[Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear FreeSurfer team,

For a case report I'm running recon-all on a patient with a giant arachnoid 
cyst in the left hemisphere. It gets stuck at this point (last message):
CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
XL defect detected...
It is stuck here since a whole day now, so I'm not expecting it to advance...
Following this post: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
looked at the wm.mgz, but did not find huge errors.
Do you have any ideas what the problem might be or what I can do to work around 
it?

Thanks,
Martin


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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear Bruce,

thanks for the quick reply! You are right, of course. I do find errors in 
lh.inflated.nofix.
I have attached a screenshot of the biggest errors I found..
Can you maybe guide me a little how to fix the issue? Do I just cancel the 
running recon-all process, and set control points and run again? Investing some 
time in manual editing would be fine as it's a case study...

Thanks for your help,
Martin



Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Bruce 
Fischl [fis...@nmr.mgh.harvard.edu]
Gesendet: Montag, 11. Dezember 2017 22:47
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

a defect that large means that something big went wrong (skull or
dura attached, etc...). Try looking at the ?h.orig.nofix and/or the
?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
defect 9

cheers
Bruce


On Mon, 11 Dec 2017, Loeffler, Martin wrote:

>
> Dear FreeSurfer team,
>
>
>
> For a case report I’m running recon-all on a patient with a giant arachnoid 
> cyst in the left
> hemisphere. It gets stuck at this point (last message):
>
> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>
> XL defect detected...
>
> It is stuck here since a whole day now, so I’m not expecting it to advance…
>
> Following this post: 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I
> looked at the wm.mgz, but did not find huge errors.
>
> Do you have any ideas what the problem might be or what I can do to work 
> around it?
>
>
>
> Thanks,
>
> Martin
>
>
>
>
>
>
>
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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot. 
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von 
> "Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura 
> attached, etc...). Try looking at the ?h.orig.nofix and/or the 
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find 
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant 
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to 
>> advance.
>>
>> Following this post: 
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

[Loeffler, Martin]

Dear Bruce,
Dear Bram,

Thanks a lot for having a look. Unfortunately the left hemisphere is equally 
important as the right one for our question of interest. With a lot of patience 
the recon-all has finished and the result looks surprisingly ok. I have 
additionally re-run it (recon-all -autorecon2-cp -autorecon3 -s Case) after 
setting control points to correct errors in the wm.mgz. Some errors were 
corrected, but not all. Next I would like to correct the surfaces.
My questions:

-  I know that recon-all is not designed for such a subject. But is 
there any argument against continuing the analysis now?

-  What can I do for those errors where the wm.mgz is still false, 
despite control points?
I have uploaded the respective files.

Best,
Martin


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Diamond, Bram 
Ryder
Gesendet: Mittwoch, 13. Dezember 2017 23:23
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst


Hi Martin,



We've taken a look at the scans you uploaded, and unfortunately it won't be 
possible to run the standard recon-all on your subject.  Recon-all is not 
designed to work on scans with such large lesions.  If you are interested, 
there may be a way to generate a reasonable model of the right hemisphere.



Best,

Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Loeffler, Martin 
mailto:martin.loeff...@zi-mannheim.de>>
Sent: Tuesday, December 12, 2017 11:57:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Dear Bruce,
I have uploaded the respective files. If there is something missing let me know.
Cheers,
Martin


-Ursprüngliche Nachricht-
Von: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 12. Dezember 2017 16:35
An: Freesurfer support list
Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst

Hi Martin

we are happy to take a look, but can't really tell much from a screenshot.
Feel free to upload the subject to our ftp site if you want us to help

cheers
Bruce

On Tue, 12 Dec 2017, Loeffler, Martin wrote:

> Dear Bruce,
>
> thanks for the quick reply! You are right, of course. I do find errors in 
> lh.inflated.nofix.
> I have attached a screenshot of the biggest errors I found..
> Can you maybe guide me a little how to fix the issue? Do I just cancel the 
> running recon-all process, and set control points and run again? Investing 
> some time in manual editing would be fine as it's a case study...
>
> Thanks for your help,
> Martin
>
>
> 
> Von: 
> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von
> "Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Gesendet: Montag, 11. Dezember 2017 22:47
> An: Freesurfer support list
> Betreff: Re: [Freesurfer] CORRECTING DEFECT recon-all giant cyst
>
> Hi Martin
>
> a defect that large means that something big went wrong (skull or dura
> attached, etc...). Try looking at the ?h.orig.nofix and/or the
> ?h.inflated.nofix surfaces with the ?h.defect_labels overlayed to find
> defect 9
>
> cheers
> Bruce
>
>
> On Mon, 11 Dec 2017, Loeffler, Martin wrote:
>
>>
>> Dear FreeSurfer team,
>>
>>
>>
>> For a case report I'm running recon-all on a patient with a giant
>> arachnoid cyst in the left hemisphere. It gets stuck at this point (last 
>> message):
>>
>> CORRECTING DEFECT 9 (vertices=21935, convex hull=1992, v0=31849)
>>
>> XL defect detected...
>>
>> It is stuck here since a whole day now, so I'm not expecting it to
>> advance.
>>
>> Following this post:
>> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48891.html I 
>> looked at the wm.mgz, but did not find huge errors.
>>
>> Do you have any ideas what the problem might be or what I can do to work 
>> around it?
>>
>>
>>
>> Thanks,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>

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[Freesurfer] changing label outlines in tksurfer

[Loeffler, Martin]

External Email - Use Caution

Dear experts,

I’m visualizing a 1st level sig-map together with two specific label files 
using tksurfer (Freesurfer version 6.0). I’ve extracted those labels before 
using mri_annotation2label.
I would like to change the colours of the label outlines. This is probably a 
very simple thing to do, but I am somehow stuck and would appreciate any help.
Here my code:

tksurfer Case01 lh inflated \
-tcl my_script.tcl \
-label-outline \
-label ${label_dir}/lh.label1.label\
-label ${label_dir}/lh.label2.label\
-o ${contrast_dir}/contrast1l/sig.nii.gz

with the .tcl file containing the following:
labl_set_color 0 0 0 255
labl_set_color 1 0 255 255
make_lateral_view
rotate_brain_x -30
redraw

Thanks for your help!
Martin
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Re: [Freesurfer] changing label outlines in tksurfer

[Loeffler, Martin]

External Email - Use Caution

Dear Bruce,

thanks for your quick response! I managed to do most of what I wanted in 
freeview. My last question: Is there any possibility to increase the thickness 
of the label outlines? Here the new code:
freeview -f 
${case_dir}/surf/rh.inflated:curvature_method=binary:label=${case_dir}/extracted_label/rh.label1.label:label_color=yellow:label_outline=yes:label=${case_dir}/extracted_label/rh.label2.label:label_color=Cyan:label_outline=yes:overlay=${base_dir}/sig.nii.gz
 -viewport 3d

Thanks again,
Martin




-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Sonntag, 8. Juli 2018 17:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] changing label outlines in tksurfer

Hi Martin

can you try freeview instead? We don't support tksurfer anymore, and changing 
label color/outline color is trivial using freeview.

cheers
Bruce


On
Sun, 8 Jul 2018, Loeffler, Martin wrote:

> 
> External Email - Use Caution
> 
> Dear experts,
> 
>  
> 
> I’m visualizing a 1st level sig-map together with two specific label 
> files using tksurfer (Freesurfer version 6.0). I’ve extracted those labels 
> before using mri_annotation2label.
> 
> I would like to change the colours of the label outlines. This is 
> probably a very simple thing to do, but I am somehow stuck and would 
> appreciate any help.
> 
> Here my code:
> 
>  
> 
> tksurfer Case01 lh inflated \
> 
> -tcl my_script.tcl \
> 
> -label-outline \
> 
> -label ${label_dir}/lh.label1.label\
> 
> -label ${label_dir}/lh.label2.label\
> 
> -o ${contrast_dir}/contrast1l/sig.nii.gz
> 
>  
> 
> with the .tcl file containing the following:
> 
> labl_set_color 0 0 0 255
> 
> labl_set_color 1 0 255 255
> 
> make_lateral_view
> 
> rotate_brain_x -30
> 
> redraw
> 
>  
> 
> Thanks for your help!
> 
> Martin
> 
> 
>

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[Freesurfer] 1) single subject surface activation in volume space and 2) small volume correction

[Loeffler, Martin]

External Email - Use Caution

Dear experts,

I'm running a sensory mapping experiment, which I would like to analyse in 
single subject space. Everything seems to be working fine (see code excerpt 
below). Now I'd  like to do two additional things:

1)  show the surface results in single subject volume space (as overlay on 
T1).

2)  Limit my surface analysis to BA3b, using correction for multiple 
comparisons in that region only. I've read that this should be possible with 
monte carlo simulation, but can't figure out how to do this for one subject 
only.
Any help is much appreciated!

Best,
Martin


mkanalysis-sess -fsd bold  -surface self lh -fwhm ${fwhm_par} -event-related  
-paradigm Onsets.par -nconditions 5 -spmhrf 1 -TR 1.5 -refeventdur 12 -hpf 0.01 
-nskip 3 -polyfit 2 -analysis MR.lh -force -per-run

mkcontrast-sess -analysis MR.lh -contrast digit1_lh -a 1 -c 0
#...

bbregister --s $subj --mov f.nii.gz --init-fsl --int whole.nii.gz --t2 --reg 
register.partial.dat

preproc-sess -s $subj -fsd bold -surface self lhrh -fwhm ${fwhm_par} -projfrac 
0.5 -per-run -update -regfile register.partial.dat

selxavg3-sess -s $subj -analysis MR.lh -force

freeview -f 
${ANAT}/${subj}/surf/lh.inflated:curvature_method=binary:overlay=${FUNC}/${subj}/bold/MR.lh/digit1_lh/sig.nii.gz


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[Freesurfer] small volume correction in native space

[Loeffler, Martin]

External Email - Use Caution

Dear experts,

I'm running an analysis on sensory mapping. It's a simple event-related design 
and my analysis stream seems to work fine. I need to analyze all the data in 
single subject space, because I'd like to calculate surface distances later 
(using mris_pmake), which must not be in standard space.
I'd like to run my analysis for each single subject, but limit the analysis to 
a specific area (e.g. BA3b). Is this possible using FS? If yes, could you show 
me a way how this can be done?

Thanks a lot for your help!
Best,
Martin



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[Freesurfer] Postdoc available at the Central Institute of Mental Health

[Loeffler, Martin]

External Email - Use Caution

The Central Institute of Mental Health (CIMH) stands for cutting-edge 
international research and groundbreaking treatment concepts in psychiatry, 
psychotherapy, child and adolescent psychiatry, psychosomatics and addiction 
medicine.
The Department of Cognitive and Clinical Neuroscience (Scientific Director: 
Prof. Dr. Dr. h. c. Dr. h. c. Herta Flor) is looking for a talented, highly 
motivated postdoctoral fellow, to join a multimodal human neuroimaging research 
group with strong roots in experimental psychology.

Our BMBF funded research examines neural circuits underlying chronic 
musculoskeletal pain. In the current project we focus on the improvement of the 
treatment of chronic musculoskeletal pain disorders through a personalized 
therapy approach with cross-disease multilevel diagnostics and 
mechanism-oriented interventions. We employ learning models and machine 
learning approaches to improve patient stratification. Our methods concentrate 
on experimental psychological designs, neuropsychological assessments, 
functional magnetic resonance imaging (fMRI), and peripheral physiology

Our requirements

  *   Ph.D. in psychology, neuroscience or related fields
  *   Experience in at least one of the imaging modalities (fMRI, MEG, EEG, 
fNIRS)
  *   Excellent teamwork, time management and organizational skills
  *   Expertise in statistics (R, JASP, SPSS) and experimental designs 
(Presentation,
Matlab)
  *   Programming skills (Matlab, Python) and experience with neuroimaging 
analysis software (e. g. FSL, SPM, FreeSurfer)
  *   Strong publication record in peer-reviewed scientific journals
  *   German language skills are an advantage

Responsibilities

  *   Become part of a multidisciplinary team working on psychobiological and 
clinical research questions
  *   Participation in grant writing and scientific publications
  *   Participation to clinical interviews and questionnaires as well as 
patient recruitment
  *   Presentation of study-related outcomes at key scientific meetings

What you can expect

  *   An interesting job in a clinical center and leading research institute
  *   Pleasant colleagues and a friendly working atmosphere
  *   Departmental introduction and familiarization
  *   Internal and external further education and training opportunities
  *   Job ticket
  *   Good accessibility and central location in the heart of Mannheim
  *   Good compatibility of work and family
  *   Remuneration according to TV-L and the associated social benefits 
according to the collective bargaining regulations of the public service

Severely disabled, who are equally qualified will be preferred. Salary is based 
on the German TV-L pay scale, including the social benefits of the German 
public service sector

Contact

If you have any questions, please contact Herta Flor, email: 
herta.f...@zi-mannheim.de, phone number +49 
621 1703-6302 or Martin Löffler, email: 
martin.loeff...@zi-mannheim.de +49 621 
1703-6349. We are pleased to receive your application via the online career 
portal until April, 15th, 2022 
(https://secure-web.cisco.com/1VLfuJU_rnnl9fgjvpflyO_Ee8Uy_9ByRDPS1PRf-PsbHUZz7lG6-nv1L0Pr9BjXGYIDIDqFt5UM0t3bnOpqayBAzbiyNe3VEXN810gumRuc5OHGVFu8QgJh22tyTGj-32zJaJj8WdsP5fdhIfKBehixwmOpFLryl5bMAvt8pSpuPCHKSgWYyoPHish6FOWPEDvBNPYh1y2bnXrGjRsumFrIFJ_xGfSHAKp3UGlIFzSXg2B13_f-Soyv6n1F7RFsOcph9UD4kK9FZ_qSRdTrVDljWWA4eaZ5jg-nz0JxPtBOB-EDnd3_jfJnRvtsXFxCvQJeVJ_fGr6pMJRB3cAG3Sw/https%3A%2F%2Fjobs.zi-mannheim.de%2FVacancies%2F508%2FDescription%2F1)
 .


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[Freesurfer] design is ill-conditioned

[Loeffler, Martin]

External Email - Use Caution

Dear experts,

I’m running into an error when running selxavg3. It says the design is 
ill-conditioned. I’m a bit stuck, because the same pipeline works in most 
subjects, but not all. Also, if I exchange the functional scan (f.nii.gz) with 
a scan from a working session of the same subject (same number of volumes etc.) 
I don’t get any errors. I’m grateful for any advice that helps to track down 
the mistake I’m doing.

Here the content of the selxavg3.log file:
cd /home/hector/SENS_MAPPING_BLOCK/sessions
/opt/software/freesurfer/fsfast/bin/selxavg3-sessbc -s HEC_035_1 -analysis 
MPBDandefs_orig_lhrh_revd11.5_sm2.lh -no-preproc -fwhm -force
Found 42449/139130 (30.5) voxels in mask
Creating Design Matrix
... creation time =  0.004 sec
DoMCFit = 1
ntptot = 500, nX = 33, DOF = 467
XCond = 2.63784e+16 (normalized)
ERROR: design is ill-conditioned

Before the error it gives a warning that the design matrix is singular or badly 
scaled:
[Warning: Matrix is close to singular or badly scaled. Results may be
inaccurate. RCOND =  1.271035e-17.]
[> In fast_selxavg3bc (line 318)]
norm(inv(XtX),2) = [14601308845709730.0]
Saving X matrix to 
/home/hector/SENS_MAPPING_BLOCK/sessions/HEC_035_1/bold/MPBDandefs_orig_lhrh_revd11.5_sm2.lh/Xtmp.mat
XCond = 2.63784e+16 (normalized)
ERROR: design is ill-conditioned
>> --
ERROR: fast_selxavg3bc() failed\n

Many thanks in advance,
Martin

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