[Freesurfer] segmentHA_T2.sh

[Eva Hilland]

Dear FS experts,

 I am now trying the dev version for centos6 to run the segmentHA_T2.sh
script.

 I get the following error:

/bin/.: Permission denied.

I have tried to change persmissions in freesurfer/bin and still get the
same error.

Does anyone have experience with this?


Best regards,
Eva
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[Freesurfer] Problems transforming T1 to talairach

[Helen Beaumont]

I am using the command 
mri_convert -at transforms/talairach.xfm  brain.mgz brain_in_tal.nii.gz

to convert a native-space skull-stripped T1 image to talairach space. I used 
recon-all to generate the transform matrix, and the segmentation and everything 
look good. But the T1_in_talairach image is not good - the brains are ending up 
different sizes, and frequently have the posterior chopped off. 
Please what am I doing wrong? Should I be applying the inverse of the 
transform? 

Helen Beaumont PhD
University of Manchester
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[Freesurfer] mpr2mni305 talaraich transformation error

[Dijkshoorn, A.B.C. (Aicha)]

Hello free surfer developers,

I am attempting to compute cortical thickness for anatomical ROIs in neonates, 
but for some of my subjects I get the following error when I run the 
auto-recon1 command:



\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun  4 
21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64

recon-all -s N192_con_recon exited with ERRORS at Fri Feb  2 12:32:02 CET 2018


Is there any way I can work around this error?
I've also attached the recon-all.log and the talaraich_avi.log in case it's of 
any use.

Kind regards,
Aicha Dijkshoorn



recon-all.log
Description: recon-all.log


talairach_avi copy.log
Description: talairach_avi copy.log
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[Freesurfer] One Group (One Factor), Two Covariates

[stdp82]

Hi list,

in reference to One Group (One Factor), Two Covariates

https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V#Contrast2age.mtx

that has been applied on FS-FAST fcMRI data

I obtain three folder, respectively, for "main", "covariate 1", "covariate 2".

What's meaning the sig.nii.gz that it is produced by mri_glmfit in each folder?
Please correct my conclusions if they are wrong.

1 - In the "Main" folder, the sig.nii.gz contains the results of One-sample t 
test regressing out the effect of the two covariates.

2 - In the "Covariate 1" folder, the sig.nii.gz contains the significant 
cluster that are associated with the covariate 1 regressing out the effect for 
the covariate 2.

3 - In the "Covariate 2" folder, the sig.nii.gz contains the significant 
cluster that are associated with the covariate 2 regressing out the effect for 
the covariate 1.

Thanks


Stefano


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[Freesurfer] Group and ROI analyses in qdec

[Backhausen, Lea]

Dear freesurfer experts,

I started using qdec for comparing cortical measures in adolescent patients 
with ADHD versus typically developing adolescents and I have a few questions 
concerning the ROI analysis as well as the Desikan-Killiany versus Destrieux 
atlas.

English is not my native language so please excuse typing errors or wrong 
expressions.
1)  Is it somehow possible to have the significant clusters mapped onto the 
Destrieux atlas in qdec instead of the Desikan-Killiany one?

2)  I would like to export the mean thickness/surface area from significant 
clusters to SPSS to correlate them with clinical symptoms. I understand you can 
either use means from the stats tables (aparc_thikness_lh.txt etc.) or manually 
draw a ROI and then map the lable back to other subjects. But is there also a 
way to simply export the measures from the significant clusters that show up 
without drawing around them or export measures from the peak vertices?

3)  If I use methods as described in 2), do I have to be concerned about 
‘double dipping’ or ‘circular analysis’?

4)  Does the measure ‘area.pial’ you can select during design creation 
correspond to ‘cortical surface area’ and the measure ‘area’ to ‘WM surface 
area’? Which measure do the aparc_area_lh.txt files that I get when generating 
stats data tables correspond to? I do not see aparc_area.pial.txt files, should 
I be getting them?

5)  After reading a lot about correcting for global brain measures I am 
still confused about the best way to do it. I am quite sure that for the 
volume-based measures it is best to control for ICV/eTIV but for thickness and 
surface area I read different approaches from not controling to using total 
brain volume, global thickness or ICV. Is it safe not to control for anything 
for thickness measures as I do not expect any kind of atrophy in my sample? 
What should my decision be based on?

Sorry, these are many questions – I appreciate any thoughts on these problems, 
thank you so much!

Lea Backhausen, B.Sc.

Research Assistant
Department of Child and Adolescent Psychiatry, Faculty of Medicine of the 
Technische Universität Dresden, Dresden, Germany



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[Freesurfer] talaraich transformation error

[Dijkshoorn, A.B.C. (Aicha)]

Hello free surfer developers,

I am attempting to compute cortical thickness for anatomical ROIs in neonates, 
but for some of my subjects I get the following error when I run the 
auto-recon1 command:



\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun  4 
21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64

recon-all -s N192_con_recon exited with ERRORS at Fri Feb  2 12:32:02 CET 2018


Is there any way I can work around this error?

Kind regards,
Aicha Dijkshoorn

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Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

[Bruce Fischl]

Hi Kyung

you should look at the mris_convert help. It has an example of how to 
convert a scalar overlay like a curv file to ascii:



Convert a scalar overlay file to ascii:
  mris_convert -c lh.thickness lh.white lh.thickness.asc


it needs the surface as an input to do the conversion properly.

cheers
Bruce

On Fri, 2 Feb 2018, 
박경일 wrote:



Hi Bruce
I found a directory having a file with ".curv", open terminal and run following 
command.

[root@localhost surf]# mris_convert rh.curv rh.curv.asc
nquads=4587523,  nvertices=476
ERROR: MRISread: file 'rh.curv' has many more faces than vertices!
Probably trying to use a scalar data file as a surface!
No such file or directory

what is wrong?

Thanks as always.

Kyung

2018-01-31 0:04 GMT+09:00 Bruce Fischl :
  Hi Kyung

  the thickness values are stored as "curvature" file format that you can 
load into matlab
  with read_curv.m. Alternatively, you can convert them to ascii with 
mris_convert and do
  what you want with them. For each index, you can look up its location on 
the white or
  pial (or whatever surface). That is, for the 2nd thickness value (index 
1), you would go
  find vertex #1 on the other surface and read its location that way

  cheers
  Bruce
  On Tue, 30 Jan 2018, 박경일 wrote:

Hi Bruce, I am very new for FS, so did not understand you comments
completely. sorry..

For cortical thickness from each vertex in one subject, which 
scripts should
follow "mris_convert"?
And another question is how to recognize the location of each 
vertex in
brain finally.

thank you so much

Kyung
 

2017-11-13 10:06 GMT+09:00 Bruce Fischl 
:
      p.s. if you want the vertices to correspond, first run 
recon-all
-qcache for each
      subject. That will generate a set of thickness maps in 
fsaverage space
at predefined
      smoothing levels (so that the vertex numbers correspond across
subjects)

      On Mon, 13 Nov 2017, 박경일 wrote:

            Hi Bruce,What I want is the values of cortical 
thickness in each
vertex in
            each subject. Is that
            possible?
            Thanks so much.

            Kyung

             

            2017-11-13 0:43 GMT+09:00 Bruce Fischl
:
                  Hi Kyung

                  you can load them into matlab or convert them to 
ascii if
you want
                  Bruce
                  On Sun, 12 Nov 2017, 박경일 wrote:

                        Dear FS experts,
                        I could get QDEC image comparing two groups.
                        However, is there a way to get numerical 
values of
cortical
            thickness in
                        each vertex?

                        Thank you

                        Best,
                        Kyung




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            --

            Kyung-Il Park, MD, PhD.

            Professor,  

            Department of Neurology, Seoul National University
Hospital; Seoul National
            University Hospital
            Healthcare System Gangnam Center.

            Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 

            Email: kip...@snuh.org / ideo...@gmail.com



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Re: [Freesurfer] Control Points Not Working

[Boyd, Emma]

Hi Arsenije,


You should never need to add hundreds of control points, just a few dispersed 
through the problematic area should work. Would you mind uploading your recon 
to our file drop site and I'll take a look at it? You can send it to my email, 
ebo...@nmr.mgh.harvard.edu.

https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,

Emma


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Arsenije Subotic 

Sent: Thursday, February 1, 2018 5:54:20 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Control Points Not Working

Dear experts,

I’m currently performing quality control for my data, and most of my issues so 
far have been that in many cases adding control points has not been able to 
extend the white surface. I’ve also noticed that most of the regions where I 
have needed to add CPs are in the parietal regions of the brain. Does anyone 
know how many control points are usually recommended to be added? I have so far 
had cases where I have had to add hundreds of CPs and I have still had mixed 
success.

Thank you,
Arsenije

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Re: [Freesurfer] mpr2mni305 talaraich transformation error

[Boyd, Emma]

Hi Aicha,


Have you visually inspected your input image, rawavg.mgz or orig.mgz to make 
sure they look ok?


Emma



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Dijkshoorn, A.B.C. 
(Aicha) 
Sent: Friday, February 2, 2018 7:37:25 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mpr2mni305 talaraich transformation error

Hello free surfer developers,


I am attempting to compute cortical thickness for anatomical ROIs in neonates, 
but for some of my subjects I get the following error when I run the 
auto-recon1 command:



\n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n

ERROR: mpr2mni305 failed, see transforms/talairach_avi.log

Darwin leia.ds.umcutrecht.nl 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun  4 
21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64

recon-all -s N192_con_recon exited with ERRORS at Fri Feb  2 12:32:02 CET 2018



Is there any way I can work around this error?

I've also attached the recon-all.log and the talaraich_avi.log in case it's of 
any use.

Kind regards,
Aicha Dijkshoorn

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Re: [Freesurfer] segmentHA_T2.sh

[Hoopes, Andrew]

Hi Eva, I believe this should be fixed in the most recent El Capitan dev 
version. Let me know if the issue persists.

best
Andrew



On February 1, 2018 at 7:02:19 AM, Iglesias Gonzalez, Eugenio 
(e.igles...@ucl.ac.uk) wrote:
We are looking into all this. We’ll have updates soon.
Cheers,
/Eugenio

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


From:  on behalf of Eva Hilland 

Reply-To: Freesurfer support list 
Date: Wednesday, 31 January 2018 at 22:26
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] segmentHA_T2.sh


Dear freesurfer experts,

I have tried the dev version of Segmentation of hippocampal subfields and 
nuclei of the amygdala
for OSX el Capitan, downloaded today.
I did get an error message similar to a previous error I found on this mailing 
list:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973.html

I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below

Is this a matlab runtime problem?

Many thanks in advance

Eva



#@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 CET 2018
--
Setting up environment variables
---
DYLD_LIBRARY_PATH is 
.:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64:
Invalid MEX-file 
'/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64':
 
dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64,
 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv
  Referenced from: 
/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64
 (which was built for Mac OS X 10.11)
  Expected in: /usr/lib/libstdc++.6.dylib
 in 
/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64

Error in kvlClear (line 11)



Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135)



MATLAB:invalidMEXFile
Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 
18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018
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Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

[Dorit Kliemann]

ops. I guess that should have been obvious to me!

Thanks!
Dorit



smime.p7s
Description: S/MIME cryptographic signature
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