Re: [Freesurfer] using different Freesurfer versions for cross-sectional & longitudinal processing

[Greve, Douglas N.,Ph.D.]

I think it should be ok in principle, though it might fail because the v6 long 
stream expects there to be certain files with certain names, and they might not 
be there with 5.1.

On 12/16/2019 2:49 PM, Morgan Botdorf wrote:

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Dear Freesurfer Experts,

We have child data that was previously processed cross-sectionally using 
version 5.1. We are now interested in looking at the data longitudinally. Can 
the longitudinal processing stream in version 6.0 be used on data that was 
processed cross-sectionally using 5.1? Or is it better that we reprocess the 
data using 6.0. We appreciate any help you can provide!

Thank you,


Morgan Botdorf, M.S.

Doctoral Candidate

Neurocognitive Development Lab

University of Maryland, College Park

mbotd...@terpmail.umd.edu

Office: 301.405.5922





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Re: [Freesurfer] Conversion fMRI volumes to surface

[Bruce Fischl]

Hi Marina

yes, mri_vol2surf will sample volumes onto the surface. You will need to 
register them first (we typically use Doug Greve's bbregister for this). 
What preprocessing did you do? For cortical data we don't recommend 
smoothing in the volume - you are much better off sampling to the surface 
then smoothing on the surface


cheers
Bruce


On Tue, 17 Dec 2019, Marina Fernández wrote:



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Dear experts,

I’ve done the fMRI preprocessing and now I would like to convert each file
(that contains 250 volumes) to surface.

Is it correct to use the function mri_vol2surf? Should I use any specific
flag because they are 4D files? What is the best way to transform the
volumes to surface?

Thank you in advance.

 

Best regards,

Marina.


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Re: [Freesurfer] Conversion fMRI volumes to surface

[Greve, Douglas N.,Ph.D.]

Yes, use mri_vol2surf. Make sure to use --projfrac 0.5 to sample in the middle 
of cortex. Run it with --help to get examples.

On 12/17/2019 11:16 AM, Marina Fernández wrote:

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Dear experts,
I’ve done the fMRI preprocessing and now I would like to convert each file 
(that contains 250 volumes) to surface.
Is it correct to use the function mri_vol2surf? Should I use any specific flag 
because they are 4D files? What is the best way to transform the volumes to 
surface?
Thank you in advance.

Best regards,
Marina.



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Re: [Freesurfer] (no subject)

[Greve, Douglas N.,Ph.D.]

OK, I'm still at a loss. The one suspicious thing is that it only took a few 
min to run. So you have never looked at that volume? What is in the atlas?

On 12/16/2019 3:42 PM, Boris Rauchmann wrote:

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This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label 
$SUBJECTS_DIR/1122/mri/brain.mgz 
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z 
$SUBJECTS_DIR/BN_Atlas_subcortex.gca 
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz


== Number of threads available to mri_ca_label for OpenMP = 1 ==
reading 1 input volumes
reading classifier array from 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was 
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed 
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec146.184667
mri_ca_label stimesec1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss0
mri_ca_label ru_idrss0
mri_ca_label ru_isrss0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
reading frame -1 of gca
Volume information for 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
  type: GCA
dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 3
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 0.
  : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   128.
0.   0.   1.  -128.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   128.
   -0.  -0.  -1.   128.
   -0.   1.  -0.   128.
   -0.  -0.  -0. 1.




Am 16.12.2019 um 21:21 schrieb Boris Rauchmann 
mailto:boris.rauchm...@gmail.com>>:

Thanks, it was created using:

mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

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Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
-1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu> 
>:

mri_info N_Atlas_subcotex.mgz


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[Freesurfer] Conversion fMRI volumes to surface

[Marina Fernández]

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Dear experts,

I’ve done the fMRI preprocessing and now I would like to convert each file
(that contains 250 volumes) to surface.

Is it correct to use the function mri_vol2surf? Should I use any specific
flag because they are 4D files? What is the best way to transform the
volumes to surface?

Thank you in advance.



Best regards,

Marina.
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[Freesurfer] Doctoral student positions in fMRI of visual illusions

[Zaretskaya, Natalia (natalia.zaretsk...@uni-graz.at)]

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Dear all,

We are looking for three doctoral students to join our Experimental Psychology 
and Cognitive Neuroscience group in Graz to work on fMRI of visual illusions.

You will find the official job ad below

(Please note that doctoral students in Austria are employed under a work 
contract with health and pension benefits. There are no tuition fees associated 
with getting a PhD degree.)



The Institute of Psychology of the University of Graz is looking for three
Doctoral Candidates within the framework of the BioTechMed Young Researcher 
Group
"Neural basis of subjective visual experience"

(Project-Assistant; 30 hours a week; fixed-term employment for the period of 4 
years; position to be filled as of now)


Your profile

  *   Master's degree or diploma in psychology, biology, neuroscience, medicine 
computer sicence or similar fields
  *   Excellent English skills
  *   Interest in the topic of the project and in neuroscience research in 
general
  *   Scientific curiosity, ability and readiness to learn new things
  *   Excellent organization, communication and social skills
  *   Independence and reliability
  *   Preferably sound knowledge in conducting/analyzing fMRI experiments and 
programming skills (MATLAB, Python, etc.)

Your duties

  *   Writing a dissertation and publishing activities in the research area of 
the Young Researcher Group
  *   Participation in planning, preparing and conducting fMRI experiments, 
fMRI data analysis
  *   Preparing scientific manuscripts and publications
  *   Participation in scientific conferences and workshops
  *   Contribution to supervising scientific thesis

Our offer

The project provides an opportunity to learn advanced (f)MRI techniques 
(including quantitative morphometry, surface-based analysis, pRF mapping, MVPA, 
high-resolution structural and functional MRI), while addressing exciting 
scientific questions. More information about the project can be found at 
https://psychologie.uni-graz.at/en/cognitive/researching/projects/neural-basis-of-subjective-visual-experience/

Classification

Salary scheme of the Universitäten-KV (University Collective Agreement): B1

Minimum salary

The minimum salary as stated in the collective agreement and according to the 
classification scheme is EUR 2148.40 gross/month. This minimum salary may be 
higher due to previous employment periods eligible for inclusion and other 
earnings and remunerations.

We offer you a job with a lot of responsibility and variety. You can expect an 
enjoyable work climate, flexible work hours and numerous possibilities for 
further education and personal development. Take advantage of the chance to 
enter into a challenging work environment full of team spirit and enthusiasm 
for your job.

Application Deadline: January 1st 2020
Reference Number: MB/24/99 ex 2019/20

The University of Graz strives to increase the proportion of women in 
particular in management and faculty positions and therefore encourages 
qualified women to apply.

Especially with regard to academic staff, we welcome applications from persons 
with disabilities who meet the requirements of the advertised position.

If you are interested, please submit your application documents before the 
stated deadline. Make sure to indicate the reference number on your application 
(Motivation letter, CV, degree certificates, names of two scientists who can 
provide a reference letter upon request) to:

bewerb...@uni-graz.at

For further Information please contact Mrs Dr. Natalia Zaretskaya 
(http://bit.ly/2youGD6).


--
Dr. Natalia Zaretskaya
Institute of Psychology, University of Graz
BioTechMed-Graz
Universitaetsplatz 2
8010 Graz
Austria
+43 316 380 - 5117
natalia.zaretsk...@uni-graz.at
http://bit.ly/2youGD6

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[Freesurfer] Problem with the segmentation of subregions

[Marina Fernández]

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Hi experts,

We are doing the segmentation of the subfields of the hippocampal and
amygdala subfields, brainstem subestructures and thalamic nuclei. When we
used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found'
appears.

On the other hand, we used segmentBS.sh and we got the following message:
'Software requires 4 arguments:
segmentSFnewT1.sh matlabRuntimeDirectory FShomeDirectory subjectName
subjectDir'.
But, when we typed 'segmentSFnewT1.sh'  we got  'Command not found' again.


Note:  We have FS v6.0 and the runtime Matlab 2014b.

Best wishes,
Marina
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