[Freesurfer] Tracula / 0 slices processed in Bedpostx before queuing post processing stage

[Anna Mynick]

Hi, 

I’m having difficulty making BedpostX work on non-tutorial data per the 
tutorial located here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula 


The preprocessing has worked without errors, but now that I’m using BedpostX, 
the output is producing: 

subjectdir is {subject's directory}/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
Queuing post processing stage

Obviously, it shouldn’t be going straight from 0 slices processed to the post 
processing stage. I’m running the command directly (i.e. bedpostx {subject's 
directory}/dmri ), and when the process is done ( it ends in 25 seconds) the 
dmri folder has files that are in the format data_slice_00**.nii.gz and 
nodif_brain_mask_slice_00**.nii.gz. 

I’ve also tried running the command: trac-all -bedp -c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial on a cluster, which produces 
the same output. 

Has anyone else had this issue? 

Thanks for any help,
Anna 

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[Freesurfer] TRACULA error "R: Subscript out of range"

[Anna Mynick]

Hi all, 

I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is 
exiting with the output below. Most notably, I think, is the section of the 
output that says "R: Subscript out of range.” repeatedly and then the section 
afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8 9 / ERROR: valid frame 
numbers are between 0 and 0”. Does anyone have thoughts on what might be going 
on here? 

I’ve attached my bvecs and bvals too, in case there is trouble there too. 

Thanks very much for any help. 

Best,
Anna 


0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.00 0.00 0.00
0.99649667739868 0.06475614756346 -0.05292384698987
0.60556709766388 0.42478442192078 0.67293894290924
0.86823248863220 0.03115228191018 -0.49517852067947
0.67013686895370 0.45375373959541 -0.58738726377487
-0.08319617807865 -0.97095906734467 0.22431358695030
0.19819127023220 -0.76370823383331 0.61438584327698
-0.38230711221695 0.40581783652306 0.83015239238739
0.21735191345215 -0.75227254629135 -0.62196791172028
0.02298471517861 0.97281080484390 -0.23045811057091
-0.07650605589151 0.04117560386658 0.99621850252151
-0.14655694365501 0.75338035821915 0.64104521274567
-0.57700997591019 -0.78357273340225 0.23037599027157
0.12379934638739 -0.96946108341217 -0.21170438826084
0.04432926326990 0.02168774046004 -0.99878138303757
0.26761892437935 -0.38499519228935 -0.88326603174210
-0.28756865859032 0.78847736120224 -0.54369783401489
0.38445866107941 0.07492686808109 0.92009633779526
-0.83095681667328 0.54706901311874 0.10112489014864
0.32437109947205 0.77897244691849 0.53664255142212
0.52829635143280 0.79588997364044 -0.29573988914490
-0.16789475083351 0.45606943964958 -0.87396329641342
-0.59607589244843 0.39722976088524 -0.69778358936310
-0.42442059516907 0.90444123744965 -0.04304528608918
0.37679037451744 -0.90613275766373 0.19222989678383
-0.62092286348343 -0.47927498817444 0.62028235197067
-0.07215544581413 0.96755516529083 0.24213692545891
-0.25669917464256 -0.76215481758118 0.59432780742645
-0.52350831031799 -0.05601207166910 0.85017740726471
0.18893271684647 0.76144242286682 -0.62008827924728
-0.93878203630447 -0.25041463971138 -0.23660232126713
0.92434495687485 -0.25977137684822 0.27947291731834
-0.85333710908890 -0.08729962259531 0.51399856805801
0.61280375719070 -0.55279505252838 0.56470263004303
-0.40714001655579 -0.01904341205955 -0.91316711902618
0.36646711826324 0.92621129751205 0.08851362764835
-0.77262413501740 -0.05901937559247 -0.63211452960968
-0.71511095762253 -0.66166228055954 -0.22543147206306
-0.17854259908199 -0.41829714179039 0.89058959484100
-0.88413268327713 -0.43072432279587 0.18106889724731
-0.24447374045849 -0.79100799560547 -0.56083726882935
-0.60315960645676 -0.48198029398918 -0.63552600145340
0.90175306797028 0.24873784184456 0.35351192951202
0.72955089807510 -0.10027404874563 0.67653554677963
-0.91682189702988 0.25997617840767 -0.30306729674339
-0.68014901876450 0.66064327955246 -0.31772288680077
0.86024975776672 0.48736852407455 -0.14980775117874
-0.19012457132339 -0.44323825836182 -0.87600934505463
-0.52820658683777 0.75576055049896 0.38707065582275
0.13211445510387 0.46795129776001 0.87382322549820
0.89498126506805 -0.39065974950790 -0.21539171040058
0.55196392536163 -0.00862982682884 -0.83382308483124
0.74213677644730 -0.65859544277191 0.12443807721138
-0.34717303514481 -0.92652040719986 -0.14502120018005
-0.75233423709869 0.36954036355019 0.54537409543991
0.28638312220573 -0.37944245338440 0.87977713346481
0.30121210217476 0.39795523881912 -0.86654651165009
0.71197289228439 0.66156578063965 0.23542550206184
-0.98868387937546 0.09445825219154 0.11654109507799
0.55790656805038 -0.78184622526169 -0.27831059694290
0.65419042110443 -0.44598758220673 -0.610843658447270.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00
700.00


——

INFO: SUBJECTS_DIR is 
/mindhive

[Freesurfer] Reset view command in freeview

[Anna Mynick]

Hi all,

I’m wondering whether there's a command-line equivalent to the the Reset View 
tool found in the Freeview GUI when you right-click a volume in 3d view. I 
tried using the -viewport tag (e.g. freeview -v myvolume.nii.gz -viewport 
coronal), but the problems with this are:

(1) Though the tag does change the viewpoint in which my volume is displayed, 
which is what I want, it also switches out of the 3d view, and my goal is to 
maintain the 3d view so I can view my region as an isosurface

(2) I’d like the option of choosing between anterior, posterior, superior, 
inferior, and left and right views, as in the Reset View tool menu, rather than 
just coronal, sagittal, and axial.

In other words, is there a way to open a volume to a specific view from the 
command line while maintaining 3d view?

Thanks for any help!

Best,
Anna
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[Freesurfer] Custom color map in Freeview

[Anna Mynick]

Hi all,

I’m wondering whether there’s a way to create a custom color map in Freeview 
that would operate as a alternative to the preset Greyscale, Heatmap, NIH, PET, 
Jet and GE Color options.

Ideally, I could assign each number value a given color, e.g. every “0” value 
in an .nii file is black, every “1” value is red, every “2” value is blue, 
every “3" is green and so on. I already have the RGB values worked out for each 
number value; I just need to know how to format this information and where to 
put it so that I can my custom colormap as an option in Freeview.

For my purposes, there would be no need to adjust the assigned colors based on 
the overall range of values. For instance, there would be no need to assign a 
different color value to a “1” value depending on whether the highest value in 
the overall .nii file is 1 or 100.

I did try reading the related conversation 
here
 but I can’t seem to find the file it references, annotval2surfoverlay.m, in 
the Freesurfer directory.

Thanks very much for your help!
Anna

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[Freesurfer] Register individual functional volume to MNI152

[Anna Mynick]

External Email - Use Caution

Hi all,

I’m having some trouble getting an an accurate registration between an 
individual functional volume and MNI152 space. Presently, I’m using the 
commands:

bbregister --s MNI152_FS --mov volumeInFunctional  --reg 
mniDir/filename2mni.lta --init-fsl --bold
mri_vol2vol --mov volumeInFunctional  --reg  mniDir/filename2mni.lta --fstarg 
--o ‘ mniDir/filename.nii --no-resample

I’ve also tried using the strategy detailed 
here,
 without much luck (the registration was very distorted).

Is there a different method for registration to MNI152  that yields more 
accurate results?

Thanks very much for any suggestions!

Best,
Anna

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[Freesurfer] Compiling same-subject data across multiple scanning sessions

[Anna Mynick]

External Email - Use Caution

Hi all, 

I'm wondering whether there's a way to compile same-subject data across 
multiple sessions into the same analysis. 

More specifically, I've run all my individual scanning sessions through 
preproc-sess (same subject, different scanning days) and am now hoping to 
compile same-subject sessions into a file that can be fed into mkanalysis-sess, 
mkcontrast-sess and selxavg3-sess. 

One concern I have is that all of the .para files that list stimulus onsets and 
durations are separate, so I imagine those would need to be concatenated along 
with the preprocessed functional data. 

Thanks very much for any help, 
Anna 

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[Freesurfer] Running selxavg with many (~5000) different conditions

[Anna Mynick]

External Email - Use Caution

Hi, 

I'm currently running an analysis that requires defining each of 5000 stimuli 
as a condition during processing, and for each subject, I have about 140 runs. 

As a result, selxavg is taking a very long time and huge amounts of memory to 
run. 

For instance, it has gotten about 5 runs into "GLS Beta Pass" after 60 hours of 
running with 200G. 

Is there a way to 
(a) predict based on runs and conditions how long and how much compute power 
selxavg will need to run? 
(b) speed up running selxavg (maybe there is a lighter-weight version of 
selxavg that requires less compute power? 

Thanks very much for any input, 
Anna 

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