Re: [Freesurfer] error glm-fit-sim (message 11)

[Caroline Beelen]

External Email - Use Caution

Few clusters survive glm fit. No clusters seem to survive glm-fit-sim (when 
visualizing). However, I'm not sure if I should also see this in a text file. 
Opening cache.th40(or 30).abs.sig.cluster.summary it seems to have found no 
clusters. At least, under the line ClusterNo Max VtxMax Size MNIX MNIY etc. 
nothing is written.

But does a lack of significant clusters also explain the weird messages of 
"colortable with 1 entries read (originally none)" (& "CTABisEntryValid: index 
-1 was OOB" & "Resource temporarily unavailable") that show up in the terminal?

Thanks very much, Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens 
freesurfer-requ...@nmr.mgh.harvard.edu
Verzonden: dinsdag 9 oktober 2018 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 176, Issue 9

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Today's Topics:

   1. FW: RE: error glm-fit-sim (Caroline Beelen)
   2. Re: output values of vertices on surface into a   textfile
  (Sims, Sara A)
   3. Re: output values of vertices on surface into a textfile
  (Bruce Fischl)
   4. Re: output values of vertices on surface into a   textfile
  (Sims, Sara A)
   5. Re: Hippocampal segmentation with an additional scan ERROR
  kvlGEMSMatlab (Pradeep)
   6. Re: Hippocampal segmentation with an additional scan ERROR
  kvlGEMSMatlab (Iglesias Gonzalez, Eugenio)
   7. hippocampal subfields (Marcel Heers)
   8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio)
   9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert)
  10. Talairach failed in monkey brain (Frehiwot Woldeyes)
  11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.)
  12. Mri Convert Help (Justin Arnett)
  13. Re: Mri Convert Help (Greve, Douglas N.,Ph.D.)
  14. Re: Recon-all with/without T2 give the same stats
  (Greve, Douglas N.,Ph.D.)
  15. Re: Recon-all with/without T2 give the same stats (Jianzhong Chen)
  16. m.khalil...@sutech.ac.ir sent you files via WeTransfer
  (WeTransfer)
  17. very bad result using "mris_ca_train" and "mris_ca_label"
  (Maedeh Khalilian)
  18. Re: Talairach failed in monkey brain (Greve, Douglas N.,Ph.D.)
  19. Re: Recon-all with/without T2 give the same stats
  (Greve, Douglas N.,Ph.D.)
  20. Re: very bad result using "mris_ca_train" and "mris_ca_label"
  (Bruce Fischl)
  21. Re: Extract individual vertex thickness values from cortical
  parcellations (Greve, Douglas N.,Ph.D.)
  22. Re: nu_correct disk i/o issues (Greve, Douglas N.,Ph.D.)
  23. Re: masking cortical thickness (Greve, Douglas N.,Ph.D.)


------

Message: 1
Date: Mon, 8 Oct 2018 16:12:06 +
From: Caroline Beelen 
Subject: [Freesurfer] FW: RE: error glm-fit-sim
To: "freesurfer-boun...@nmr.mgh.harvard.edu"
,
"freesurfer@nmr.mgh.harvard.edu"
Message-ID:
<4051d561c94b40e0b641202b7bad7...@icts-s-exmbx25.luna.kuleuven.be>
Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

The command:

gop@gop-linux:~/freesurfer$ freeview -f 
$SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
 -viewport 3d

The output:

reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)

The command with a bit less strict significance level:

gop@gop-linux:~/freesurfer$ freeview -f 
$SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
 -viewport 3d

The output:

reading colortable from annotation file...
colortable with 1 entries read (originally none)
col

[Freesurfer] FW: RE: error glm-fit-sim

[Caroline Beelen]

External Email - Use Caution

The command:

gop@gop-linux:~/freesurfer$ freeview -f 
$SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
 -viewport 3d

The output:

reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)
CTABisEntryValid: index -1 was OOB
Resource temporarily unavailable
Resource temporarily unavailable
B
ginally none)

The command with a bit less strict significance level:

gop@gop-linux:~/freesurfer$ freeview -f 
$SUBJECTS_DIR/avgsubject/surf/lh.inflated:overlay=lh.area.glmdir/groupeffect/cache.th40.abs.sig.cluster.mgh:overlay_threshold=3,5:annot=lh.area.glmdir/groupeffect/cache.th40.abs.sig.ocn.annot
 -viewport 3d

The output:

reading colortable from annotation file...
colortable with 1 entries read (originally none)
colortable with 1 entries read (originally none)

(and then it says no more).

Both commands visualize the data, but no clusters are found.
Is this how it should be? Does it mean that there is a problem with reading 
colortables or not?

Best, Caroline

Message: 2
Date: Mon, 1 Oct 2018 17:10:28 +
From: "Greve, Douglas N.,Ph.D." 
mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] error glm-fit-sim
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu<mailto:504d6069-399f-163d-39a9-dcc6c02d3...@mgh.harvard.edu>>
Content-Type: text/plain; charset="Windows-1252"

What says that? What command are you running? What is the other terminal
output?


On 10/01/2018 04:54 AM, Caroline Beelen wrote:
>
> External Email - Use Caution
>
> Dear FS,
>
> I followed the group analysis page for glm analysis and it worked fine
> until the final step. I?m using version 5.3. After performing
> glm-fit-sim it says ?glm-fit done? (for all files), but when trying to
> open these it says:
>
> ?Reading colortable from annotation file?
>
> Colortable with 1 entries read (originally none)
>
> Colortable with 1 entries read (originally none)
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> CTABisentryvalid: index -1 was 00B
>
> Resource temporarily unavailable
>
> Resource temporarily unavailable?
>
> (etc..)
>
> It opens, but nothing is visible and I have the feeling it cannot open
> color files??
>
> MRI glmfit gives positive clusters for some values. I therefore used
> the abs sign for glm-fit-sim.
>
> What might be wrong?
>
> Thanks. Caroline

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[Freesurfer] error glm-fit-sim

[Caroline Beelen]

External Email - Use Caution

Dear FS,

I followed the group analysis page for glm analysis and it worked fine until 
the final step. I'm using version 5.3. After performing glm-fit-sim it says 
"glm-fit done" (for all files), but when trying to open these it says:

"Reading colortable from annotation file...
Colortable with 1 entries read (originally none)
Colortable with 1 entries read (originally none)
CTABisentryvalid: index -1 was 00B
Resource temporarily unavailable
CTABisentryvalid: index -1 was 00B
Resource temporarily unavailable
Resource temporarily unavailable"
(etc..)

It opens, but nothing is visible and I have the feeling it cannot open color 
files??
MRI glmfit gives positive clusters for some values. I therefore used the abs 
sign for glm-fit-sim.

What might be wrong?

Thanks. Caroline





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Re: [Freesurfer] Manuel edits (message 5)

[Caroline Beelen]

Dear Bruce,

Thank you for answering my question. However, I'm still in a bit confused... 
Therefore, I have one more question:

Would it then be best to choose a particular WM intensity value to rely upon 
for adding control points or to rely upon sight?

Thank you very much!

Kind regards, Caroline Beelen

-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens 
freesurfer-requ...@nmr.mgh.harvard.edu
Verzonden: donderdag 18 mei 2017 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Freesurfer Digest, Vol 159, Issue 31

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freesurfer@nmr.mgh.harvard.edu

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


Today's Topics:

   1. Postdoctoral position in psychosis studies - Oslo,Norway
  (Tiril Pedersen Gurholt)
   2. manuel edits (Caroline Beelen)
   3. Re: Question of longitudinal processing (jahanvi patel)
   4. Re: Mean gray-white contrast for each ROI (Douglas N Greve)
   5. Re: manuel edits (Bruce Fischl)
   6. Re: Freesurfer white matter outer edge to volume (Douglas N Greve)
   7. Re: mri_mcsim for individual subjects and references
  {Disarmed} (Douglas N Greve)
   8. Improving the brainmask.mgz using aseg.mgz for gettingrid of
  dura (Karteek Popuri)
   9. Re: Improving the brainmask.mgz using aseg.mgz for getting
  rid of dura (Douglas N Greve)
  10. Re: Improving the brainmask.mgz using aseg.mgz for getting
  rid of dura (Bruce Fischl)


--

Message: 1
Date: Thu, 18 May 2017 12:04:49 +
From: Tiril Pedersen Gurholt 
Subject: [Freesurfer] Postdoctoral position in psychosis studies -
Oslo,   Norway
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID: <9e8a081e-d148-4b08-b276-dd5b58c20...@medisin.uio.no>
Content-Type: text/plain; charset="utf-8"

Dear All,

At the NORMENT ? K.G. Jebsen Research Centre for Psychosis Research, a Centre 
of Excellence, Institute of Clinical Medicine, University of Oslo, Oslo 
University Hospital and Diakonhjemmet Hospital, Norway, there is a position 
available as a postdoctoral student with employment at Diakonhjemmet hospital. 
The research area is psychiatric neuroimaging with focus on obstetric 
complications and the analysis of structural and functional, DTI and ASL MR 
imaging datasets with regard to developmental trajectories and genetic, 
environmental and phenotypic variation. Applicants should have a doctoral 
degree (PhD) in psychiatry or a related medical discipline, neuroimaging, 
computer science, bioinformatics, psychology, or equivalent. Applicants who 
have handed in their dissertation for evaluation are also encouraged to apply, 
caveat the dissertation is approved. Application deadline is June 15th, 2017. 
For further information and to submit an application please see the website of 
Diakonh  jemmet
  H  ospital, Oslo, Norway:
https://www.webcruiter.no/WcMain/advertviewpublic.aspx?oppdragsnr=3420277973&company_id=201412&Link_source_id=0&use_position_site_header=0&culture_id=NB-NO

Best regards,

Tiril Gurholt
---
Tiril Gurholt
Postdoctoral Fellow
Psychosis Research Centre, NORMENT
Institute of Clinical Medicine, University of Oslo, Norway

http://www.med.uio.no/norment/


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------

Message: 2
Date: Thu, 18 May 2017 12:40:12 +
From: Caroline Beelen 
Subject: [Freesurfer] manuel edits
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:
<02267843e84c41ad9d0490fc5939f...@icts-s-exmbx25.luna.kuleuven.be>
Content-Type: text/plain; charset="us-ascii"

Dear FS team,

I have two questions regarding manuel editing. We were looking at inter-rater 
reliability, but noticed it was not too high... However, during editing we used 
different criteria. Therefore I would like to ask:



1.  Does the order of pial correction, topological deficit, wm corrections 
and control points editing matters? You seem to assume on your website for 
instan

[Freesurfer] manuel edits

[Caroline Beelen]

Dear FS team,

I have two questions regarding manuel editing. We were looking at inter-rater 
reliability, but noticed it was not too high... However, during editing we used 
different criteria. Therefore I would like to ask:



1.  Does the order of pial correction, topological deficit, wm corrections 
and control points editing matters? You seem to assume on your website for 
instance that pial corrections would come before wm corrections/control points, 
but is this necessarily the case?


2.  When the wm intensity value is below 110, voxel inclusions might be 
needed. On the website is written: "when you feel like there is wm underneath 
you can add control points (...)". How to make a decision on this matter: based 
on sight or on wm intensity values?
For instance, often the WM values are either 0 or 80 or above... Would it be 
good to assume that wm intensity values above 80 are actually wm, regardless of 
how it visually would look like? Likewise, would it be good to assume that 
areas where it says the wm intensity value is 0, that these areas are actually 
not wm, regardless of whether it might look like wm?  So, basically, it is 
correct to make your decision only based on wm intensity values?

Thank you for your reply.

Kind regards,

Caroline Beelen
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[Freesurfer] visualize corrected results

[Caroline Beelen]

Dear FS,

I have a question on visualizing results from GLM analysis... How can I 
visualize corrected results in Freeview after having applied bonferroni/FDR 
correction (somewhere else)?
I saw it is not possible (error: masking file missing) -and was told it is not 
necessary- to apply monte carlo simulation on results obtained via aparc-files 
from DK-atlas.

Thank you very much!

Regards, Caroline

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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
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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 150, Issue 14

[Caroline Beelen]

sert your 
> lesions. First run recon-all with -autorecon1 -autorecon2 instead of 
> -all. Then, in matlab,
>
>
> aseg = MRIread('aseg.auto.mgz'); % FreeSurfer aseg
>
> manlesion = MRIread('manlesion.nii.gz'); % Manual lesion, whatever 
> format, but should be binary
>
> ind = find( (aseg.vol == 2 | aseg.vol == 41) & manlesion.vol != 0);
>
> newaseg = aseg;
>
> newaseg.vol(ind) = 77;
>
> MRIwrite(newaseg,'aseg.mgz'); % This will overwrite the aseg.mgz, so 
> make a backup
>
>
> Then run recon-all with -autorecon2-cp -autorecon3
>
>
>
> On 8/1/16 7:35 AM, Silas wrote:
>>
>>
>> Dear FreeSurfer team,
>>
>>
>> I'm doing a structural analysis with 50 MS patients and 50 healthy 
>> controls (T1, T2 and FLAIR). The MS patients have multiple lesions 
>> mainly in white matter. My co-worker did manual editing (bullet 
>> points) in the FLAIR images, and i would like to use these edits when 
>> running recon-all in order to avoid further manual editing.
>>
>>
>> The data i'm working with is already resliced to 1 mm and 
>> co-registered in MNI-space.
>>
>> 1) Can i use this data or would it be preferable to use the original 
>> T1's?
>>
>>
>> My thought was to run the following command:
>>
>> recon-all -subject subjectname -i /path/to/input_volume -FLAIR 
>> /path/to/FLAIR_volume_with_edits-FLAIRpial  -all
>> 2) Does this look correct? Is there anything i should be aware of? -> 
>> update: Does this command only improve the pial surface? How can i 
>> also improve the white mater segmentation (white) using FLAIR 
>> corrections?
>>
>> 3) Does it make a difference running recon-all -all with the FLAIR 
>> image - compared to running recon-all -autorecon3 with the FLAIR 
>> after running recon-all -all with only the T1?
>>
>> 4) I've also thought about using the lesion segmentation toolbox for 
>> SPM and completely avoid manual editing - is this preferable to using 
>> the FLAIR with manual editing?
>>
>> 5) How is the general strength of analysing corpus callosum 
>> structurally in MS patients using FreeSurfer?
>>
>>
>> Best, Silas
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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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
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/



--

Message: 13
Date: Wed, 10 Aug 2016 17:57:31 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] myaparc
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57aba34b.7030...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

what is the error?

On 08/10/2016 04:45 AM, Caroline Beelen wrote:
>
> Dear FS,
>
> I figured out how to list my ctabe-file (attached). Again, the file 
> myaparc was created but this time I got the following error:
>
> Colortable:aparc.annot.ctab
>
> Annotname: myaparc
>
> Nhitsfile nhits.mgh
>
> Nlabels 6
>
> Labeltresh 0  0.0
>
> Loading freesurfer/fsaverage/surf/lh.orig
>
> 1   9345678 fusiform
>
> 2  145768794 inferiorparietal
>
> 3   79873658 inferiortemporal
>
> (etc)
>
> Mapping unhit to unknown
>
> Found 137851 unhit vertices
>
> Writing annot to freesurfer/fsaverage/lh.myaparc.annot
>
> What goes wrong?
>
> My command line is:
>
> mris_label2annot --subject fsaverage --hemi  lh  --ctab 
> aparc.annot.ctab --annot myaparc  --l lh.fusiform.label
>
> --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh
>
> (I have version 5.3)
>
> Thanks for your help,
>
> Caroline
>
> My command line is:
>
> mris_label2annot --subject fsaverage --hemi  lh  --ctab 
> aparc.annot.ctab --annot myaparc  --l lh.fusiform.label
>
> --l lh.inferiorparietal.label (etc.) --nhits nhits.mgh
>
> (I have version 5.3)
>
> Regards, Caroline
>
> Message: 3
>
> Date: Wed, 3 Aug 2016 09:30:48 -0400
>
> From: Douglas Greve  <mailto:gr...@nmr.mgh.harvard.edu>>
>
> Subject: Re: [Freesurfe

[Freesurfer] myaparc

[Caroline Beelen]

Dear FS,

I figured out how to list my ctabe-file (attached). Again, the file myaparc was 
created but this time I got the following error:

Colortable:aparc.annot.ctab
Annotname: myaparc
Nhitsfile nhits.mgh
Nlabels 6
Labeltresh 0  0.0
Loading freesurfer/fsaverage/surf/lh.orig

1   9345678 fusiform
2  145768794 inferiorparietal
3   79873658 inferiortemporal
(etc)
Mapping unhit to unknown
Found 137851 unhit vertices
Writing annot to freesurfer/fsaverage/lh.myaparc.annot

What goes wrong?

My command line is:
mris_label2annot --subject fsaverage --hemi  lh  --ctab aparc.annot.ctab 
--annot myaparc  --l lh.fusiform.label
  --l lh.inferiorparietal.label (etc.)  --nhits nhits.mgh

(I have version 5.3)

Thanks for your help,

Caroline





My command line is:
mris_label2annot --subject fsaverage --hemi  lh  --ctab aparc.annot.ctab 
--annot myaparc  --l lh.fusiform.label
  --l lh.inferiorparietal.label (etc.)  --nhits nhits.mgh
(I have version 5.3)

Regards, Caroline

Message: 3
Date: Wed, 3 Aug 2016 09:30:48 -0400
From: Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mapping error
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID: 
mailto:f3f77469-16ad-6fdf-f647-80aee162d...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="windows-1252"

what is your command line?


On 8/3/16 6:00 AM, Caroline Beelen wrote:
>
>
>
>



aparc.annot.ctab
Description: aparc.annot.ctab
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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
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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] Freesurfer Digest, Vol 150, Issue 6

[Caroline Beelen]

My command line is:
mris_label2annot --subject fsaverage --hemi  lh  --ctab aparc.annot.ctab 
--annot myaparc  --l lh.fusiform.label 
  --l lh.inferiorparietal.label (etc.)  --nhits nhits.mgh
(I have version 5.3)

Regards, Caroline

Message: 3
Date: Wed, 3 Aug 2016 09:30:48 -0400
From: Douglas Greve 
Subject: Re: [Freesurfer] mapping error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 
Content-Type: text/plain; charset="windows-1252"

what is your command line?


On 8/3/16 6:00 AM, Caroline Beelen wrote:
>
> Dear FS,
>
> An aparc.annot ctab file was created but I got the following error:
>
> Colortable:aparc.annot.ctab
>
> Annotname: myaparc
>
> Nhitsfile nhits.mgh
>
> Nlabels 6
>
> Labeltresh 0 0.0
>
> Loading freesurfer/fsaverage/surf/lh.orig
>
> 1 -1 not found
>
> 2 -1 not found
>
> 3 -1 not found
>
> Etc?
>
> Mapping unhit to unknown
>
> Found 132101 unhit vertices
>
> Writing annot to freesurfer/fsaverage/lh.myaparc.annot
>
> I guess my ctab file is incorrect? I included an example of a label 
> with it.
>
> Thanks again for your help.
>
> Caroline
>
>

-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
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Verzonden: woensdag 3 augustus 2016 18:00
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Onderwerp: Freesurfer Digest, Vol 150, Issue 6

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Today's Topics:

   1. Re: brain mask and T1 are not the same size (Isabelle Deschamps)
   2. Re: Coordinates in TRACULA group analysis (Anri WATANABE)
   3. Re: mapping error (Douglas Greve)
   4. Re: Multiple Comparison Question for surface-based analyses
  (Douglas Greve)
   5. Re: Coordinates in TRACULA group analysis (Anastasia Yendiki)
   6. Re: brain mask and T1 are not the same size (Douglas N Greve)


--

Message: 1
Date: Wed, 3 Aug 2016 10:50:30 +
From: Isabelle Deschamps 
Subject: Re: [Freesurfer] brain mask and T1 are not the same size
To: ""

Message-ID: <8f31a8f6-59c6-4d12-a2a4-2ef526465...@ulaval.ca>
Content-Type: text/plain; charset="us-ascii"

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Message: 2
Date: Wed, 3 Aug 2016 20:19:09 +0900
From: Anri WATANABE 
Subject: Re: [Freesurfer] Coordinates in TRACULA group analysis
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

Hi Anastasia,

Thank you for your kind explanation. I can be understanding how TRACULA
tracts white matter pathways.
At each position (in training subjects, not in new subjects of my data)
probability that next goes for which direction to every labels in the
aparc+aseg (not with setting a certain ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects
(your publication in 2011) and they are based on manual labeling (the
manual labeling tracts are referred to Wakana et al. 2007). Then when white
matter pathways are reconstructed in my subjects, TRACULA computes
anatomical priors in each subjects in my data in pre-processing and
probability distributions from anatomical priors and by fitting
ball-and-stick model.
Is this comprehension ok?

Best Regards,
Anri



**


?? ??
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - Instead of hard-coding some ROIs in the white matter that the
> tract is forced to go through, TRACULA uses information like "what is the
> probability that this tract goes lateral/anterior/etc to XXX", where XXX
> any of the labels in the aparc+aseg. TRACULA computes these prior
> probabilities from a set of training subjects, where the tracts have been
> labeled manually. So it knows how likely a tract is to go through a certain
> aparc+aseg label, or to he left, right, ante

[Freesurfer] mris_label2annot

[Caroline Beelen]

Dear FS,

Sorry to bother again, but I'm currently in need for some quick help.
Today, I also ran into another problem. I tried to display only few ROI's in 
Freeview instead of the whole brain. Therefore, I tried to create a new 
annotation file consisting of only few labels (from regions of DK-atlas) and I 
used the mri_annotation2label on my own created fsaverage to get these labels. 
This worked fine.
Then I used the command of mris_label2annot to create the annotation file, but 
part of the command, --ctab aparc.annotation.ctab, is not recognized. Replacing 
it by -ctab  fsaverage/label/lh.aparc.annot (file exists in the label folder of 
fsaverage) gives me the following error: CTABreadASCII: badly formed file. 
ERROR: reading fsaverage/label/lh.aparc.annot. I couldn't find, or create, any 
other aparc.annot file.

What would be the right command (for the part of ctab) to get mris_label2annot 
working? Or is there perhaps a better way to only display certain ROI's in 
Freeview? (the latter I could still explore but assistance is certainly 
appreciated)

Thanks a lot!
Caroline


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[Freesurfer] significance overlay Freeview

[Caroline Beelen]

Dear FS,

Yes, I'm running FS 5.3. :)
How can I visualize the significance overlay (correctly)?  Which command should 
I use to view a significance overlay in freeview in FS 5.3? See also my email 
below.

Thank you very much in advance!
Best, Caroline

Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 
6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

> On Jul 29, 2016, at 9:11 AM, Caroline Beelen 
> mailto:caroline.bee...@kuleuven.be>> wrote:
>
> Dear FS team,
>
> Apologies in advance for perhaps again a rather basic question. I attempted 
> to load the aparc overlay in freeview by using the written command from the 
> group analysis page, however it failed to load correctly.
>
> I used the following command:
> freeview -f 
> fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
> and dyslect is the contrast folder within this file (main effect of 
> dyslexia), containing a sig.mgh file (all seems fine)
>
> Unfortunately, I got an error that it does not recognize 
> overlay_treshold=4,5. I used freeview ?h and tried certain commands alike, 
> but they didnt work. When leaving out this part, I got another error that it 
> failed to recognize annot_outline=1. Again, leaving this out too, freeview 
> loads itself and the DK-regions become visible. However, nothing else seems 
> to get activated, and even not when putting configure overlay (which is set 
> to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.
> When looking at the command line it says that it implemented the colortable 
> of DK-atlas (even twice), but it tells me nothing else. Also, after closing 
> and reloading Freeview by using the similar command and then clicking on 
> configure overlay the screen sometimes gets stuck, giving me the impression 
> that something must be wrong with the command.
>
> Could you please help me out and provide me the right command-line for 
> loading the overlay of the significance map of 
> roi.lh.area.dyslect_basic.glmdir/dyslect?
>
> Thanks in advance!
>
> Kind regards, Caroline
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Phd-candidate KU Leuven
Gezins-en Orthopedagogiek
Vanderkelenstraat 32, 3000 Leuven
Belgium

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Re: [Freesurfer] significance overlay in freeview

[Caroline Beelen]

Dear Ruopeng,



Yes, I'm running FS 5.3. :)

But then how can I see the correct significance overlay? Cause even when 
leaving out some commands (which may or may not work in 5.3), freeview does 
load, but seems to only display the DK-atlas on fs average (... and gets stuck 
sometimes too), as I described below.

I cant find the right command ...



So I guess my actual question is: Which command should i use to view a 
(correct) significance overlay in FS 5.3?



Thank you very much for your help!



Regards, Caroline


 Hi Caroline,

Are you running FS 5.3? The command on the webpage is based on the upcoming 
6.0, I believe. So some of the command line options are not available in 5.3.

Best,
Ruopeng

> On Jul 29, 2016, at 9:11 AM, Caroline Beelen  
> wrote:
>
> Dear FS team,
>
> Apologies in advance for perhaps again a rather basic question. I attempted 
> to load the aparc overlay in freeview by using the written command from the 
> group analysis page, however it failed to load correctly.
>
> I used the following command:
> freeview -f 
> fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
>  -viewport 3d
> ? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
> and dyslect is the contrast folder within this file (main effect of 
> dyslexia), containing a sig.mgh file (all seems fine)
>
> Unfortunately, I got an error that it does not recognize 
> ?overlay_treshold=4,5?. I used freeview ?h and tried certain commands alike, 
> but they didn?t work. When leaving out this part, I got another error that it 
> failed to recognize ?annot_outline=1?. Again, leaving this out too, freeview 
> loads itself and the DK-regions become visible. However, nothing else seems 
> to get activated, and even not when putting ?configure overlay? (which is set 
> to sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.
> When looking at the command line it says that it implemented the colortable 
> of DK-atlas (even twice), but it tells me nothing else. Also, after closing 
> and reloading Freeview by using the similar command and then clicking on 
> ?configure overlay? the screen sometimes gets stuck, giving me the impression 
> that something must be wrong with the command.
>
> Could you please help me out and provide me the right command-line for 
> loading the overlay of the significance map of 
> ?roi.lh.area.dyslect_basic.glmdir/dyslect??
>
> Thanks in advance!
>
> Kind regards, Caroline
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[Freesurfer] significance overlay in freeview

[Caroline Beelen]

Dear FS team,

Apologies in advance for perhaps again a rather basic question. I attempted to 
load the aparc overlay in freeview by using the written command from the group 
analysis page, however it failed to load correctly.

I used the following command:
freeview -f 
fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=roi.lh.area.dyslect_basic.glmdir/dyslect/sig.mgh:overlay_threshold=4,5
 -viewport 3d

? roi.lh.area.dyslect_basic.glmdir is the file obtained from the GLM-analysis 
and dyslect is the contrast folder within this file (main effect of dyslexia), 
containing a sig.mgh file (all seems fine)


Unfortunately, I got an error that it does not recognize 
"overlay_treshold=4,5". I used freeview -h and tried certain commands alike, 
but they didn't work. When leaving out this part, I got another error that it 
failed to recognize "annot_outline=1". Again, leaving this out too, freeview 
loads itself and the DK-regions become visible. However, nothing else seems to 
get activated, and even not when putting "configure overlay" (which is set to 
sig.mgh) to 1.3 as minimum and 3 as maximum. So basically nothing happens.
When looking at the command line it says that it implemented the colortable of 
DK-atlas (even twice), but it tells me nothing else. Also, after closing and 
reloading Freeview by using the similar command and then clicking on "configure 
overlay" the screen sometimes gets stuck, giving me the impression that 
something must be wrong with the command.

Could you please help me out and provide me the right command-line for loading 
the overlay of the significance map of 
"roi.lh.area.dyslect_basic.glmdir/dyslect"?

Thanks in advance!

Kind regards, Caroline




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[Freesurfer] GLM significance table

[Caroline Beelen]

Dear FS team,

I tried to run GLM-analysis using aparc stats files. At first I created these 
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and 
checked whether they looked ok, which they did (values were pretty similar). 
Then I used the following command (for example):

Mri_glmfit
-- table aparc_rh_thickness_stats.txt
-- fsgd gender_dys.fsgd (see attached; example of a fsgd-file)
-- C Int.mtx
-- C Dys.mtx
-- C Gender.mtx
-- glmdir roi.gender_dyslect.rh.thickness.glmdir

The file was created and it contained a sig.table.dat folder. However, the 
values in this folder are all quite low. According to information found on your 
website they should correspond to (-)log10(p) values. I found mainly values 
between -1 and 1, but even of -0.03, which would correspond to a p-value of 1.5 
(non-existing). Could you please explain to me what I did wrong?

Thank you very much!

Kind regards,
Caroline



gender_dys.fsgd.docx
Description: gender_dys.fsgd.docx
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[Freesurfer] GLM significance table

[Caroline Beelen]

Dear FS team,

I tried to run GLM-analysis using aparc stats files. At first I created these 
files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and 
checked whether they looked ok, which they did (values were pretty similar). 
Then I used the following command (for example):

Mri_glmfit
-- table aparc_rh_thickness_stats.txt
-- fsgd gender_dys.fsgd (see attached; example of a fsgd-file)
-- C Int.mtx
-- C Dys.mtx
-- C Gender.mtx
-- glmdir roi.gender_dyslect.rh.thickness.glmdir

The file was created and it contained a sig.table.dat folder. However, the 
values in this folder are all quite low. According to information found on your 
website they should correspond to (-)log10(p) values. I found mainly values 
between -1 and 1, but even of -0.03, which would correspond to a p-value of 1.5 
(non-existing). Could you please explain to me what I did wrong?

Thank you very much!

Kind regards,
Caroline



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[Freesurfer] 3 analyses questions

[Caroline Beelen]

Dear FS team,

I would like to correct for multiple comparisons after I run command-line GLM 
analysis on aparc.stats tables (my ROI's are few regions from DK-atlas). I 
tried to do the Monte Carlo simulation but get an error that a masking-file is 
missing. In general, how could I correct for multiple comparisons when using 
aparcstats2tables in GLM?

Alternatively I performed the analysis in Qdec (excluding a nuisance factor to 
be able to do so). I tried to implement few ROI's from DK-atlas, one at a time, 
such as left fusiform area. However, when running the analysis it seems to take 
into account the whole area of the brain and investigates its correlation with 
a particular selected ROI (i.e. left fusiform area). Would this kind of 
analysis give me the same results as when only performing stats on this 
particular region?

Actually, for my analysis I'm only interested in few regions of DK-atlas and, 
if possible, would like to perform it on only these regions, leaving out all of 
the rest (I'm correcting for ICV anyways). In that case I would also have to 
correct for fewer multiple comparisons... How could I achieve this in Qdec 
and/or command-line GLM?

Thanks in advance for your help.

Regards, Caroline
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Re: [Freesurfer] Freesurfer Digest, Vol 147, Issue 29

[Caroline Beelen]

nd 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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Message: 3
Date: Tue, 17 May 2016 12:48:07 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] ERROR: cannot unpack mosiacs without ASCII
header
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <573b4b47.2020...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Please remember to include previous correspondence otherwise we can't keep 
track of the problem!
Eg, I don't have the previous email to see what the error was. Is it possible 
that the disk filled up?

On 05/17/2016 09:49 AM, Aloi, Joseph wrote:
> Hi Doug,
>
> Yes, you are correct- data I have previously processed without any 
> problems is no longer being processed.
>
> My version of freesurfer is 5.3.0; I only downloaded it a few weeks 
> ago so I have not changed my freesurfer version recently.
>
> Thanks!
>
> Joseph Aloi
> Graduate Student, MD/PhD Scholars Program Department of Pharmacology 
> and Experimental Neuroscience University of Nebraska Medical Center
>
> Neurobehavioral Research Assistant, Center For Neurobehavioral 
> Research Boys Town National Research Hospital
>
>
>
> The information in this e-mail may be privileged and confidential, 
> intended only for the use of the addressee(s) above. Any unauthorized 
> use or disclosure of this information is prohibited. If you have 
> received this e-mail by mistake, please delete it and immediately 
> contact the sender.
>
>
> ___
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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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Message: 4
Date: Tue, 17 May 2016 13:03:39 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] wm parcellation
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <573b4eeb.70...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Add  --a2009s to your command line. Note that the colors will not differ 
between the ctx and wm labels.

On 05/17/2016 07:28 AM, Caroline Beelen wrote:
>
> Dear FS team,
>
> Thank you for your answers before (email: WmParc). We now realize that 
> we?ve formulated our question wrong, since our problem is mainly in 
> creating the wmparc.a2009s.mgz file. We ran the following command:
>
> mri_aparc2aseg --s  --labelwm --hypo-as-wm --rip-unknown 
> --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz 
> ( was replaced by our subject and the ribbon command was set 
> to ?noribbon? because we otherwise received the message the that the 
> ribbon command was unknown.)
>
>
> If we run this command, we can extract grey matter labels with 
> fslmaths (e.g. 11136 for the left planum temporale), but not the white 
> matter labels we are looking for (this is 13136 for the left planum 
> temporale).
>
> The problem seems to be in the labelling of the white matter.
>
> Many thanks.
>
> Jolijn & Caroline
>
>
>
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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/



--

Message: 5
Date: Tue, 17 May 2016 13:04:01 -0400
From: Douglas N Greve 
Subject: Re: [Freesurfer] Same coordinates for all labels
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <573b4f01.8010...@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed

Set the threshold to be something non-zero (eg, ---thmin .0001)

On 05/17/2016 10:47 AM, Nabin Koirala wrote:
> Dear FS team,
>
> I am trying to find the centroid using mri_surfcluster

[Freesurfer] wm parcellation

[Caroline Beelen]

Dear FS team,
Thank you for your answers before (email: WmParc). We now realize that we've 
formulated our question wrong, since our problem is mainly in creating the 
wmparc.a2009s.mgz file. We ran the following command:
mri_aparc2aseg --s  --labelwm --hypo-as-wm --rip-unknown --ribbon --o 
mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by 
our subject and the ribbon command was set to 'noribbon' because we otherwise 
received the message the that the ribbon command was unknown.)

If we run this command, we can extract grey matter labels with fslmaths (e.g. 
11136 for the left planum temporale), but not the white matter labels we are 
looking for (this is 13136 for the left planum temporale).
The problem seems to be in the labelling of the white matter.

Many thanks.
Jolijn & Caroline

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[Freesurfer] WmParc

[Caroline Beelen]

Dear FS team,

We want to create a ROI based on the wm parcellation in the 2009s atlas. We ran 
the following command:
mri_aparc2aseg --s  --labelwm --hypo-as-wm --rip-unknown --ribbon --o 
mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz ( was replaced by 
our subject)

We get the following error: option --ribbon unknown.

The ribbon.mgz folders exist and are located in the right directory. We also 
tried to re-create them and this worked fine, but again after running the 
command above we got the same error.
If we changed the command --ribbon to -- no ribbon, the script ran, but when we 
looked at the stats-file, only cortical grey matter labels were segmented (no 
wm).
The same applies to other subjects we tried.

Could you please help us out?

Many thanks.
Jolijn & Caroline

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Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Hi Bruce,

Thank you very much! :) 
I think somethings wrong with gnumeric indeed just discovered that gedit 
works fine. 

As for 3, that would mean that the data are not in native space? I'm trying to 
understand this concept of "summary statistics" :-).

Thanks again in advance.

Caroline



-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 13:59
Aan: Freesurfer support list 
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
something strange with gnumeric and I'm not sure we are qualified to help you.

As for 3, the tables contain summary stats and so don't need to be mapped into 
any common space.

cheers
Bruce


On Thu, 17 Mar 2016, Caroline
Beelen wrote:

> 
> Dear FS,
> 
>  
> 
> 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects 
> A01_T1
> 
> > A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed 
> > by)
> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, 
> it generated the table attached. Why are the mean cortical thickness 
> values sometimes depicted wrong and how can I change this (or do I 
> need to do this by hand)?
> 
>  
> 
> 2. I noticed aparcstats2table doesn’t generate a mean volume (column 
> AJ is empty). Is that supposed to be the case?
> 
>  
> 
> 3. A final question: the aparcstats2table and asegstats2table contain 
> data in native space. Before loading Qdec data needs to be smoothed 
> onto the average subject (using qcache). As s I understand correctly 
> from your answer below and the tutorial I could either just use these 
> values to create the qdectable.dat file or just load the tables in Qdec 
> itself.
> 
> Does that mean that the values of these tables somehow (have) 
> change(d) during the smoothing process?
> 
>  
> 
> Sorry if my questions are rather basic…, but I try to fully 
> understand. J
> 
> Thanks again for responding in advance.
> 
>  
> 
> Kind regards,
> 
>  
> 
> Caroline
> 
> > 
> 
>  
> 
>  
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
> Verzonden: woensdag 16 maart 2016 15:38
> Aan: freesurfer@nmr.mgh.harvard.edu
> Onderwerp: Re: [Freesurfer] gnumeric file
> 
>  
> 
>  
> 
> On 3/16/16 6:52 AM, Caroline Beelen wrote:
>
>   Hi FS team,
>
>    
>
>   Sorry for these rather basic questions…
>
>    
>
>   I'm not sure whether the gnumeric file is an ascii file (see
>   mails below). Attached you'll find the file. It seems the case
>   when you open it in the terminal screen that the nr's look fine
>   (with command cat). However as soon as you type the command
>   gnumeric and so on, it creates a wrong table from the start (see
>   file attached). Can I somehow change this?
> 
> How did you create this file? The aparcstats2table command produces a 
> simple ascii file.
>
>    
>
>   I have an additional question:
>
>   I was looking at the Qdec info (tutorial) and I am not totally
>   sure how to create the table.dat file… Where to get the volume
>   measures from, if you’d like to include those? The statistical
>   folder (where the tables are from)?
> 
> Run asegstats2table and/or aparcstats2table to create a table of the 
> volumes, then extract the values you need. BTW, you don't have to have 
> volume measures in the qdec table.
>
>    
>
>   Thank you for responding in advance.
>
>    
>
>   Kind regards, Caroline
>
>    
>
>   -Oorspronkelijk bericht-
>
>   Van: freesurfer-boun...@nmr.mgh.harvard.edu
>   [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N
>   Greve
>
>   Verzonden: dinsdag 8 maart 2016 0:24
>
>   Aan: freesurfer@nmr.mgh.harvard.edu
>
>   Onderwerp: Re: [Freesurfer] mean thickness
>
>    
>
>   the table file lh.aparc.thickness.table should be an ascii file.
>   when you look at it with cat/more/less, what do you see? Can you
>   send that table file?
>
>    
>
>    
>
>    
>
>   On 03/07/2016 04:33 AM, Caroline Beelen wrote:
>
>   > Hi Bruce,
>
>   >
>
>   > I'm a beginner in FS, so I just followed tutorial instructions
>   for generating the files carefully...
>
>   > I generated it by typing in for instance (after rec

Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Dear FS

I typed in: aparcstats2table --hemi lh --meas thickness --subjects A01_T1
> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed by) 
> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, it 
> generated the table attached in the previous mail.

Thank you with regards to the second question.. However, for volumes 
aparcstats2table it doesn't generate a mean volume (column AJ is empty). Is 
that supposed to be?

Kind regards,
Caroline
>

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
Verzonden: woensdag 16 maart 2016 15:38
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] gnumeric file


On 3/16/16 6:52 AM, Caroline Beelen wrote:
Hi FS team,

Sorry for these rather basic questions...

I'm not sure whether the gnumeric file is an ascii file (see mails below). 
Attached you'll find the file. It seems the case when you open it in the 
terminal screen that the nr's look fine (with command cat). However as soon as 
you type the command gnumeric and so on, it creates a wrong table from the 
start (see file attached). Can I somehow change this?
How did you create this file? The aparcstats2table command produces a simple 
ascii file.


I have an additional question:
I was looking at the Qdec info (tutorial) and I am not totally sure how to 
create the table.dat file... Where to get the volume measures from, if you'd 
like to include those? The statistical folder (where the tables are from)?
Run asegstats2table and/or aparcstats2table to create a table of the volumes, 
then extract the values you need. BTW, you don't have to have volume measures 
in the qdec table.


Thank you for responding in advance.

Kind regards, Caroline

-Oorspronkelijk bericht-
Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas N Greve
Verzonden: dinsdag 8 maart 2016 0:24
Aan: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: Re: [Freesurfer] mean thickness

the table file lh.aparc.thickness.table should be an ascii file. when you look 
at it with cat/more/less, what do you see? Can you send that table file?



On 03/07/2016 04:33 AM, Caroline Beelen wrote:
> Hi Bruce,
>
> I'm a beginner in FS, so I just followed tutorial instructions for generating 
> the files carefully...
> I generated it by typing in for instance (after recon-all process was
> done): aparcstats2table --hemi lh --meas thickness --subjects A01_T1
> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table followed by
> the command: gnumeric lh.aparc.thickness.table
>
> It's a linux pc with Ubuntu 12.04 LTS (processor intel core i7-3770
> CPU @ 3.4GHz x 8)
>
> Attached the log file (A09).
>
> Thank you very much!
>
> Greetings, Caroline





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Re: [Freesurfer] gnumeric file

[Caroline Beelen]

Hi Bruce,

Ok, very clear. Thank you! :-)

Regards, Caroline

-Oorspronkelijk bericht-
Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
Verzonden: donderdag 17 maart 2016 15:47
Aan: Freesurfer support list 
Onderwerp: Re: [Freesurfer] gnumeric file

Hi Caroline

the data are in native space. Summary statistics means e.g. the volume of the 
left hippocampus. You don't need any registration algorithm for this type of 
thing - you just tabulate it across subjects

cheers
Bruce


On Thu, 17 Mar 2016, Caroline Beelen wrote:

> Hi Bruce,
>
> Thank you very much! :)
> I think somethings wrong with gnumeric indeed just discovered that gedit 
> works fine.
>
> As for 3, that would mean that the data are not in native space? I'm trying 
> to understand this concept of "summary statistics" :-).
>
> Thanks again in advance.
>
> Caroline
>
>
>
> -Oorspronkelijk bericht-
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl
> Verzonden: donderdag 17 maart 2016 13:59
> Aan: Freesurfer support list 
> Onderwerp: Re: [Freesurfer] gnumeric file
>
> Hi Caroline
>
> have you looked at the  lh.aparc.thickness.table? If it is correct then it is 
> something strange with gnumeric and I'm not sure we are qualified to help you.
>
> As for 3, the tables contain summary stats and so don't need to be mapped 
> into any common space.
>
> cheers
> Bruce
>
>
> On Thu, 17 Mar 2016, Caroline
> Beelen wrote:
>
>>
>> Dear FS,
>>
>>  
>>
>> 1. I typed: aparcstats2table --hemi lh --meas thickness --subjects
>> A01_T1
>>
>>> A02_T1 etc... A10_T1 --tablefile lh.aparc.thickness.table (followed
>>> by)
>> gnumeric lh.aparc.thickness.table. As soon as I typed in the latter, 
>> it generated the table attached. Why are the mean cortical thickness 
>> values sometimes depicted wrong and how can I change this (or do I 
>> need to do this by hand)?
>>
>>  
>>
>> 2. I noticed aparcstats2table doesn’t generate a mean volume (column 
>> AJ is empty). Is that supposed to be the case?
>>
>>  
>>
>> 3. A final question: the aparcstats2table and asegstats2table contain 
>> data in native space. Before loading Qdec data needs to be smoothed 
>> onto the average subject (using qcache). As s I understand correctly 
>> from your answer below and the tutorial I could either just use these 
>> values to create the qdectable.dat file or just load the tables in Qdec 
>> itself.
>>
>> Does that mean that the values of these tables somehow (have)
>> change(d) during the smoothing process?
>>
>>  
>>
>> Sorry if my questions are rather basic…, but I try to fully 
>> understand. J
>>
>> Thanks again for responding in advance.
>>
>>  
>>
>> Kind regards,
>>
>>  
>>
>> Caroline
>>
>>>  
>>
>>  
>>
>>  
>>
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Douglas Greve
>> Verzonden: woensdag 16 maart 2016 15:38
>> Aan: freesurfer@nmr.mgh.harvard.edu
>> Onderwerp: Re: [Freesurfer] gnumeric file
>>
>>  
>>
>>  
>>
>> On 3/16/16 6:52 AM, Caroline Beelen wrote:
>>
>>   Hi FS team,
>>
>>    
>>
>>   Sorry for these rather basic questions…
>>
>>    
>>
>>   I'm not sure whether the gnumeric file is an ascii file (see
>>   mails below). Attached you'll find the file. It seems the case
>>   when you open it in the terminal screen that the nr's look fine
>>   (with command cat). However as soon as you type the command
>>   gnumeric and so on, it creates a wrong table from the start (see
>>   file attached). Can I somehow change this?
>>
>> How did you create this file? The aparcstats2table command produces a 
>> simple ascii file.
>>
>>    
>>
>>   I have an additional question:
>>
>>   I was looking at the Qdec info (tutorial) and I am not totally
>>   sure how to create the table.dat file… Where to get the volume
>>   measures from, if you’d like to include those? The statistical
>>   folder (where the tables are from)?
>>
>> Run asegstats2table and/or aparcstats2table to create a table of the 
>> volumes, then extract the values you need. BTW, you don't have to 
>> have volume measures in th

[Freesurfer] mean thickness

[Caroline Beelen]

Dear Freesurfer team,

Forgive me if this is a foolish question...

I wanted to overlook cortical thickness, area and volume measures in Gnumeric 
file after recon-all (checking edits made). However, for several subjects I 
noticed that the values of mean thickness (final column) were calculated wrong, 
whereas this is not the case for their independent cortical thickness values. 
For instance, this happened to subject A09. I'm including the excel file to 
show the example. In the gnumeric file the number for this subject was depicted 
as 2/4964 instead of 2.4 etc.. What could have went wrong?

Thank you for your answer in advance.

Kind regards, Caroline


Map1.xlsx
Description: Map1.xlsx
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Re: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016

[Caroline Beelen]

Hi Christophe,

Apologies, I wanted to forward the mail but instead replied to it. ;)

Regards, Caroline

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Christophe Destrieux
Verzonden: vrijdag 12 februari 2016 10:45
Aan: Freesurfer support list 
Onderwerp: Re: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016

Dear Caroline
could you please resend it in english or in French ; I’m not too familiar with 
Flamish ; )
thanks

Christophe Destrieux,
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de 
Tours
http://www.u930.tours.inserm.fr/

Service de Neurochirurgie
et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours 
- France
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07




Le 12 févr. 2016 à 09:53, Caroline Beelen 
mailto:caroline.bee...@ppw.kuleuven.be>> a 
écrit :

Dag Jolijn,

Heb jij je al aangemeld voor onderstaande Freesurfer course? Er is volgens mij 
nog steeds niets van die andere beschikbaar, dus ik twijfel ook om te gaan (zou 
wel nuttig zijn!). Al is het een beetje achter de feiten aan…

Vriendelijke groet,

Caroline

Van: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Christophe Destrieux
Verzonden: woensdag 3 februari 2016 18:00
Aan: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Onderwerp: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016

Dear FreeSurfers,

It is our pleasure to welcome you the FreeSurfer course organized in Tours, 
Loire Valley, France, 2016 26-27th may.
This event is coorganized by the brain and imaging laboratory, INSERM 
U930-Université François Rabelais of Tours (France) and by the Martinos Center 
for Biomedical Imaging in Charlestown, MA (USA) which develops and distributes 
FreeSurfer.<http://freesurfer.net/>
This course will be limited to 64 participants. It will focus on surface-based 
analysis of individual and group morphological data and on tractographic 
analysis using FreeSurfer tools.
This course will be organized in the Ecole Polytechnique de l'Université de 
Tours
For online registration, please visit : 
http://freesurfer2016.sciencesconf.org/?lang=en
See you in Tours next May
 C Destrieux, F Andersson, L Barantin, S Love, M Sta, C Tauber


Christophe Destrieux,
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de 
Tours
http://www.u930.tours.inserm.fr/

Service de Neurochirurgie
et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours 
- France
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07




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The information in this e-mail is intended only for the person to whom it is
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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] FreeSurfer Course Tours, France, 26-27/05/2016

[Caroline Beelen]

Dag Jolijn,

Heb jij je al aangemeld voor onderstaande Freesurfer course? Er is volgens mij 
nog steeds niets van die andere beschikbaar, dus ik twijfel ook om te gaan (zou 
wel nuttig zijn!). Al is het een beetje achter de feiten aan…

Vriendelijke groet,

Caroline

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Christophe Destrieux
Verzonden: woensdag 3 februari 2016 18:00
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: [Freesurfer] FreeSurfer Course Tours, France, 26-27/05/2016

Dear FreeSurfers,

It is our pleasure to welcome you the FreeSurfer course organized in Tours, 
Loire Valley, France, 2016 26-27th may.
This event is coorganized by the brain and imaging laboratory, INSERM 
U930-Université François Rabelais of Tours (France) and by the Martinos Center 
for Biomedical Imaging in Charlestown, MA (USA) which develops and distributes 
FreeSurfer.
This course will be limited to 64 participants. It will focus on surface-based 
analysis of individual and group morphological data and on tractographic 
analysis using FreeSurfer tools.
This course will be organized in the Ecole Polytechnique de l'Université de 
Tours
For online registration, please visit : 
http://freesurfer2016.sciencesconf.org/?lang=en
See you in Tours next May
 C Destrieux, F Andersson, L Barantin, S Love, M Sta, C Tauber


Christophe Destrieux,
Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de 
Tours
http://www.u930.tours.inserm.fr/

Service de Neurochirurgie
et Laboratoire d'Anatomie - Faculté de Médecine - 10 Bd Tonnellé - 37032 Tours 
- France
tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07




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[Freesurfer] Qdec

[Caroline Beelen]

Dear Freesurfer experts,

I just started using Freesurfer for performing MRI (T1)- group-based ROI 
analysis and managed to go through the first recon-all processing stream and 
making few manual edits. Then I followed first steps of the Qdec -procedure. 
However, there is a separate section on ROI-analysis as well. Are they 
complementary or not (which one to follow best)?
I tried both. However, at the Qdec section I got lost at creating the table: 
how to know volumes of pre-specified structures?
At the ROI-section I got lost at the point of adding labels to the average 
subject:

cd $freesurfer (directory)
mri_label2label \
  --srcsubject avgsubject \
  --srclabel avgsubject/label/lh.BA45.label \
  --trgsubject A06_T1 \
  --trglabel A06_T1/label/lh.BA45.label \
  --hemi lh \
  --regmethod surface
(followed the example)

I got the error of:
subject_dir .../freesurfer
Freesurfer_home .../freesurfer
Loading source lab: 'no such file or directory'...etc. ... ERROR reading 
lh.BA45.label.
What am I doing wrong?

Thank you very much for your response in advance.

Kind regards, Caroline





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