[Freesurfer] Reminder: FSurf webinar tomorrow

[Suchandra Thapa]

Dear FreeSurfer Community,

The Open Science Grid consortium (http://www.opensciencegrid.org) offers a
service “FSurf” which allows large scale batch processing of MRI scans
using FreeSurfer.   FSurf supports the standard FreeSurfer workflow
(autorecon-all) or workflows with arbitrary FreeSurfer options.  FSurf
currently uses FreeSurfer 5.3 but support for FreeSurfer 6.0 will be added
in the near future.  Note that no proposal for an allocation is required to
use the service.

We are hosting a 30 minute webinar on Thursday, April 13th, 2pm CDT to
cover the basics of batch processing using FSurf.  The webinar will be
accessible from a PC, Mac, Linux, iOS, or Android device at
https://IU.zoom.us/j/644966220.

Instructions for getting started with FSurf can be found here:
http://bit.ly/freesurferopensciencegrid.

We hope to see you there, and best regards.

The OSG FSurf support team


Suchandra Thapa
sth...@ci.uchicago.edu
Computation Institute
Searle Chemistry Laboratory #201A
5735 South Ellis Avenue
Chicago, IL 60637
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Re: [Freesurfer] Longitudinal Pipeline

[Arman Eshaghi]

Thanks Martin. Should I be worried about affine transform masking out the
global atrophy if I am using the whole brain (no skull stripping)?

Arman

On Wed, Apr 12, 2017 at 9:36 PM, Martin Reuter 
wrote:

> Hi Arman,
>
> should be possible by passing the - - affine flag. I think I also
> experimented around with a -base-affine flag to recon-all for that (instead
> of -base). It is experimental!
>
> Best, Martin
>
>
> > On 07 Apr 2017, at 13:34, Arman Eshaghi  wrote:
> >
> > Hi,
> >
> > I wonder if there is a way for mri_robust_template to perform iterative
> registration with 9 DOF rather than 6-7 default. The rational is to allow
> for a bit of scaling to adjust for potential scanner drifts in a
> longitudinal study over years.
> >
> > Thanks,
> > Arman
> > ___
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>
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[Freesurfer] trac-all -stat

[Versace, Amelia]

Hi Anastasia, 

I am having some issues with the -stat option. Below is the error. I am not 
sure of what's causing the issue. Any idea?
Thanks a lot!! Amelia

-
trac-all -c scripts/dmrirc.stats -stat

INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer
INFO: Diffusion root is /data/dprojects/BIOS/tracula
Actual FREESURFER_HOME /data/software/freesurfer6
ERROR: no pathway reconstructions found
-

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Re: [Freesurfer] trac-all -stat

[Yendiki, Anastasia]

Hi Amelia - This means that it can't find any of the tracts that you've 
specified (or any tracts period, if you haven't specified a list) for the 
subjects that you've specified in your config file. It'd be looking under:

/data/dprojects/BIOS/tracula/$subj/dpath/

Best,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Versace, Amelia 
[versa...@upmc.edu]
Sent: Wednesday, April 12, 2017 5:00 PM
To: Freesurfer support list
Subject: [Freesurfer] trac-all -stat

Hi Anastasia,

I am having some issues with the -stat option. Below is the error. I am not 
sure of what's causing the issue. Any idea?
Thanks a lot!! Amelia

-
trac-all -c scripts/dmrirc.stats -stat

INFO: SUBJECTS_DIR is /data/dprojects/BIOS/freesurfer
INFO: Diffusion root is /data/dprojects/BIOS/tracula
Actual FREESURFER_HOME /data/software/freesurfer6
ERROR: no pathway reconstructions found
-

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Re: [Freesurfer] Longitudinal Pipeline

[Martin Reuter]

Hi Arman, 

should be possible by passing the - - affine flag. I think I also experimented 
around with a -base-affine flag to recon-all for that (instead of -base). It is 
experimental!

Best, Martin


> On 07 Apr 2017, at 13:34, Arman Eshaghi  wrote:
> 
> Hi,
> 
> I wonder if there is a way for mri_robust_template to perform iterative 
> registration with 9 DOF rather than 6-7 default. The rational is to allow for 
> a bit of scaling to adjust for potential scanner drifts in a longitudinal 
> study over years.
> 
> Thanks,
> Arman
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Survey on inputs for surface-based analysis pipelines

[Christopher Markiewicz]

Hi list,

We're working on FMRIPREP , a 
pipeline aimed at performing baseline preprocessing, and producing cleaned 
structural and functional data which can be fed into any of a number of 
analysis pipelines.

We've recently begun incorporating surface reconstruction and surface-mapped 
functionals, and we'd like to get feedback on what outputs would be most 
valuable to people, in terms of formats, spaces and sampling strategies.

1) What surfaces do you use for sampling functional data and visualization? If 
you use down-sampled surfaces, do you have a preferred down-sampling strategy 
or target mesh?

2) What statistical analyses and model-fitting tools do you use for 
surface-based analyses? And are there any particular considerations you have 
for preparing your data for use by these tools?

I appreciate your time and any input you may have to help us build a tool that 
fits the needs of the community.

Thanks,
-- 
Chris Markiewicz
Center for Reproducible Neuroscience
Stanford University


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Re: [Freesurfer] TRACULA tract reconstruction

[Yendiki, Anastasia]

Hi Joelle – I tested one of your dicoms and the gradient table that mri_convert 
reads from it works just fine. So you can just pass your dicoms to TRACULA and 
it’ll do the rest. No need for you to specify the gradient tables.

Best,
a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 
>
Date: Friday, March 31, 2017 at 7:44 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Anastasia,


I sent the links for the dicom files to you and just want to make sure - did 
you receive them?


Best,


Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 de la part de Yendiki, Anastasia 
>
Envoyé : jeudi 30 mars 2017 15:20
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle - Can you please send the filedrop upload to me too? Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
[joelle.vandermo...@etu.unige.ch]
Sent: Thursday, March 30, 2017 7:27 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA tract reconstruction


​Hi Barbara,


Thank you for the tip, I managed to anonymize my dicom images. I uploaded them 
on filedrop. ​

The scanner used for the acquisition is a Siemens Prisma 3 Tesla.


Best,

Joëlle


De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 de la part de Barbara Kreilkamp 
>
Envoyé : mercredi 29 mars 2017 14:18
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction


Hi Joëlle,

Which scanner was used to acquire the images? I have used Osirix light in the 
past to anonymize my dicom images, maybe you'd like to try that?

Best wishes,

Barbara

On 29/03/2017 13:30, Joëlle Ismay Rosanne Van Der Molen wrote:

​Hi Anastasia,


Yes, I use dicom images as input for Tracula. I also specify the bvecs files, 
as Tracula returns an error if I try to run it with a configuration file that 
does not contain them.



Unfortunately, our dicom images are not anonymised, so I cannot provide them.


Best,


Joëlle



De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 de la part de Yendiki, Anastasia 

Envoyé : mercredi 22 mars 2017 15:40
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA tract reconstruction

Hi Joëlle – What images do you pass as input to TRACULA? Do you pass the dicom 
itself, or a converted file? Happy to look at your dicom, if it’s anonymized.

a.y

From: 
>
 on behalf of Joëlle Ismay Rosanne Van Der Molen 
>
Reply-To: Freesurfer support list 
>
Date: Wednesday, March 22, 2017 at 3:55 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] TRACULA tract reconstruction

Hi Anastasia and Antonin,

I apologize for the late response.
Thank you very much for the explanations!

Regarding the gradient tables, I realized that I was indeed using the old 
version of mrtrix3, and was getting tables with a flipped x component (sign 
inversion), which corresponds to the bug that is highlighted in the blog link 
you sent me. After having updated mrtrix3, the tables now look correct.

What seems odd, however, is that in fact mri_convert outputs the same gradient 
tables as the old version of mrtrix3, that is, with a flipped x component.
I tried running tracula on one of our subjects using gradient tables obtained 
with the updated mrtrix3, versus those obtained with mri_convert, and the 
results are quite different. I attached several files, so that you could maybe 
take a look and tell me how to best interpret this:

Re: [Freesurfer] correlation coefficient R

[tom parker]

Thank you so much Doug!

It worked! I was just wondering which value I should report as the
correlation coefficient of my analysis.

This is the output I got:

# ColHeaders  Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max
Range
  1  -4 2037320373.0  Seg-004-0.1596 0.0468-0.3134
-0.1017 0.2117

Should I report the mean (-0.1596) or the min (-0.3134)?

Thanks again

Try something like

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



2017-04-08 1:35 GMT+01:00 tom parker :

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

 I made some correlations between cortical thickness and age in qdec.

 Is it possible to get the correlation coefficient value of this
 analysis?

 I just need to put it in a table with the significant results.

 Thank you so much!

>>>
>>>
>>
>
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[Freesurfer] Fwd: wm edits not incorporated

[Octavian Lie]

Dear All,

Regarding wm.mgz edits not incorporated into wm surface, which seems to
have been reported on by several of us with FS 6.00. I followed Antonin's
idea of editing 001.mgz by switching wm-intensity voxels clearly not wm
(mostly in the subtemporal regions, at times close to bright dural portions
in the crown) to gm intensities and ran recon-all -all, and this time all
was OK. So it seems that the problem is that on re-initializing during
-autorecon2-wm rerun, the routine does not edit out high intensity voxels
even if manually excluded in wm.mgz. This seems to be different to some
extent with how FS 5.3 was reacting, although I did not look at this
systematically. There may be a reason that manual editing is just part of
the story during rerun and does not automatically override the recon
stream, but I do not know it.
Octavian




-- Forwarded message --
From: Octavian Lie 
Date: Sun, Apr 2, 2017 at 7:59 PM
Subject: wm edits not incorporated
To: octavian lie 



Dear Bruce,

I just transferred subject r02.tar.gz.

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

FOr example, the complete command line for  a rerun is

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


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


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


I mention this is not the only subject where I have this problem.
Thank you for your help.
Octavian
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Re: [Freesurfer] manual edits

[David Semanek]

Hi John,

Yes understanding how freesurfer deals with edits can be a bit confusing. I 
have a lot of experience doing edits to the wm.mgz and brainmask.mgz for cross 
sectional data in Freesurfer 5.3 so perhaps I can help.

Recon-all is basically a script which runs a series of about 25 or so 
processing steps in a defined sequence. The software generally will be able to 
recognize when an edit has been done at a particular intervention point and 
will take those edits into account when running that step unless you 
specifically instruct it not to.

The most common types of edits are edits to the wm.mgz to fix white matter 
defects and tissue incorrectly identified as white matter, and edits to the 
brainmask.mgz to fix cases where the skull strip is insufficient to prevent 
dura and other non-cortical tissue from making it into the gray matter/pial 
surfaces. White matter edits need to be done directly on the wm.mgz and gray 
matter/skull strip edits need to be done on the brainmask.mgz. Editing those 
two files and saving them directly in freeview is sufficient to register those 
edits for recon-all.

If you have edited only the brainmask.mgz, it is sufficient to run 
–autorecon-pial since the white matter surfaces will not need to be 
regenerated. If you have edited the wm.mgz, you must run –autorecon2-wm (or 
–autorecon2-cp  if you used control points as well as white matter edits). If 
you have edited both the brainmask.mgz and the wm.mgz, then you only need to 
run –autorecon2-wm since the pial surfaces will be regenerated taking into 
account the brainmask.mgz edits as part of that workflow. Keep in mind that you 
still need to run –autorecon3 to complete the reprocessing of these data 
(-autorecon-pial includes the steps from –autorecon3) but that can be done when 
you are happy with your final surfaces if you want to save processing time on 
iterative edits.

Here is the wiki page referring to edits: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData

I hope this is helpful.

Best,

David P. Semanek, HCISPP
Research Technician, Posner Lab
Division of Child and Adolescent Psychiatry
Columbia University Medical Center
New York State Psychiatric Institute
1051 Riverside Drive, Pardes Bldg. Rm. 2424
New York, NY 10032
PH: (646) 774-5885

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From: John Anderson 
Reply-To: John Anderson 
Date: Wednesday, April 12, 2017 at 6:45 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] manual edits

Dear Freesurfer experts,
I am not an expert in manual edits, so I highly appreciate any feedback 
regarding the issues in my questions below. I ran the following command line 
“recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing 
the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached.
Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz"

1.   When I reviewed “wm.mgz” I see interactions between the white matter 
(wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by 
removing the wm voxels from the cortex, and the data was saved in the file 
“wm.seg.mgz”

2.   I found many holes in many slices similar to the (black arrow). I 
filled all these holes. The data saved in “wm.seg.mgz”

3.   I fixed some issues related to dura and bad skullstipping
Then I ran the command:
“recon-all -autorecon2-wm -autorecon3 -subjid ” which output the file 
“brain.finalsurfs.mgz”
and the command
“recon-all -autorecon-pial -subjid ”
Now, I want to understand where Freesurfer implement the new edits? Which files 
will be used as the main files that include the new edits. Logically, the edits 
must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I 
open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original 
non-edited files. I am not sure what I am doing wrong so I highly appreciate 
any help.
John

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but 

Re: [Freesurfer] mri_concat pet images into 1 template image

[Shane S]

Hi Doug,

There is a bit of movement across the 3 acquisitions. How may I align 
everything together before running mri_concat?

1. Run bbregister or mri_coreg to register 1 acquisition to T1
2. Use the reg file to move the remaining 2 acquisitions ?

Is there a quicker way?

Thank you.

-- 
Shane Schofield

On 9 March 2017 at 17:01:28, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote:

If the 3 volumes are in register (ie, no motion between them), then I  
would just run the mri_concat command to create a single volume which is  
the average of the 3, then proceed as described.  


On 03/09/2017 11:58 AM, Shane S wrote:  
> Hi Doug,  
>  
> I want to derive a single averaged PET volume from the three  
> reconstructed 5 min acquisitions, expressed in detected counts. Then  
> we will divide the counts based on the cerebellum. Following that, I  
> want to use PetSurfer for partial volume correction and GLM  
> comparisons. May I upload the 3 images per subject?  
>  
> Thank you.  
>  
> --  
> Shane S  
>  
> On 9 March 2017 at 16:18:33, Douglas N Greve  
> (gr...@nmr.mgh.harvard.edu ) wrote:  
>  
>> How are you planning on analyzing the different time points?  
>>  
>>  
>> On 03/08/2017 05:33 PM, Shane S wrote:  
>> > Dear Doug,  
>> >  
>> > My PET data is 3 x 5 minute acquisitions. Each subject has  
>> > subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am  
>> > supposed to align and average them.  
>> >  
>> > Please advise.  
>> >  
>> > Thanks!  
>> >  
>> > --  
>> > Shane Schofield  
>> >  
>> > On 8 March 2017 at 22:31:06, Douglas Greve (gr...@nmr.mgh.harvard.edu  
>> > ) wrote:  
>> >  
>> >> No, the template is a within subject template used for registration.  
>> >> If your pet data only has one frame (eg, FDG SUV), then you don't  
>> >> need to run mri_convert or mri_concat, just use your pet image as the  
>> >> template  
>> >>  
>> >>  
>> >> On 3/8/17 11:11 AM, Shane S wrote:  
>> >>> Hello Freesurfer,  
>> >>>  
>> >>> I have 3 PET images per individual. I am learning PetSurfer based on  
>> >>> the Greve et al., 2014 paper.  
>> >>>  
>> >>> On the PetSurfer link, there are 2 methods.  
>> >>>  
>> >>> mri_convert pet.nii.gz —frame frameno template.nii.gz  
>> >>> or  
>> >>> mri_concat pet.nii.gz --mean —0 template.nii.gz  
>> >>>  
>> >>> What are the differences? My files are listed as  
>> >>> subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz  
>> >>>  
>> >>> Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz,  
>> >>> subject123_c.nii.gz —mean —o template.nii.gz” correct?  
>> >>>  
>> >>> Thank you for helping.  
>> >>>  
>> >>> Best Wishes,  
>> >>>  
>> >>> S  
>> >>> --  
>> >>> Shane Schofield  
>> >>>  
>> >>>  
>> >>> ___  
>> >>> Freesurfer mailing list  
>> >>> Freesurfer@nmr.mgh.harvard.edu  
>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>> >>  
>> >> ___  
>> >> Freesurfer mailing list  
>> >> Freesurfer@nmr.mgh.harvard.edu  
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>> >>  
>> >>  
>> >> The information in this e-mail is intended only for the person to  
>> >> whom it is  
>> >> addressed. If you believe this e-mail was sent to you in error and  
>> >> the e-mail  
>> >> contains patient information, please contact the Partners Compliance  
>> >> HelpLine at  
>> >> http://www.partners.org/complianceline . If the e-mail was sent to  
>> >> you in error  
>> >> but does not contain patient information, please contact the sender  
>> >> and properly  
>> >> dispose of the e-mail.  
>> >  
>> >  
>> > ___  
>> > Freesurfer mailing list  
>> > Freesurfer@nmr.mgh.harvard.edu  
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  
>>  
>> --  
>> 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  

[Freesurfer] Bits of dura being captured as GM ..

[Shane S]

Hi Freesurfer Users,

I am checking my data and there are many scans with a bit of dura being 
captured as GM. I have attached some screenshots below. This happens in more 
than 50% of my subjects.  I am removing them manually them using Freeview, then 
running the autorecon-pial. But this will take a lot of time on 200+ subjects.. 
Does anyone have any tips to deal with these little inclusions? 
Thanks =)



Best Wishes,
Shane___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

I added --surf mytemplate lh to the command and now it works.

Thank you so much!!

- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 11. April 2017 20:13:21
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

oh, I think I see the problem now. The input is surface-based data, but 
you did not include a --surf subject hemi option, so it thinks that it 
is a volume.


On 04/11/2017 12:58 PM, Clara Kühn wrote:
> Hi Doug,
>
> attached you find the rmanova directory after I ran the mri_glmfit command. I 
> hope this can shed some light on the problem...
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 11. April 2017 18:29:52
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> Still a bit of a mystery. Can you tar up and send me the rmanova folder?
>
>
> On 04/11/2017 11:18 AM, Clara Kühn wrote:
>> Oh, yes, sorry:
>> command line:
>> mri_glmfit --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>>  --fsgd 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>>  doss --C 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>>
>> output:
>> gdfReadHeader: reading 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>> Continuous Variable Means (all subjects)
>> 0 pre-vs-post 0 1
>> Class Means of each Continuous Variable
>> 1 Subject1   0.
>> 2 Subject2   0.
>> 3 Subject3   0.
>> 4 Subject4   0.
>> 5 Subject5   0.
>> 6 Subject6   0.
>> 7 Subject7   0.
>> 8 Subject8   0.
>> 9 Subject9   0.
>> 10 Subject10   0.
>> 11 Subject11   0.
>> 12 Subject12   0.
>> 13 Subject13   0.
>> 14 Subject14   0.
>> 15 Subject15   0.
>> 16 Subject16   0.
>> 17 Subject17   0.
>> 18 Subject18   0.
>> 19 Subject19   0.
>> 20 Subject20   0.
>> 21 Subject21   0.
>> 22 Subject22   0.
>> 23 Subject23   0.
>> 24 Subject24   0.
>> 25 Subject25   0.
>> 26 Subject26   0.
>> 27 Subject27   0.
>> 28 Subject28   0.
>> 29 Subject29   0.
>> 30 Subject30   0.
>> 31 Subject31   0.
>> 32 Subject32   0.
>> 33 Subject33   0.
>> 34 Subject34   0.
>> 35 Subject35   0.
>> 36 Subject36   0.
>> 37 Subject37   0.
>> 38 Subject38   0.
>> 39 Subject39   0.
>> 40 Subject40   0.
>> INFO: gd2mtx_method is doss
>>
>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> cwd 
>> /data/p_npsy001_neurotrain/new_syntax_training/Pilot2-NachtestungPilot0/logfiles
>> cmdline mri_glmfit --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>>  --fsgd 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>>  doss --C 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>> sysname  Linux
>> hostname etsch
>> machine  x86_64
>> user ckuehn
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 0
>> y
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>> logyflag 0
>> usedti  0
>> FSGD 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>> glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
>> IllCondOK 0
>> ReScaleX 1
>> DoFFx 0
>> Creating output directory 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
>> Loading y from 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>> INFO: gd2mtx_method is doss
>> Saving design matrix to 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//Xg.dat
>> Normalized matrix condition is 1
>> Matrix condition is 40
>> Pruning voxels by thr: 0.00
>> Found 97361 voxels in mask
>> Saving mask to 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//mask.mgh
>> search space = 97361.00
>> DOF = 39
>> Starting fit and test
>> Fit completed in 0.551233 minutes
>> Computing spatial AR1 in volume.
>> fMRIspatialAR1(): hit 0 voxels
>> WARNING: no voxels in AR1 computation
>> Residual: ar1mn = (-nan,-nan,-nan) fwhm = (-nan,-nan,-nan) -nan
>> Writing results
>> C-pre-vs-post
>>   maxvox sig=3.9739  F=18.6032  at  index 4623 0 0