subjects. 
I applied the first command on all the subjects. 
I never tried the second command, but I was inquiring because I thought that 
maybe the first command is missing some flags so "mri-segstats" is unable to 
read the cerebellum parcellates

For the subjects who have zeros for the cerebellum parcellates. I checked the 
functional images one by one ( the registration is perfect) and the images are 
fine.

I can't explain why this is happening so thank you for any suggestion.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 5:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

What do you mean you got 0s only for the cblum segs? Did all other segs have 
non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?

On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
> Thank you very much Doug for your answer.
> Kindly I have one more question:
> Although the registration between my functional data and "wmparc.mgz" is 
> perfect. When I run the first command bellow, I get zeros ( in the report  
> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
> many of my subjects.
> Is this issue related to a missing  flags in my "mri_segstats" command line?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Thursday, July 7, 2016 12:17 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> The first one
>
> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>> Dear FS experts,
>>
>> I have PET image "pet.anat.mgz" in subject space. I want to calculate 
>> the mean PET signal for every parcellate and segment in the atlas 
>> "wmparc.mgz".
>>
>> _Which one of the following commands is more accurate? _
>>
>> __
>>
>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum 
>> PET.wmparc.stats
>>
>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR 
>> --subject ${subj} --surf-wm-vol --ctab 
>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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suvr.wmparc.stats
Description: suvr.wmparc.stats
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Re: [Freesurfer] FSGD error: class Input not defined

[Douglas N Greve]

You have a rogue non-ascii character between HM-HR10-002Rest and Group1 
(between others). Make sure you create your fsgd file in a simple ascii 
text editor.

On 06/23/2016 01:48 AM, Jarek Rokicki wrote:
> Dear Freesurfer experts,
>
> I am trying to perform the resting state fMRI analysis as in: 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>
> I got stuck with the STEP8, when I tried to use my own fsgd file. I 
> tried to test for two group difference, no covariance as in: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
>
> But I am getting this error:
> mri_glmfit --y fc.lpccseed.surf.lh/L_PCC/ces.nii.gz  --wls 
> fc.lpccseed.surf.lh/L_PCC/cesvar.nii.gz --fsgd ../glm_file.fsgd --C 
> ../group.diff.mtx --surface fsaverage lh --glmdir my-glm.wls --nii.gz
> gdfRead(): reading ../glm_file.fsgd
> Input line 1, subjid = HM-HR10-002Rest　Group1, class Input not defined
> FSGDF Format Error: file = ../glm_file.fsgd, tag=Input
>
> I am testing the pipeline so just 8 subjects so far.
> I've checked the ces.nii.gz and cesvar.nii.gz and both of them have 
> correct dimensions of 163842 x 1 x 1 x 8.
>
> Thank you for your help in advance.
> *
>
> fsdg_file is:*
> GroupDescriptorFile 1
> Title OSGM
> Class Group1
> Class Group2
> Input HM-HR10-002Rest　Group1
> Input HM-HR10-005Rest　Group1
> Input HM-HR10-007Rest　Group1
> Input HM-HR10-010Rest　Group1
> Input PD0001Rest　Group2
> Input PD0002Rest Group2
> Input PD0004Rest　Group2
> Input　PD0005Rest　Group2
>
> *mtx file is:*
> 1 -1
>
>
>
> 宜しくお願い致します。*
>
> *
> Sincerely,
> Jarek Rokicki, Ph.D.
>
> Integrative Brain Imaging Center (IBIC)
> National Center of Neurology and Psychiatry (NCNP)
> /4-1-1 Ogawahigashi-chyo, Kodaira,
> Tokyo 187-8551 Japan/
>
> TEL: +81-80-6628-5709
>
> 国立精神・神経医療研究センター
> 脳病態統合イメージングセンター(IBIC)
> 臨床脳画像研究部 画像情報解析研究室
> /〒187-8551　東京都小平市小川東町4-1-1/
>
>
>
>
>
>
> ___
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_segstats

[Alshikho, Mohamad J.]

Thank you Doug!

Attached is a report for one of the subjects showing how the cerebellum 
structures have zeros for the mean, SD , ...etc  ( red circles)
Also if we scroll down ( not included), all the cerebellum parcellates ( white 
and cortex) are zeros.
 I have this issue with 70 % of the subjects. 
I applied the first command on all the subjects. 
I never tried the second command, but I was inquiring because I thought that 
maybe the first command is missing some flags so "mri-segstats" is unable to 
read the cerebellum parcellates

For the subjects who have zeros for the cerebellum parcellates. I checked the 
functional images one by one ( the registration is perfect) and the images are 
fine.

I can't explain why this is happening so thank you for any suggestion.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Monday, July 18, 2016 5:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_segstats

What do you mean you got 0s only for the cblum segs? Did all other segs have 
non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline?

On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
> Thank you very much Doug for your answer.
> Kindly I have one more question:
> Although the registration between my functional data and "wmparc.mgz" is 
> perfect. When I run the first command bellow, I get zeros ( in the report  
> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
> many of my subjects.
> Is this issue related to a missing  flags in my "mri_segstats" command line?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N 
> Greve
> Sent: Thursday, July 7, 2016 12:17 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> The first one
>
> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>> Dear FS experts,
>>
>> I have PET image "pet.anat.mgz" in subject space. I want to calculate 
>> the mean PET signal for every parcellate and segment in the atlas 
>> "wmparc.mgz".
>>
>> _Which one of the following commands is more accurate? _
>>
>> __
>>
>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum 
>> PET.wmparc.stats
>>
>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR 
>> --subject ${subj} --surf-wm-vol --ctab 
>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_convert : ERROR: cannot unpack mosiacs without ASCII header

[Douglas N Greve]

Is this still a problem? If so, can you upload the dicom files to our 
file drop?

On 07/05/2016 11:24 AM, Koubiyr, Ismail wrote:
> The file has not been anonymized.
>
> Thanks,
>
> Ismail
>
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
>> wrote:
>>
>> can you answer the question that it asks?
>>
>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>>> Hi everyone,
>>>
>>> I’m having some issues converting my DICOMs (DWI) into NIFTI using
>>> mri_convert. I looked for other topics with people having the same
>>> kind of problem but couldn’t find an answer.
>>>
>>> Each time I run mri_convert on my DICOMs I get the following error :
>>> WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931
>>> does not contain a Siemens ASCII header
>>> has this file been anonymized?
>>> ERROR: cannot unpack mosiacs without ASCII header
>>>
>>> Here are the following DICOMs informations :
>>> Identification
>>> NumarisVer   syngo MR D13
>>> ScannerModel Skyra
>>> PatientName   x
>>> Date and time
>>> StudyDate 20140918
>>> StudyTime 121037.203000
>>> SeriesTime   123450.60
>>> AcqTime   123257.367500
>>> Acquisition parameters
>>> PulseSeq ep_b0
>>> Protocol AX DTI no angle MS NEX 4 2
>>> PhEncDir COL
>>> EchoNo   1
>>> FlipAngle 90
>>> EchoTime 96
>>> InversionTime -1
>>> RepetitionTime   4700
>>> PhEncFOV 0
>>> ReadoutFOV   0
>>> Image information
>>> RunNo 4
>>> SeriesNo 5
>>> ImageNo   1
>>> NImageRows   990
>>> NImageCols   990
>>> NFrames   64
>>> SliceArraylSize   0
>>> IsMosaic 1
>>> ImgPos   1075.1575 1069.8385 -48.6769
>>> VolRes 2.1818   2.1818   2.
>>> VolDim 000
>>> Vc -1.  -0.   0.
>>> Vr -0.  -1.   0.
>>> Vs 0.   0.   0.
>>> VolCenter   0.   0.   0.
>>> TransferSyntaxUID 1.2.840.10008.1.2.1
>>>
>>>
>>> Then I try using mri_convert -it dicom, it converts the files but not
>>> as it is expected, you could notice the difference when I run mri_info
>>> on my output :
>>> Volume information for output.nii.gz
>>>   type: nii
>>> dimensions: 990 x 990 x 1 x 64
>>>voxel sizes: 2.1818, 2.1818, 2.
>>>   type: SHORT (4)
>>>fov: 2160.000
>>>dof: 0
>>> xstart: -1080.0, xend: 1080.0
>>> ystart: -1080.0, yend: 1080.0
>>> zstart: -1.0, zend: 1.0
>>> TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip
>>> angle: 0.00 degrees
>>>nframes: 64
>>>PhEncDir: UNKNOWN
>>> ras xform present
>>> xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =
>>>   -4.8425
>>>   : x_a =  -0., y_a =  -1., z_a = -0., c_a =
>>> -10.1615
>>>   : x_s =   0., y_s =   0., z_s = 1., c_s =
>>> -47.6769
>>> Orientation   : LPS
>>> Primary Slice Direction: axial
>>>
>>> voxel to ras transform:
>>>-2.1818  -0.  -0.  1075.1575
>>>-0.  -2.1818  -0.  1069.8385
>>> 0.   0.   2.   -48.6769
>>> 0.   0.   0. 1.
>>>
>>> voxel-to-ras determinant 9.52066
>>>
>>> ras to voxel transform:
>>>-0.4583   0.   0.   492.7805
>>> 0.  -0.4583   0.   490.3426
>>>-0.  -0.   0.500024.3384
>>> 0.   0.   0. 1.
>>>
>>> I would really appreciate your help, thank you.
>>>
>>> Best,
>>>
>>> Ismail
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

[Hibert, Matthew Louis]

It did, I removed 2 of them and it's running fine now.  Thanks!

Matt

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: Monday, July 18, 2016 5:48 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

Check the contents of

  /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname

It may have the subjectname repeated 3 times


On 07/18/2016 05:45 PM, Hibert, Matthew Louis wrote:
> Attached.  I took a quick look and it seems that I wrote the subject name 3 
> times, on new lines, to the subjectname file.  I removed 2 of them and re-ran 
> selxavg3-sess and it appears to be working.
>
> Thanks for the help Doug.
>
> Matt
> 
> 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: Monday, July 18, 2016 5:23 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
>
> Can you run the command below and send me dng.log?
>
> register-sess -debug -s nmr00978 -d
> /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6
> -per-run -nolog -update |& tee dng.log
>
> On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote:
>> Hi All,
>> I'm running into an error analyzing some fMRI data with FS-FAST in
>> Freesurfer version 5.3.  The analysis runs fine until it gets to the
>> register-sess part, which quits before actually starting to do any
>> registration.  The last line of the log file, attached, is "if:
>> Expression syntax", but there are no other errors prior to that.  The
>> command I'm using, analysis, and contrasts have all worked on several
>> other similar data sets. Has anyone encountered this problem before,
>> or know what's causing it?
>>
>> Thanks,
>> Matt
>>
>> Clinical Research Coordinator
>> Stufflebeam Lab
>> Athinoula A. Martinos Center
>> Massachusetts General Hospital
>> 149 13th Street, Room 1115S
>> Charlestown, MA 02129
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

[Douglas N Greve]

Check the contents of

  /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/subjectname

It may have the subjectname repeated 3 times


On 07/18/2016 05:45 PM, Hibert, Matthew Louis wrote:
> Attached.  I took a quick look and it seems that I wrote the subject name 3 
> times, on new lines, to the subjectname file.  I removed 2 of them and re-ran 
> selxavg3-sess and it appears to be working.
>
> Thanks for the help Doug.
>
> Matt
> 
> 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: Monday, July 18, 2016 5:23 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error
>
> Can you run the command below and send me dng.log?
>
> register-sess -debug -s nmr00978 -d
> /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6
> -per-run -nolog -update |& tee dng.log
>
> On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote:
>> Hi All,
>> I'm running into an error analyzing some fMRI data with FS-FAST in
>> Freesurfer version 5.3.  The analysis runs fine until it gets to the
>> register-sess part, which quits before actually starting to do any
>> registration.  The last line of the log file, attached, is "if:
>> Expression syntax", but there are no other errors prior to that.  The
>> command I'm using, analysis, and contrasts have all worked on several
>> other similar data sets. Has anyone encountered this problem before,
>> or know what's causing it?
>>
>> Thanks,
>> Matt
>>
>> Clinical Research Coordinator
>> Stufflebeam Lab
>> Athinoula A. Martinos Center
>> Massachusetts General Hospital
>> 149 13th Street, Room 1115S
>> Charlestown, MA 02129
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

[Hibert, Matthew Louis]

Attached.  I took a quick look and it seems that I wrote the subject name 3 
times, on new lines, to the subjectname file.  I removed 2 of them and re-ran 
selxavg3-sess and it appears to be working.

Thanks for the help Doug.

Matt

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: Monday, July 18, 2016 5:23 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

Can you run the command below and send me dng.log?

register-sess -debug -s nmr00978 -d
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6
-per-run -nolog -update |& tee dng.log

On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote:
> Hi All,
> I'm running into an error analyzing some fMRI data with FS-FAST in
> Freesurfer version 5.3.  The analysis runs fine until it gets to the
> register-sess part, which quits before actually starting to do any
> registration.  The last line of the log file, attached, is "if:
> Expression syntax", but there are no other errors prior to that.  The
> command I'm using, analysis, and contrasts have all worked on several
> other similar data sets. Has anyone encountered this problem before,
> or know what's causing it?
>
> Thanks,
> Matt
>
> Clinical Research Coordinator
> Stufflebeam Lab
> Athinoula A. Martinos Center
> Massachusetts General Hospital
> 149 13th Street, Room 1115S
> Charlestown, MA 02129
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 11 != 0 )

set flag = $argv[1] ; shift ;
set flag = -s
shift

switch ( $flag )
switch ( -s )
case "-sf":
case -sf:
case "-df":
case -df:
case "-d":
case -d:
case "-g":
case -g:
shift ;
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 9 != 0 )

set flag = $argv[1] ; shift ;
set flag = -d
shift

switch ( $flag )
switch ( -d )
case "-g":
case -g:
shift ;
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 7 != 0 )

set flag = $argv[1] ; shift ;
set flag = -fsd
shift

switch ( $flag )
switch ( -fsd )
if ( $#argv < 1 ) goto arg1err ;
if ( 6 < 1 ) goto arg1err
set fsd = $argv[1] ; shift ;
set fsd = sycabs
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;
set flag = -dof
shift

switch ( $flag )
switch ( -dof )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set dof = $argv[1] ; shift ;
set dof = 6
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 3 != 0 )

set flag = $argv[1] ; shift ;
set flag = -per-run
shift

switch ( $flag )
switch ( -per-run )
case "-perrun":
case -perrun:
set PerRun = 1 ;
set PerRun = 1
set PerSess = 0 ;
set PerSess = 0
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 2 != 0 )

set flag = $argv[1] ; shift ;
set flag = -nolog
shift

switch ( $flag )
switch ( -nolog )
set nolog = 1 ;
set nolog = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 1 != 0 )

set flag = $argv[1] ; shift ;
set flag = -update
shift

switch ( $flag )
switch ( -update )
set UpdateOnly = 1 ;
set UpdateOnly = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

set SessList = `getsesspath $inputargs` ;
set SessList = `getsesspath $inputargs`
getsesspath -debug -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 11 != 0 )

set flag = $argv[1] ; shift ;
set flag = -s
shift

switch ( $flag )
switch ( -s )
if ( $#argv == 0 ) goto arg1err ;
if ( 10 == 0 ) goto arg1err
set SessList = ( $SessList $argv[1] ) ; shift ;
set SessList = ( nmr00978 )
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 9 != 0 )

set flag = $argv[1] ; shift ;
set flag = -d
shift

switch ( $flag )
switch ( -d )
if ( $#argv == 0 ) goto arg1err ;
if ( 8 == 0 ) goto arg1err
if ( ! -d $argv[1] ) then
if ( ! -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) then
if ( ! -r $argv[1] ) then
if ( ! -r /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects ) then
set srchdir = $argv[1] ; shift ;
set srchdir = /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects
shift
set SearchPathList = ( $SearchPathList 

Re: [Freesurfer] DeMean Flag

[Douglas N Greve]

The DeMeanFlag in what tool?

On 07/08/2016 05:16 AM, Clara Kühn wrote:
> Dear Freesurfer experts,
>
> is there an explanation somewhere for the DeMeanFlag? I can't find it in the 
> wiki but I would like to use it to demean my covariates for the GLM and LME.
>
> Cheers
> Clara
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] mri_segstats

[Douglas N Greve]

What do you mean you got 0s only for the cblum segs? Did all other segs 
have non-zeros, but clbum have 0s? And did you get non-0s in the 2nd 
commandline?

On 07/07/2016 05:16 PM, Alshikho, Mohamad J. wrote:
> Thank you very much Doug for your answer.
> Kindly I have one more question:
> Although the registration between my functional data and "wmparc.mgz" is 
> perfect. When I run the first command bellow, I get zeros ( in the report  
> wmparc.stats) only for the cerebellum parcellates, and this was prominent in 
> many of my subjects.
> Is this issue related to a missing  flags in my "mri_segstats" command line?
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Thursday, July 7, 2016 12:17 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_segstats
>
> The first one
>
> On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote:
>> Dear FS experts,
>>
>> I have PET image "pet.anat.mgz" in subject space. I want to calculate
>> the mean PET signal for every parcellate and segment in the atlas
>> "wmparc.mgz".
>>
>> _Which one of the following commands is more accurate? _
>>
>> __
>>
>> 1.mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab
>> $FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum
>> PET.wmparc.stats
>>
>> 2.mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv
>> mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/
>> PET.anat.mgz--in-intensity-name norm --in-intensity-units MR --subject
>> ${subj} --surf-wm-vol --ctab
>> /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv
>>
>> Best,
>>
>> Mohamad
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Question about NULL event with Optseq2

[Douglas N Greve]

Some of this might be fixed with a newer version of optseq:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2

The long last NULL might not be fixed. It is just hard to get all the 
things to add up to get the right amount of time, so it time is left 
over, it adds it to the end


On 07/08/2016 07:39 PM, Feng Zhou wrote:
> Dear experts,
> I'd like to use optseq2 to optimize the order of events as well as 
> inter stimulus intervals. My experiment contains 3 runs and each run 
> contains 3 events, say Cp, Cn and Pobe events
> Each stimulu will be presented 4, 4 and 1 sec and the numbers of times 
> that each event type will be presented during the course of the run 
> are 12 12 and 4 respectively, and interstimulus interval ranges from 
> 8–12 sec. So each run would last around 380 sec. I used the following 
> code:
> optseq2 --ntp 380 --tr 1 --psdwin 0 20 1 --ev Cp 4 12 --ev Cn 4 12 
> --ev Prob 1 3 --evc 1 -1 0 --tnullmin 8 --tnullmax 12 --nkeep 3 --o 
> IAPS --nsearch 1
> However, the durations of some NULL events were more than 12 sec and 
> the last NULL events were more than 30 sec.
> Did I use optseq2 in the right way? How could I fix it?
> Thanks in advance & Best regards,
> Feng Zhou
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Inquiries about thickness and lgi group analysis

[Douglas N Greve]

Well you can start by telling us what you did. There is not much info 
down there

On 07/14/2016 10:40 AM, Mahtab Farahbakhsh wrote:
> Dear FreeSurfer,
>
> I am doing group analysis for thickness and LGI values. I have just 
> got the output and the output of both analyses (sig.mgh file view in 
> Freeview) are exactly the same. Would you please guide me with this?
>
> Best Regards,
> Mahtab.
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] mri_glmfit error

[Douglas N Greve]

I can't tell from the glmfit command line what you are trying to do. 
Generally, the GLM is run on group data and you specify an average brain 
(eg, fsaverage) as the --surf.

On 07/14/2016 06:10 AM, Chatzi, Vasiliki wrote:
>
>
> Dear Developers,
>
>
> I am trying to run the mri_glmfit command and I get two 
> different errors for two different subjects. Please find 
> details below. I would be really grateful if you could provide any advice.
>
>
>
> Error1
>
> setenv SUBJECTS_DIR ./
>
> mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject1 lh
>
> gdfReadHeader: reading fsgd_test2.txt
>
> INFO: gd2mtx_method is dods
>
> Reading source surface .//subject1/surf/lh.white
>
> Number of vertices 167703
>
> Number of faces335402
>
> Total area 108706.031250
>
> AvgVtxArea   0.648206
>
> AvgVtxDist   0.881642
>
> StdVtxDist   0.250483
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>
> cwd /home/test
>
> cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject1 lh
>
> sysname  Linux
>
> hostname
>
> machine  x86_64
>
> user
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing 1
>
> OneSampleGroupMean 0
>
> y/home/test/lh.10.lgi.mgh
>
> logyflag 0
>
> usedti  0
>
> FSGD fsgd_test2.txt
>
> labelmask  .//subject1ii/label/lh.cortex.label
>
> maskinv 0
>
> glmdir ./
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory ./
>
> Loading y from /home/test/lh.10.lgi.mgh
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to .//Xg.dat
>
> Normalized matrix condition is 1
>
> Matrix condition is 1
>
> Found 158404 points in label.
>
> ERROR: mri_reshape: number of elements cannot change
>
>   nv1 = 167703, nv1 = 163842
>
> Pruning voxels by thr: 0.00
>
> Found 163842 voxels in mask
>
> Saving mask to .//mask.mgh
>
> Reshaping mriglm->mask...
>
> ERROR: mri_reshape: number of elements cannot change
>
>   nv1 = 163842, nv1 = 167703
>
> search space = 108705.102552
>
> DOF = 0
>
> ERROR: DOF = 0
>
>
>
> Error 2
> setenv SUBJECTS_DIR ./
> mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject2 lh
> gdfReadHeader: reading fsgd_test2.txt
> INFO: gd2mtx_method is dods
> Reading source surface .//subject2/surf/lh.white
> Number of vertices 129318
> Number of faces258632
> Total area 86174.742188
> AvgVtxArea   0.666379
> AvgVtxDist   0.893985
> StdVtxDist   0.260921
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/test
> cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject2 lh
> sysname  Linux
> hostname
> machine  x86_64
> user
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y/home/test/lh.10.lgi.mgh
> logyflag 0
> usedti  0
> FSGD fsgd_test2.txt
> labelmask  .//subject2/label/lh.cortex.label
> maskinv 0
> glmdir ./
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory ./
> Loading y from /home/test/lh.10.lgi.mgh
> INFO: gd2mtx_method is dods
> Saving design matrix to .//Xg.dat
> Normalized matrix condition is 1
> Matrix condition is 1
> Found 121215 points in label.
> ERROR: mri_reshape: number of elements cannot change
>   nv1 = 129318, nv1 = 163842
> Pruning voxels by thr: 0.00
> Segmentation fault
>
> Bets wishes,
> Vasiliki
>
>
>
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] FS-FAST "If: Expression Syntax" Error

[Douglas N Greve]

Can you run the command below and send me dng.log?

register-sess -debug -s nmr00978 -d 
/autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 
-per-run -nolog -update |& tee dng.log

On 07/14/2016 02:51 PM, Hibert, Matthew Louis wrote:
> Hi All,
> I'm running into an error analyzing some fMRI data with FS-FAST in 
> Freesurfer version 5.3.  The analysis runs fine until it gets to the 
> register-sess part, which quits before actually starting to do any 
> registration.  The last line of the log file, attached, is "if: 
> Expression syntax", but there are no other errors prior to that.  The 
> command I'm using, analysis, and contrasts have all worked on several 
> other similar data sets. Has anyone encountered this problem before, 
> or know what's causing it?
>
> Thanks,
> Matt
>
> Clinical Research Coordinator
> Stufflebeam Lab
> Athinoula A. Martinos Center
> Massachusetts General Hospital
> 149 13th Street, Room 1115S
> Charlestown, MA 02129
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Comparing between a group of subject

[Douglas N Greve]

Use the GLM approach (cross-sectional, not longitudinal). You don't need 
a variable to regress against, just set up two groups, with one group 
being your single subject. Though I'm not sure what you want to gain out 
of this.

On 07/15/2016 04:08 PM, Aman Montazeri wrote:
> Hi Freesurferes,
>
> Sorry for my simple and rookie question, I'm a new user and couldn't 
> find my answer after a bit googling.
>
> I have a group of subjects and want to compare their thickness with a 
> baseline (average of my subjects).
>
> I thought to use the mri_avarage to make the baseline (Average of all 
> of my subjects), but don't know how to compare them with the baseline 
> after making the baseline.
>
>
> Any help would be highly appreciated
>
>
> Thanks,
>
> Aman
>
> Ps. I have looked into GLM and longitudinal processing tutorials; GLM 
> doesn't work for me as I don't have any variable to regress against; 
> longitudinal processing is also for comparing different time shots of 
> the same subject (my case are 40 different subjects).
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] BrainSegVolNotVent

[Douglas N Greve]

I think you may be using a very old version of mri_segstats. The version 
5.3 mri_segstats gives:

# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 
1290472.00, mm^3
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume 
Without Ventricles, 1279674.00, mm^3




On 07/18/2016 02:46 PM, Eryilmaz, H. Hamdi wrote:
> Hi Doug,
>
> Thanks for your reply. I just sent you this subject's directory via file 
> drop. Please note that there are two aseg.stats files under the 'stats' 
> folder:
>
> aseg.stats: generated by the mri_segstats command I ran including the 
> --brainmask mri/brainmask.mgz --brain-vol-from-seg flags.
> aseg_original.stats: generated by the original recon-all command.
>
> Let me know if you need anything else.
>
> Best,
> Hamdi
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, July 18, 2016 1:33 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] BrainSegVolNotVent
>
> That does look suspicious, esp since BrainSegNotVent should be smaller
> than BrainSeg. Can you tar up the subject and send it to me? It may be
> some strange incompatibility with v5
>
>
> On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote:
>> Hello Doug and Freesurfers,
>>
>> I am trying to compute a structural measure called
>> 'BrainSegVolNotVent' as an approximate value of total brain volume.
>> 'BrainSegVolNotVent' is now present in aseg.stats files but the
>> dataset I'm working on was preprocessed using FS 5.0, which did not
>> produce this variable. Per your advice I found in a previous email, I
>> reran mri_segstats adding the flags --brainmask mri/brainmask.mgz
>> --brain-vol-from-seg.
>>
>> The new aseg.stats file contains the following lines that were added
>> after running this command:
>>
>> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels,
>> 1667093, unitless
>> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3
>> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation
>> Volume Without Ventricles, 232145.00, mm^3
>> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels,
>> 1410666, unitless
>> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume,
>> 1410666.00, mm^3
>>
>> The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should
>> normally be close to each other, right? Also unitless values such as
>> BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding
>> volumetric values.
>>
>> Do you have any idea what might have gone wrong? Here's the command I
>> ran:
>>
>> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
>> --subcortgray --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
>> --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt
>> --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg
>>
>>
>> Thanks very much for your help!
>>
>> Best,
>> Hamdi
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Douglas N Greve]

It does not look like the variables are demeaned (your FSGD file below)

Variables Age eTIV EnglishParityRT
Input Math_5001m Monolingual_male 18 1865790.30866 -8952.208
Input Math_5002m Monolingual_female 19 1520429.68796 -4605.208
Input Math_5003m Monolingual_male 19 1749716.72939 -39407.208333
Input Math_5004m Monolingual_female 18 1589109.27022 -17967.208333
Input Math_5005m Monolingual_male 21 1472295.15211 19531.791667
Input Math_5006m Monolingual_male 18 1580381.40566 -17027.208333
Input Math_5007m Monolingual_male 20 1813373.55024 16152.791667
Input Math_5008m Monolingual_male 21 1638616.48007 -9074.208
Input Math_5009m Monolingual_female 21 1297920.49281 61860.791667
Input Math_5010m Monolingual_female 18 1634762.57845 -22671.208333
Input Math_5011m Monolingual_female 21 1602611.42141 12763.791667
Input Math_5014m Monolingual_male 21 1632452.66476 9395.2916669


On 07/18/2016 01:31 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thank you for your response.  The current fsgd file I sent you was 
> with the covariates demeaned x 100, as I saw you recommend that to 
> someone else.  We previously tried doing just the demeaned values 
> without multiplying by 100, and that still had the badly scaled 
> error.  Do you think we should take the demeaned x 100 covariates and 
> divide them by the standard deviation?  Or would it be better to take 
> regular demeaned values and divide them by the standard deviation?
>
> Best,
>
> Jennifer Legault
>
> On Mon, Jul 18, 2016 at 12:43 PM, Douglas N Greve 
> > wrote:
>
> This is almost surely a problem with scaling as your covariates are
> huge. Try subtracting the mean and dividing by the stddev before
> entering into the FSGD file. Compute the means and stddevs across all
> subjects.
> doug
>
> On 07/11/2016 03:20 PM, Jennifer Legault wrote:
> > Hi Freesurfer Experts,
> >
> > I am trying to run mri_glmfit and while 90% of my files work,
> some of
> > them display the error below.  I have tried demeaning, and then
> tried
> > multiplying this value by 100, and I still get the same error.  Any
> > feedback would be greatly appreciated.
> >
> > mris_preproc done
> > srcsubject = fsaverage
> > srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
> > srctype=
> > trgsubject = fsaverage
> > trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= rh
> > trghemi= rh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> >
> /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
> > Loading source data
> > INFO: trgsubject = srcsubject
> > Saving target data
> > Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > gdfReadHeader: reading
> >
> 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 Age 19.5833 1.32025
> > 1 eTIV 1.61645e+06 145343
> > 2 EnglishParityRT 0.00012207 25139.1
> > Class Means of each Continuous Variable
> > 1 Monolingual_male  19.7143 1678946.5893 -4197.2796
> > 2 Monolingual_female  19.4000 1528966.6750 5876.1917
> > INFO: gd2mtx_method is dods
> > Reading source surface
> > /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
> > Number of vertices 163842
> > Number of faces327680
> > Total area 65020.765625
> > AvgVtxArea   0.396850
> > AvgVtxDist   0.717994
> > StdVtxDist   0.193566
> >
> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> > cwd /gpfs/scratch/jtl190/Math_reconstruction
> > cmdline mri_glmfit --y
> > rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
> >
> 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > --C
> >
> 
> /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
> > --surf fsaverage rh --cortex --glmdir
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > sysname  Linux
> > hostname cyberstar129.hpc.rcc.psu.edu
> 
> > 
> > machine  x86_64
> > user jtl190
> > FixVertexAreaFlag = 1
> > UseMaskWithSmoothing 1
> > OneSampleGroupMean 0
> > y
> >
> 
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh

[Freesurfer] Checking segmentations with aseg.mgz

[Reema Jayakar]

Hello FS Listserv members,

With regard to checking amygdala segmentation, is it appropriate to overlay
the aseg.mgz file on the brainmask.mgz? Or should I be overlaying aseg.mgz
on norm.mgz? I am aware of the general rule of thumb that editing the
subcortical segmentations generally is not recommended.

Also, where can I find documentation on the Freeview options "Resample to
standard RAS space" and

"Apply registration file". I am trying to understand whether or not it
is necessary for me to use any of these options for what I am doing
with the subcortical segmentations.


Thanks in advance for your help!

Reema



-- 
*Reema Jayakar, M.A.*
Doctoral Candidate - Clinical Neuropsychology
Health Resources and Services Administration (HRSA) Fellow
Department of Psychology
Georgia State University
Email: rjayak...@student.gsu.edu
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[Freesurfer] T2 vs. T2-FLAIR update

[Michelle T Kassel]

Hello,


I am beginning a new study and would like to determine the optimal T2 
acquisition parameters for improved pial surface results from FreeSurfer. I am 
wondering if there is a difference in using a T2 or T2-FLAIR. I have found a 
discussion post from 2014 which provided useful information 
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039580.html), 
however, it seems from reading the post that newer developments were underway, 
and I was wondering if I could get an updated answer to the question:


is there any difference from freesurfer's perspective of using T2-space or 
T2-space-flair?


Thank you for your help!


Michelle
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Re: [Freesurfer] BrainSegVolNotVent

[Eryilmaz, H. Hamdi]

Hi Doug, 

Thanks for your reply. I just sent you this subject's directory via file drop. 
Please note that there are two aseg.stats files under the 'stats' folder: 

aseg.stats: generated by the mri_segstats command I ran including the 
--brainmask mri/brainmask.mgz --brain-vol-from-seg flags.
aseg_original.stats: generated by the original recon-all command.

Let me know if you need anything else. 

Best,
Hamdi



From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, July 18, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] BrainSegVolNotVent

That does look suspicious, esp since BrainSegNotVent should be smaller
than BrainSeg. Can you tar up the subject and send it to me? It may be
some strange incompatibility with v5


On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote:
> Hello Doug and Freesurfers,
>
> I am trying to compute a structural measure called
> 'BrainSegVolNotVent' as an approximate value of total brain volume.
> 'BrainSegVolNotVent' is now present in aseg.stats files but the
> dataset I'm working on was preprocessed using FS 5.0, which did not
> produce this variable. Per your advice I found in a previous email, I
> reran mri_segstats adding the flags --brainmask mri/brainmask.mgz
> --brain-vol-from-seg.
>
> The new aseg.stats file contains the following lines that were added
> after running this command:
>
> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels,
> 1667093, unitless
> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation
> Volume Without Ventricles, 232145.00, mm^3
> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels,
> 1410666, unitless
> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume,
> 1410666.00, mm^3
>
> The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should
> normally be close to each other, right? Also unitless values such as
> BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding
> volumetric values.
>
> Do you have any idea what might have gone wrong? Here's the command I
> ran:
>
> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent
> --subcortgray --in mri/norm.mgz --in-intensity-name norm
> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol
> --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt
> --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg
>
>
> Thanks very much for your help!
>
> Best,
> Hamdi
>
>
>
>
>
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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] registering to fsaverage

[Trisanna Sprung-Much]

Hi Doug

My apologies for the delay - I just returned from vacation.

Ok, so when I take a volumetric spam created using minc tools and create an
overlay from it using mri_vol2surf, the min and max seems to be between 1
and 255. I am wondering if there is any where to change this into a %? When
I open the spam using a minc software, for instance, it shows me the %.

best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Jul 6, 2016 at 1:28 PM, Douglas N Greve 
wrote:

> Trisanna, has this issue been resolved?
> doug
>
> On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
> > Hi Bruce
> >
> > here is the output of my mri_vol2surf for a volumetric spam created in
> > minc tools. When I then overlay this result in Freeview, it displays a
> > Min of 127 and a Max of 255.
> >
> > trisanna@kaplan:~$ mri_vol2surf --mov
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> > --o
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> > --hemi lh --surf pial --regheader MNI_average_2009a_asymm
> > srcvol =
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> > srcreg unspecified
> > srcregold = 0
> > srcwarp unspecified
> > surf = pial
> > hemi = lh
> > reshape = 0
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > INFO: changing type to float
> > Done loading volume
> > Computing registration from header.
> >   Using
> > /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz as
> > target reference.
> > Reading surface
> > /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial
> > Done reading source surface
> > Mapping Source Volume onto Source Subject Surface
> >  1 0 0 0
> > using old
> > Done mapping volume to surface
> > Number of source voxels hit = 95521
> > Writing to
> >
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> > Dim: 152257 1 1
> >
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl
> > > wrote:
> >
> > Can you send the full output of that command?
> >
> > On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much
> >  > > wrote:
> >
> >> Hi Bruce
> >>
> >> I simply use
> >>
> >> mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader
> >> subject --hemi lh --surf pial
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. Candidate
> >> McGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl
> >> >
> >> wrote:
> >>
> >> how do you create the overlay?
> >> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
> >>
> >> Hi Bruce
> >>
> >> To create the spam I used minctools:
> >>
> >>  mincaverage  input.mnc output.mnc
> >>
> >> I blurred the spam using
> >>
> >> mincblur input.mnc output.mnc -fwhm 3
> >>
> >> When I open the spams using minc software, the % shown is
> >> from about 10-40%
> >> (i.e. the max overlap). For some reason when I create an
> >> overlay from this
> >> it displays the % from 1-255.
> >>
> >> Trisanna
> >>
> >> --
> >> Ph.D. CandidateMcGill University
> >> Integrated Program in Neuroscience
> >> Psychology
> >>
> >>
> >> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl
> >>  >> >
> >> wrote:
> >>   Hi Trisanna
> >>
> >>   what commands did you use to generate the
> >> volumetric probability
> >>   map?
> >>
> >>   Bruce
> >>
> >>
> >>
> >>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
> >>
> >> Hi Bruce
> >> So, when I take a probability map formed using
> >> linear volumetric
> >> registration with minc tools and saved as
> >> .mnc and
> >> convert it to an
> >> overlay.mgz and open it in Freeview, the
> >> probability
> >> seems to be out of 255
> >> (See the image attached). This is different
> >> from my
> >> Freesurfer generated
> >> probability 

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

[Douglas N Greve]

Try running make_average_volume. This will produce an aseg.mgz file with 
all the ROIs merged across all subjects


On 07/13/2016 07:10 AM, Dr Sampada Sinha wrote:
> Dear Bruce, I am trying to generate the following picture (please see 
> attached) for eod vs lod groups. Can you please tell me how to do this?
>
> Thanks and regards,
>
> Sampada
>
> On Tue, Jul 12, 2016 at 6:44 PM, Bruce Fischl 
> > wrote:
>
> Hi Sampada
>
> why not just take the volume of the hippocampus from the
> aseg.stats?  Why do you want an mgz? You just want one number per
> subject, right?
>
> Bruce
>
>
>
> On Tue, 12 Jul 2016, Dr Sampada Sinha wrote:
>
> Dear Bruce,
>
> Thanks for you for your response. I am trying to  generate an
> average
> hippocampal volume and its correlation with HAM-D score in
> early and late
> onset depression (eod vs lod). One way I tried to do it was by
> binarizing
> and concatanating the hippocampal volumes and then run
> mri_glmfit. But, I am
> stuck at glm_fit and would be grateful if you can let me know
> how to proceed
> from here. How do I run the glm_fit between eod and lod
> patients? Secondly,
> after running glm_fit how do I calculate the significance from
> sig.mgh?
>
> Appreciate all your help.
>
> Thanks and regards,
>
> Sampada
>
> On Sun, Jul 10, 2016 at 7:15 PM, Bruce Fischl
> >
> wrote:
>   Hi Sampada
>
>   can you elaborate a bit? What are you trying to achieve?
> Do you
>   want an
>   average hippocampus? Average maps of subfields? What
> hypothesis
>   are you
>   trying to test? The individual subject data is not
> resampled to
>   a common
>   coordinate system, so just averaging them as is won't
> produce
>   anything
>   interested.
>
>   cheers
>   Bruce
>
>   On Sun, 10 Jul 2016, Dr
>   Sampada Sinha wrote:
>
>   > Dear freesurfer experts,
>   > Will you please let me know if it's possible to get one
>   average mgz image
>   > file by concatenating the hippocampal volumes of different
>   subjects using
>   > dev version? Since, I already have the hippocampal
> subfields
>   mgz volume
>   > files, I intend to run the glmfit later on between two
> groups
>   to get sig.mgh
>   > files.
>   >
>   > Thanks and regards?
>   >
>   > Sampada
>   >
>   >
>   > --
>   > Sampada
>   > Pre-doctoral student
>   > Department of Geriatric Mental Health (DGMH)
>   > King George Medical University
>   > Lucknow-226003
>   > India
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
>   >
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> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person
> to whom
> it is
> addressed. If you believe this e-mail was sent to you in error
> and the
> e-mail
> contains patient information, please contact the Partners
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> but does not contain patient information, please contact the
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> and properly
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>
>
>
>
> --
> Sampada
> Pre-doctoral student
> Department of Geriatric Mental Health (DGMH)
> King George Medical University
> Lucknow-226003
> India
>
>
>
>
>
>
>
>
>
>
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>
> The information in this e-mail is intended only for the person to
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> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> 

Re: [Freesurfer] BrainSegVolNotVent

[Douglas N Greve]

That does look suspicious, esp since BrainSegNotVent should be smaller 
than BrainSeg. Can you tar up the subject and send it to me? It may be 
some strange incompatibility with v5


On 07/07/2016 03:50 PM, Eryilmaz, H. Hamdi wrote:
> Hello Doug and Freesurfers,
>
> I am trying to compute a structural measure called 
> 'BrainSegVolNotVent' as an approximate value of total brain volume. 
> 'BrainSegVolNotVent' is now present in aseg.stats files but the 
> dataset I'm working on was preprocessed using FS 5.0, which did not 
> produce this variable. Per your advice I found in a previous email, I 
> reran mri_segstats adding the flags --brainmask mri/brainmask.mgz 
> --brain-vol-from-seg.
>
> The new aseg.stats file contains the following lines that were added 
> after running this command:
>
> # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 
> 1667093, unitless
> # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1667093.00, mm^3
> # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation 
> Volume Without Ventricles, 232145.00, mm^3
> # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 
> 1410666, unitless
> # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 
> 1410666.00, mm^3
>
> The numbers look a bit odd. BrainSegVol and BrainSegVolNotVent should 
> normally be close to each other, right? Also unitless values such as 
> BrainSegNVox and BrainMaskNVox seem to be equal to their corresponding 
> volumetric values.
>
> Do you have any idea what might have gone wrong? Here's the command I 
> ran:
>
> mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv 
> mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent 
> --subcortgray --in mri/norm.mgz --in-intensity-name norm 
> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol 
> --totalgray --ctab /usr/local/freesurfer/stable5_0_0/ASegStatsLUT.txt 
> --subject SUBJECT_ID --brainmask mri/brainmask.mgz --brain-vol-from-seg
>
>
> Thanks very much for your help!
>
> Best,
> Hamdi
>
>
>
>
>
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Jennifer Legault]

Hi Doug,

Thank you for your response.  The current fsgd file I sent you was with the
covariates demeaned x 100, as I saw you recommend that to someone else.  We
previously tried doing just the demeaned values without multiplying by 100,
and that still had the badly scaled error.  Do you think we should take the
demeaned x 100 covariates and divide them by the standard deviation?  Or
would it be better to take regular demeaned values and divide them by the
standard deviation?

Best,

Jennifer Legault

On Mon, Jul 18, 2016 at 12:43 PM, Douglas N Greve  wrote:

> This is almost surely a problem with scaling as your covariates are
> huge. Try subtracting the mean and dividing by the stddev before
> entering into the FSGD file. Compute the means and stddevs across all
> subjects.
> doug
>
> On 07/11/2016 03:20 PM, Jennifer Legault wrote:
> > Hi Freesurfer Experts,
> >
> > I am trying to run mri_glmfit and while 90% of my files work, some of
> > them display the error below.  I have tried demeaning, and then tried
> > multiplying this value by 100, and I still get the same error.  Any
> > feedback would be greatly appreciated.
> >
> > mris_preproc done
> > srcsubject = fsaverage
> > srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
> > srctype=
> > trgsubject = fsaverage
> > trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= rh
> > trghemi= rh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
> > Loading source data
> > INFO: trgsubject = srcsubject
> > Saving target data
> > Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > gdfReadHeader: reading
> >
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 Age 19.5833 1.32025
> > 1 eTIV 1.61645e+06 145343
> > 2 EnglishParityRT 0.00012207 25139.1
> > Class Means of each Continuous Variable
> > 1 Monolingual_male  19.7143 1678946.5893 -4197.2796
> > 2 Monolingual_female  19.4000 1528966.6750 5876.1917
> > INFO: gd2mtx_method is dods
> > Reading source surface
> > /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
> > Number of vertices 163842
> > Number of faces327680
> > Total area 65020.765625
> > AvgVtxArea   0.396850
> > AvgVtxDist   0.717994
> > StdVtxDist   0.193566
> >
> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> > cwd /gpfs/scratch/jtl190/Math_reconstruction
> > cmdline mri_glmfit --y
> > rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
> >
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > --C
> >
> /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
> > --surf fsaverage rh --cortex --glmdir
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > sysname  Linux
> > hostname cyberstar129.hpc.rcc.psu.edu
> > 
> > machine  x86_64
> > user jtl190
> > FixVertexAreaFlag = 1
> > UseMaskWithSmoothing 1
> > OneSampleGroupMean 0
> > y
> >
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > logyflag 0
> > usedti  0
> > FSGD
> >
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > labelmask
> >  /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
> > maskinv 0
> > glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > IllCondOK 0
> > ReScaleX 1
> > DoFFx 0
> > Creating output directory
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > Loading y from
> >
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > INFO: gd2mtx_method is dods
> > Saving design matrix to
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
> > Normalized matrix condition is 22568.9
> > Design matrix --
> >  1.000   0.000   18.000   0.000   1865790.250   0.000  -8952.208   0.000;
> >  0.000   1.000   0.000   19.000   0.000   1520429.625 0.000  -4605.208;
> >  1.000   0.000   19.000   0.000   1749716.750   0.000  -39407.207
>  0.000;
> >  0.000   1.000   0.000   18.000   0.000   1589109.250 0.000  -17967.209;
> >  1.000   0.000   21.000   0.000   1472295.125   0.000 19531.791   0.000;
> >  1.000   0.000   18.000   0.000   1580381.375   0.000  -17027.209
>  0.000;
> >  1.000   0.000   20.000   0.000   1813373.500   0.000 16152.792   0.000;
> >  1.000   0.000   21.000   0.000   1638616.500   0.000  -9074.208   0.000;
> >  0.000   1.000   0.000   21.000   0.000   1297920.500 0.000   61860.793;

[Freesurfer] vtk to mgz file

[Abbie McNulty]

So we were able to figure out how to segment the different parts of the
brain using the bert sample, but have run into another problem.
I would like to save each segmentation so that I can import it into matlab
and create a matrix in order to create a mesh. The volume segment saves a
as a .vtk file, which I don't know how to read into matlab. How can I save
it as or convert it to a .mgz file so that I can import it into matlab?

Thanks!
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Re: [Freesurfer] Re Re: Checking Surfaces vs. aseg outputs

[Bruce Fischl]

nope, I would start with the aseg and only check other things if the 
ventricles aren't accurate

On Mon, 18 Jul 2016, Tamara Tavares wrote:


Thank you again Bruce.
Since I am primarily interested in ventricular volume, do you think it is
necessary to check the the brainmask.mgz for bright or dark spots indicating
an intensity normalization error? As well, what about a skull strip error
such as removal of brain tissue? I have noticed that sometimes skull strip
removes parts of the occipital lobe and I was going to adjust the watershed
parameters and re-run recon-all. Do you think this is necessary or would
affect the ventricular volume results?

Thank you in advance for your help,
Tamara 

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[Freesurfer] can not find module 'dev'

[Yun Wang]

Dear All,

I recently tried to gain  access the read-only CVS source-code repository, 
however, I have this kind of error:

cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules

anyone have idea what is going on here? 

Thank you so much!



Best,

Yun Wang

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Re: [Freesurfer] PVE correction tool on Freesurfer 6

[Douglas N Greve]

On 07/12/2016 11:03 PM, Lee Subin Kristine wrote:
>
> Hi Doug,
>
>
> Thanks a lot for the page! It was very helpful.
>
>
> I have a few questions about one of the commands and a question for 
> one of the output files.
>
>
> 1)*mri_gtmpvc --i pet.nii.gz --reg template.reg.lta--psf FWHM--seg 
> gtmseg.mgz **--default-seg-merge --auto-mask PSF .01--mgx .01--o 
> gtmpvc.output *
>
> (a) For the psf flag, do I have to know exactly the FWHM of the 
> point-spread function of the scanner or would a default value of 6 
> work for all? I am using PET images from multiple centers and thus 
> each image are from different scanners, and I'm not sure how I would 
> find the fwhm for each scanner.
>
In theory you need the FWHM for each scanner. The FWHM can also change 
depending upon recon method and parameters and even the ligand used. If 
you get it about right, probably it will be close enough.
>
> (b) For the mgx flag, is the GM threshold .01 an optimal threshold 
> referring to the p-value?(am new to PVEcorrection and asking out of 
> curiosity) What is the difference if I enter .01 versus I don't enter it?
>
You must enter a threshold. When Muller-Gartner is implemented, there 
are two stages: (1) orthogonalization (subtracting out non-GM) and (2) 
rescaling. In the rescaling step, each voxel is divided by the fraction 
of GM in that voxel. If that fraction is 0, then you will get an error. 
If it is close to 0, you can get extreme noise amplification in that 
voxel. Setting it to .01 requires that a voxel have at least 1% GM to be 
rescaled, otherwise the voxel is set to 0.
>
>
> 2) From the *gtm.stats.dat *output file, the 5th column(number of PET 
> voxels in the ROI) of, for example, the ctx-lh-precuneus and 
> ctx-rh-precuneus are 1744 and 1805 respectively. However, in the 
> *?h.aparc.stats* files from recon-all, the 4th column(gray matter 
> volume) of lh-precuneus and rh-precuneus are 5928 and 6125 
> respectively. I am confused because I thought the number of PET voxels 
> should be equal to the number of GM voxels in the ROI?
>
You need to scale by the size of the PET voxel.
>
> Also, for output files such as gtm.nii.gz or nopvc.nii.gz, what 
> programs can I open them with? It doesn't seem it is openned with 
> mricron or gedit.
>
They are nifti files, though you probably don't want to use a nifit 
viewer. You can load them into matlab with MRIread('file.nii.gz')

>
> Thank you again in adavnce for your help.
>
>
> Best,
>
> Subin
>
> 
> *보낸 사람:* Douglas N Greve  대신 
> freesurfer-boun...@nmr.mgh.harvard.edu 
> 
> *보낸 날짜:* 2016년 7월 8일 금요일 오전 2:53:31
> *받는 사람:* freesurfer@nmr.mgh.harvard.edu
> *제목:* Re: [Freesurfer] PVE correction tool on Freesurfer 6
> Hi Subin, I just created this page this morning
> http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
> do you want to take a look and see if it answers your questions. As for
> #2, yes you still need to run gtmseg.
>
> On 06/26/2016 07:45 AM, Lee Subin Kristine wrote:
> >
> > Hello,
> >
> > I am trying to use PVE correction on preprocessed PET data downloaded
> > from the Alzheimer's Disease Neuroimaging Initiative(ADNI) database.
> > I have a couple of questions:
> >
> >
> > 1) I am using the co-registered, averaged image of the dynamic images,
> > and it seems from your answers here
> > 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html) 
>
> > 
> that
>  
>
> > for static PET images, #3~5 will be different. Could you explain how I
> > would need to enter the command differently?
> >
> > 2) I already have segmentations of my MRI images obtained via
> > FreeSurfer(v.5.2)'s cortical parcellation. Would I still have to do
> > procedure #1 (gtmeseg --s subject) ? I did try using xcerebralseg
> > because it seemed from the help command that in my case where I
> > already have some FS segmentations that I should use this one:
> >
> > /You can use your own segmentation or a modified FS segmentation. //
> > //It will be easiest if you modify apas+head.mgz to insert your//
> > //segmentations. apas+head.mgz is created by gtmseg but you can//
> > //create it with //
> > /
> > /xcerebralseg --s $subject --o $SUBJECTS_DIR/$subject/mri/apas+head.mgz/
> >
> > However when I do try I got the following error:
> >
> > /ERROR: could not open
> > 
> /usr/local/freesurfer/subjects/002_S_4213/stats/002_S_4213/mri/apas+head.stats
>  
>
> > for writing//
> > //Errno: No such file or directory/
> >
> >
> >
> > Thanks a lot in advance,
> >
> > Regards,
> > Subin
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone 

Re: [Freesurfer] Freesurfer Digest, Vol 149, Issue 31

[Tamara Tavares]

Hi Bruce,

Thank you for your quick reply.

We are primarily interested in ventricular volume but we may look at other
areas in the future; this is why I thought it would be a good idea to check
the surfaces. Is the reasoning why the surface outputs vs. aseg outputs
should be checked is because the surface outputs are used the calculate the
structure's volumes? I am fairly new to Freesurfer so I am trying to get a
good understanding of it.

Thank you in advance,
Tamara

---
Tamara Tavares, HBSc 
PhD Candidate
Brain and Mind Institute, Department of Neuroscience
The Schulich School of Medicine and Dentistry
The University of Western Ontario
519-661-2111, ext 84623

On Sun, Jul 17, 2016 at 12:00 PM, 
wrote:

> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>1. Re: Checking Surfaces vs. aseg outputs (Bruce Fischl)
>
>
> --
>
> Message: 1
> Date: Sat, 16 Jul 2016 13:35:10 -0400 (EDT)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] Checking Surfaces vs. aseg outputs
> To: Freesurfer support list 
> Message-ID:
> 
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Hi Tamara
>
> if you are more interested in things like ventricular volume then the
> surfaces aren't so important to check.
>
> cheers
> Bruce
>
>
> On Fri, 15 Jul 2016, Tamara Tavares wrote:
>
> > Hi All,
> >
> > I was hoping to get some help with understanding the surface and aseg
> > volumes. I have some patient's scans and I am interested in examining the
> > ventricular volume but may look at other areas later on. I understand
> from
> > earlier threads that it is important to check the surface volumes (pial
> and
> > wm) vs. the aseg output. Why is it more important to check the surfaces
> vs
> > the aseg outputs if I am interested in getting the volumes?
> >
> > Thank you in advance for your help.
> >
> > Best,
> > Tamara
> >
> >
>
>
> --
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 149, Issue 31
> ***
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Freesurfer Digest, Vol 149, Issue 31

[Bruce Fischl]

Hi Tamara

no, the surfaces shouldn't affect the volume of the ventricles, so if 
that is all you care about just inspect the aseg.


cheers
Bruce
On Mon, 18 Jul 2016, 
Tamara Tavares wrote:



Hi Bruce,
Thank you for your quick reply.

We are primarily interested in ventricular volume but we may look at other
areas in the future; this is why I thought it would be a good idea to check
the surfaces. Is the reasoning why the surface outputs vs. aseg outputs
should be checked is because the surface outputs are used the calculate the
structure's volumes? I am fairly new to Freesurfer so I am trying to get a
good understanding of it.

Thank you in advance,
Tamara  

---
Tamara Tavares, HBSc
PhD Candidate 
Brain and Mind Institute, Department of Neuroscience
The Schulich School of Medicine and Dentistry
The University of Western Ontario
519-661-2111, ext 84623

On Sun, Jul 17, 2016 at 12:00 PM, 
wrote:
  Send Freesurfer mailing list submissions to
          freesurfer@nmr.mgh.harvard.edu

  To subscribe or unsubscribe via the World Wide Web, visit
         
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  or, via email, send a message with subject or body 'help' to
          freesurfer-requ...@nmr.mgh.harvard.edu

  You can reach the person managing the list at
          freesurfer-ow...@nmr.mgh.harvard.edu

  When replying, please edit your Subject line so it is more
  specific
  than "Re: Contents of Freesurfer digest..."


  Today's Topics:

     1. Re: Checking Surfaces vs. aseg outputs (Bruce Fischl)


  --

  Message: 1
  Date: Sat, 16 Jul 2016 13:35:10 -0400 (EDT)
  From: Bruce Fischl 
  Subject: Re: [Freesurfer] Checking Surfaces vs. aseg outputs
  To: Freesurfer support list 
  Message-ID:
         
  
  Content-Type: text/plain; charset=US-ASCII; format=flowed

  Hi Tamara

  if you are more interested in things like ventricular volume
  then the
  surfaces aren't so important to check.

  cheers
  Bruce


  On Fri, 15 Jul 2016, Tamara Tavares wrote:

  > Hi All,
  >
  > I was hoping to get some help with understanding the surface
  and aseg
  > volumes. I have some patient's scans and I am interested in
  examining the
  > ventricular volume but may look at other areas later on. I
  understand from
  > earlier threads that it is important to check the surface
  volumes (pial and
  > wm) vs. the aseg output. Why is it more important to check the
  surfaces vs
  > the aseg outputs if I am interested in getting the volumes?
  >
  > Thank you in advance for your help.
  >
  > Best,
  > Tamara
  >
  >


  --

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

  End of Freesurfer Digest, Vol 149, Issue 31
  ***


  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
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[Freesurfer] Integrate SPM activation maps to FreeSurfer structural volumes

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am trying to register my SPM activation maps to the structural data of
each subjects. Except for the commands I could find for the registration, I
could not find a guide on the registration of activation maps from SPM to
FreeSurfer. Would you please guide me how I should do that?

Best Regards,
Mahtab.
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Beta-Zero Correction - No Phase File

[Douglas N Greve]

You can extract frames from a multi frame file with
mri_convert input.nii.gz --frame 0 output.frame0.nii.gz


On 07/12/2016 02:29 PM, Afzal, Afsana wrote:
> Hi,
>
> I'm working with a dataset that outputs only one file (not two 
> separate mag and phase files) for the fieldmap. The data was also 
> collected on non-Siemens scanners: Philips Ingenia and GE SIGNA HDx 
> (not sure if this is the reason the fieldmaps are unpacking 
> differently). I've attached the .dat file for one of the fieldmaps in 
> this email.
>
> If there a way to separate out the mag and phase from the single 
> fieldmap file so I can use epidewarp.fsl?
>
> Thanks,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_convert WARNING: files are not found to be different and cannot be sorted

[Douglas N Greve]

When FS reads a series of dicom files, it tries to sort them in time and 
space so that it can generate the appropriate 4D volume. To do this, it 
needs to get info out of the DICOM header to determine this sorting. 
This includes image number and geometry information. If that information 
is not recorded properly (eg, if all files have the same info), then it 
cannot be sorted and thus the warnings below. It looks like the dicoms 
do not contain the siemens ascii header, which could also be a source of 
the warning. If the images look ok, then it might not be anything to 
worry about.


On 07/12/2016 01:19 PM, Olivia Walton Stanley wrote:
> Hello all,
>
> I have run mri_convert on a series of dicoms and received the following error 
> for several of my images. As with the previous bug report for this I have run 
> mri_info on my dicom series and it’s output is below. My main concern is 
> since these dicoms are being jumbled up and I am not sure what that warning 
> means. Is it the dicom header it is comparing? Can you elaborate or put me on 
> track to debug this error?
>
> Thanks,
>
> Olivia
>
> mri_info is below:
>
> mri_info 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm
> Getting Series No
> Scanning Directory
> INFO: Found 9218 files in 500
> INFO: Scanning for Series Number 3076
> INFO: found 4608 files in series
> INFO: loading series header info.
>
> INFO: sorting.
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP13_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP1_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP25_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP2_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP37_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP3_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP49_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP4_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP5_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP61_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP6_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP73_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC0_CON0_PHS0_REP7_SET0_AVE0_2.dcm
> File2: 500/Image_SLC0_CON0_PHS0_REP85_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP1_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP20_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP2_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP32_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP4_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP56_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP3_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP44_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP5_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP68_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP6_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP80_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC11_CON0_PHS0_REP0_SET0_AVE0_2.dcm
> File2: 500/Image_SLC11_CON0_PHS0_REP10_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC10_CON0_PHS0_REP7_SET0_AVE0_2.dcm
> File2: 500/Image_SLC10_CON0_PHS0_REP92_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC11_CON0_PHS0_REP1_SET0_AVE0_2.dcm
> File2: 500/Image_SLC11_CON0_PHS0_REP22_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC11_CON0_PHS0_REP3_SET0_AVE0_2.dcm
> File2: 500/Image_SLC11_CON0_PHS0_REP46_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC11_CON0_PHS0_REP4_SET0_AVE0_2.dcm
> File2: 500/Image_SLC11_CON0_PHS0_REP58_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC11_CON0_PHS0_REP6_SET0_AVE0_2.dcm
> File2: 500/Image_SLC11_CON0_PHS0_REP82_SET0_AVE0_2.dcm
> WARNING: files are not found to be different and cannot be sorted
> File1: 500/Image_SLC11_CON0_PHS0_REP7_SET0_AVE0_2.dcm
> File2: 

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Douglas N Greve]

This is almost surely a problem with scaling as your covariates are 
huge. Try subtracting the mean and dividing by the stddev before 
entering into the FSGD file. Compute the means and stddevs across all 
subjects.
doug

On 07/11/2016 03:20 PM, Jennifer Legault wrote:
> Hi Freesurfer Experts,
>
> I am trying to run mri_glmfit and while 90% of my files work, some of 
> them display the error below.  I have tried demeaning, and then tried 
> multiplying this value by 100, and I still get the same error.  Any 
> feedback would be greatly appreciated.
>
> mris_preproc done
> srcsubject = fsaverage
> srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
> srctype=
> trgsubject = fsaverage
> trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
> Loading source data
> INFO: trgsubject = srcsubject
> Saving target data
> Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> gdfReadHeader: reading 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 19.5833 1.32025
> 1 eTIV 1.61645e+06 145343
> 2 EnglishParityRT 0.00012207 25139.1
> Class Means of each Continuous Variable
> 1 Monolingual_male  19.7143 1678946.5893 -4197.2796
> 2 Monolingual_female  19.4000 1528966.6750 5876.1917
> INFO: gd2mtx_method is dods
> Reading source surface 
> /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
> Number of vertices 163842
> Number of faces327680
> Total area 65020.765625
> AvgVtxArea   0.396850
> AvgVtxDist   0.717994
> StdVtxDist   0.193566
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /gpfs/scratch/jtl190/Math_reconstruction
> cmdline mri_glmfit --y 
> rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
>  
> --C 
> /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
>  
> --surf fsaverage rh --cortex --glmdir 
> rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> sysname  Linux
> hostname cyberstar129.hpc.rcc.psu.edu 
> 
> machine  x86_64
> user jtl190
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y 
>  
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> logyflag 0
> usedti  0
> FSGD 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> labelmask 
>  /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory 
> rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> Loading y from 
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> INFO: gd2mtx_method is dods
> Saving design matrix to 
> rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
> Normalized matrix condition is 22568.9
> Design matrix --
>  1.000   0.000   18.000   0.000   1865790.250   0.000  -8952.208   0.000;
>  0.000   1.000   0.000   19.000   0.000   1520429.625 0.000  -4605.208;
>  1.000   0.000   19.000   0.000   1749716.750   0.000  -39407.207   0.000;
>  0.000   1.000   0.000   18.000   0.000   1589109.250 0.000  -17967.209;
>  1.000   0.000   21.000   0.000   1472295.125   0.000 19531.791   0.000;
>  1.000   0.000   18.000   0.000   1580381.375   0.000  -17027.209   0.000;
>  1.000   0.000   20.000   0.000   1813373.500   0.000 16152.792   0.000;
>  1.000   0.000   21.000   0.000   1638616.500   0.000  -9074.208   0.000;
>  0.000   1.000   0.000   21.000   0.000   1297920.500 0.000   61860.793;
>  0.000   1.000   0.000   18.000   0.000   1634762.625 0.000  -22671.209;
>  0.000   1.000   0.000   21.000   0.000   1602611.375 0.000   12763.792;
>  1.000   0.000   21.000   0.000   1632452.625   0.000 9395.292   0.000;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y 
> rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
>  
> --C 
> 

[Freesurfer] Re Re: Checking Surfaces vs. aseg outputs

[Tamara Tavares]

Thank you again Bruce.

Since I am primarily interested in ventricular volume, do you think it is
necessary to check the the brainmask.mgz for bright or dark spots
indicating an intensity normalization error? As well, what about a skull
strip error such as removal of brain tissue? I have noticed that sometimes
skull strip removes parts of the occipital lobe and I was going to adjust
the watershed parameters and re-run recon-all. Do you think this is
necessary or would affect the ventricular volume results?

Thank you in advance for your help,
Tamara
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Re: [Freesurfer] white and pail surface editing

[Bruce Fischl]

Hi Ri

I think you can just run it all as one recon-all command.

cheers
Bruce
On Mon, 18 Jul 
2016, Ritobrato Datta wrote:

> Hi All,
>
> We have some subjects who have both wm errors and gm errors.
>
> Is the following workflow possible
>
>
> Step 1) control points for the white matter edits. DONT RUN recon-all
>
> Step 2) add the pial surface edits. DONT RUN recon-all
>
> Step 3) Run recon-all to incorporate control points for wm edits (recon-all 
> -autorecon2-cp -autorecon3 -subjid cp_before)
>
> AFTER step 3 is COMPLETE, run
>
> Step 4) Run recon-all to create a fixed pial surface (recon-all 
> -autorecon-pial -subjid pial_edits_before)
>
> OR
>
> Can step 3 and Step 4 be run together as recon-all -autorecon2-cp 
> -autorecon-pial -autorecon3 -subjid cp_before
>
> Please let me know.
>
> Thanks
>
> Ri
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>
>
>
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[Freesurfer] white and pail surface editing

[Ritobrato Datta]

Hi All,

We have some subjects who have both wm errors and gm errors. 

Is the following workflow possible


Step 1) control points for the white matter edits. DONT RUN recon-all

Step 2) add the pial surface edits. DONT RUN recon-all

Step 3) Run recon-all to incorporate control points for wm edits (recon-all 
-autorecon2-cp -autorecon3 -subjid cp_before)

AFTER step 3 is COMPLETE, run 

Step 4) Run recon-all to create a fixed pial surface (recon-all -autorecon-pial 
-subjid pial_edits_before)

OR 

Can step 3 and Step 4 be run together as recon-all -autorecon2-cp 
-autorecon-pial -autorecon3 -subjid cp_before

Please let me know.

Thanks

Ri
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[Freesurfer] can not find module 'dev'

[Yun Wang]

Dear All,

I recently tried to gain  access the read-only CVS source-code repository, 
however, I have this kind of error:

cvs server: cannot find module `dev' - ignored
cvs [checkout aborted]: cannot expand modules

anyone have idea what is going on here? 

Thank you so much!



Best,

Yun Wang

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Re: [Freesurfer] Integrate SPM activation maps to FreeSurfer structural volumes

[Bruce Fischl]

Hi Mahtab

check out bbregister. It should do the trick.

cheers
Bruce
On Mon, 18 Jul 2016, Mahtab 
Farahbakhsh wrote:

> Dear FreeSurfer,
> I am trying to register my SPM activation maps to the structural data of
> each subjects. Except for the commands I could find for the registration, I
> could not find a guide on the registration of activation maps from SPM to
> FreeSurfer. Would you please guide me how I should do that?
> 
> Best Regards,
> Mahtab.
> 
>
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[Freesurfer] LME contrasts

[Clara Kühn]

Dear FreeSurfer experts,

I am following the mass-univariate (spatiotemporal) model in the LME tutorial. 
My design matrix X has the following columns:
intercept, time, time², group1, group1*time, group1*time², group2, group2*time, 
group2*time², sex, age, mean_thickness

I actually have 3 groups but group1 and group2 in X are dummy coded.

I would like to check whether there are group differences in the quadratic term 
but I don't understand what this command expresses and how the contrast was 
formed:

CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];

Could you please explain it on the example design matrix so I can adapt it to 
mine?

Thank you!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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