[Freesurfer] Regarding XYZ coordinates information of both left and right ROIs included in lh.aparc.a2009.thickness.stats.dat

[Santosh Yadav]

Dear FreeSurfer Experts,

Can any one please guide me how to get the XYZ coordinates information of
both left and right ROIs included in lh.aparc.a2009.thickness.stats.dat,
that have 74 ROIs (below), these ROI I got after Qdec in the state_table
folder.

With best

Santosh
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[Freesurfer] mri_glmfit-sim output files

[Omar Singleton]

Hi there,

I have a couple of questions about the mri_glmfit-sim output files.

First, in the mc-z.whole.absolute.sig.cluster.summary file, is the "Max" a
z-score or t-score? I have seen it referred to as -log10pvalue, but is
there a place where I can find the z- or t-score?

Second, are the numbers in the mc-z.whole.absolute.y.ocn.dat file the
average thickness of each cluster that survives correction for each
subject?

Thanks!


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Re: [Freesurfer] fslswapdim.fsl: Command not found

[Z K]

If I understand your question correctly, your saying you already have 
fsl installed and have the fslswapdim binary. If this is the case, I 
suppose it would be possible to copy the fslswapdim into the 
FREESURFER_HOME/bin directory. But you would also have to append a 
".bin" at the end.

This is slightly risky because the fslswapdim bianry that you have might 
be different than the one that ships with freesurfer. But I suppose its 
worth a try.

-Zeke

On 03/18/2015 08:18 PM, Dr Sampada Sinha wrote:
> Hello Zeke,
>
> Thanks for you valuable reply! I will go with option first of
> reinstalling freesurfer for 64bit version. I have a quick question
> though: my fsl binaries already have fslswapdim in it. If I go with an
> option second (just in case), do I still need to download fsl binaries?
>
> Thanks and regards,
>
> Sampada
>
> On Wed, Mar 18, 2015 at 5:30 PM, Z K  > wrote:
>
> Hello Sampada,
>
> It appears you are running the 32bit version of freesurfer on your
> 64bit Mac machine. Which is fine, but you would probably get better
> performance if you installed the 64bit bit version of freesurfer
> onto your machine.
>
> In regard to the error you are experiencing, you have 2 options:
>
> 1) Delete the version of freesurfer you have on your machine and
> install the 64bit version from the following page:
> (https://surfer.nmr.mgh.__harvard.edu/fswiki/Download
> )
>
> 2) Keep the version of freesurfer you currently have on your machine
> and download the the fsl binaries from here
> 
> (ftp://surfer.nmr.mgh.harvard.__edu/pub/dist/freesurfer/__patches/freesurfer_fsl.tar.gz
> 
> )__.
> Extract the contents of the tar file into the $FREESURFER_HOME/bin
> directory. This should result in 6 new files with a .fsl extension
> in the $FREESURFER_HOME/bin directory.
>
> Both options are valid.
>
> -Zeke
>
>
>
> On 03/18/2015 06:20 PM, Dr Sampada Sinha wrote:
>
> I hope you are looking for this:
>
> Last login: Tue Mar 17 15:48:52 on ttys009
> rmbp:~ Sampada$ export FREESURFER_HOME=/Applications/__freesurfer
> rmbp:~ Sampada$ source $FREESURFER_HOME/__SetUpFreeSurfer.sh
>  freesurfer-Darwin-snowleopard-__i686-stable-pub-v5.3.0
> 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/__fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/__subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /Applications/fsl
> rmbp:~ Sampada$ tcsh
> [rmbp:~] Sampada% setenv dtimartinos
> /Users/Sampada/Desktop/__dtimartinos
> [rmbp:~] Sampada% setenv SUBJECTS_DIR $dtimartinos/diffusion_recons/
> [rmbp:~] Sampada% setenv TUTORIAL_DIR
> $dtimartinos/diffusion___tutorial/
> [rmbp:~] Sampada% set subj = Diff001
> [rmbp:~] Sampada% dt_recon --i
> $TUTORIAL_DIR/$subj/orig/*-1.__dcm --s
> $subj --o $TUTORIAL_DIR/$subj/dtrecon
> INFO: SUBJECTS_DIR is
> /Users/Sampada/Desktop/__dtimartinos/diffusion_recons/
> dt_recon logfile
> Wed Mar 18 16:38:49 CDT 2015
> VERSION $Id: dt_recon,v 1.15 2011/01/25 21:53:04 greve Exp $
> setenv SUBJECTS_DIR
> /Users/Sampada/Desktop/__dtimartinos/diffusion_recons/
> cd /Users/Sampada
> /Applications/freesurfer/bin/__dt_recon --i
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial//Diff001/orig/6-1.dcm
> --s Diff001 --o
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial//Diff001/dtrecon
> rmbp.home
> Sampada
> /Applications/fsl/bin/eddy___correct
> ECRefTP 0
> #@#---__
> Converting input
> Wed Mar 18 16:38:49 CDT 2015
> cd /Users/Sampada
> mri_convert
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial/Diff001/orig/6-1.dcm
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial/Diff001/dtrecon/dwi.__nii
> mri_convert
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial/Diff001/orig/6-1.dcm
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial/Diff001/dtrecon/dwi.__nii
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
> 
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial/Diff001/orig/6-1.dcm.__..
> Getting Series No
> INFO: Found 72 files in
> /Users/Sampada/Desktop/__dtimartinos/diffusion___tutorial/Diff001/orig
> INFO: Scanning for Se

[Freesurfer] PhD studentship at Durham University

[Paige Scalf]

Dear colleagues,

Applications are invited for a fully funded PhD position (3 years) in the
Department of Psychology at Durham University. The successful applicant
will work with Paige Scalf in the Centre for Vision and Visual Cognition
(CVVC) on the neural processes underlying vision, attention and working
memory employing combinations of research methods and tools from
psychology, neuroscience and functional neuroimaging (fMRI).

The Department of Psychology and CVVC offer an exciting and friendly
multidisciplinary research environment with ample opportunities for
training and collaboration. The centre has access to excellent technical
facilities including a 0T and 3T MRI scanner, as well as laboratories for
brain stimulation (TMS, tdCS), motion analysis systems, behavioural
experiments and eye-tracking. Dr Scalf has expertise in ultra-high
resolution fMRI and time-resolved fMRI methodology.


  The candidate is expected to have a strong academic background. A
preference is given to students with a background in psychology,
neuroscience, math or computer science at the master’s level.  Candidates
who have knowledge of fMRI analysis packages (SPM, Matlab, Freesurfer,
AFNI), statistical software (e.g., R or Stata) and programming skills
(e.g.,python, C++, matlab ) will have a strong advantage. Applications are
welcome from EU nationals.

The position is expected to begin in October 2015. Applications should
include a curriculum vitae and a cover letter. Three letters of academic
reference, assessing the applicant’s research potential and personality,
should be sent independently by the referees. Applications should be
submitted electronically and all material, including reference letters, be
sent to’psychology.off...@durham.ac.uk’  with reference to “PhD position
vision/attention" in the e-mail header. Applications must be received by
April 14th  2015.

Informal inquiries can be sent via email to Paige Scalf,
paige.sc...@durham.ac.uk
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Re: [Freesurfer] Multiple and equidistant circular ROIs on the surface

[Lee Tirrell]

The reason this problem occurs is that there is no Unknown label in the 
colortable, which causes mris_divide_parcellation to segfault. After 
adding an Unknown label to the beginning of ColorTest.txt, these commands 
completed as expected.



On Wed, 18 Mar 2015, Victor Montal Blancafort wrote:


Thank you for your fast reply, Bruce.


(1)  *** mris_label2annot:

[ejones:test] (nmr-stable53-env) mris_label2annot --s fsaverage/ --h lh --ctab
ColorTest.txt --a test --l mask_region_ROIS.label
Reading ctab ColorTest.txt
Number of ctab entries 2

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /autofs/cluster/animal/users/victor/test
cmdline mris_label2annot --s fsaverage/ --h lh --ctab ColorTest.txt --a test --l
mask_region_ROIS.label
sysname  Linux
hostname ejones
machine  x86_64
user vmblanca

subject fsaverage/
hemi    lh
SUBJECTS_DIR /autofs/cluster/animal/users/victor/test
ColorTable ColorTest.txt
AnnotName  test
nlables 1
LabelThresh 0 0.00
Loading /autofs/cluster/animal/users/victor/test/fsaverage//surf/lh.orig
 1 130 mask_atrophy
Mapping unhit to unknown
Found 163791 unhit vertices
Writing annot to
/autofs/cluster/animal/users/victor/test/fsaverage//label/lh.test.annot

(2) *** mris_divide_parcellation

mris_divide_parcellation fsaverage lh test.annot splittable.txt finalAnnot.split
reading colortable from annotation file...
colortable with 2 entries read (originally ColorTest.txt)
interpreting 4th command line arg as split file name
dividing mask_atrophy (1) into 2 parts
allocating new colortable with 2 additional units...
Segmentation fault (core dumped)

(3) Files values (splittable.txt && ColorTest.txt) in older mail.



Thank you in advance!
Victor Montal


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Re: [Freesurfer] Regarding ROIs coordinates

[Bruce Fischl]

Hi Santosh

when you say " XYZ coordinates information", what coordinate system do 
you mean? You can certainly load the surface (white or pial) and the annot 
into matlab and get the surface ras coords that way.

cheers
Bruce

On Thu, 19 Mar 2015, Santosh 
Yadav wrote:

> Dear FreeSurfer Experts,
> Can any one please guide me how to get the XYZ coordinates information of
> both left and right ROIs included in lh.aparc.a2009.thickness.stats.dat,
> that have 74 ROIs (below), these ROI I got after Qdec in the state_table
> folder.
> 
> lh_G_and_S_frontomargin_thickness
> lh_G_and_S_occipital_inf_thickness
> lh_G_and_S_paracentral_thickness
> lh_G_and_S_subcentral_thickness
> lh_G_and_S_transv_frontopol_thickness
> lh_G_and_S_cingul-Ant_thickness
> lh_G_and_S_cingul-Mid-Ant_thickness
> lh_G_and_S_cingul-Mid-Post_thickness
> lh_G_cingul-Post-dorsal_thickness
> lh_G_cingul-Post-ventral_thickness
> lh_G_cuneus_thickness
> lh_G_front_inf-Opercular_thickness
> lh_G_front_inf-Orbital_thickness
> lh_G_front_inf-Triangul_thickness
> lh_G_front_middle_thickness
> lh_G_front_sup_thickness
> lh_G_Ins_lg_and_S_cent_ins_thickness
> lh_G_insular_short_thickness
> lh_G_occipital_middle_thickness
> lh_G_occipital_sup_thickness
> lh_G_oc-temp_lat-fusifor_thickness
> lh_G_oc-temp_med-Lingual_thickness
> lh_G_oc-temp_med-Parahip_thickness
> lh_G_orbital_thickness
> lh_G_pariet_inf-Angular_thickness
> lh_G_pariet_inf-Supramar_thickness
> lh_G_parietal_sup_thickness
> lh_G_postcentral_thickness
> lh_G_precentral_thickness
> lh_G_precuneus_thickness
> lh_G_rectus_thickness
> lh_G_subcallosal_thickness
> lh_G_temp_sup-G_T_transv_thickness
> lh_G_temp_sup-Lateral_thickness
> lh_G_temp_sup-Plan_polar_thickness
> lh_G_temp_sup-Plan_tempo_thickness
> lh_G_temporal_inf_thickness
> lh_G_temporal_middle_thickness
> lh_Lat_Fis-ant-Horizont_thickness
> lh_Lat_Fis-ant-Vertical_thickness
> lh_Lat_Fis-post_thickness
> lh_Pole_occipital_thickness
> lh_Pole_temporal_thickness
> lh_S_calcarine_thickness
> lh_S_central_thickness
> lh_S_cingul-Marginalis_thickness
> lh_S_circular_insula_ant_thickness
> lh_S_circular_insula_inf_thickness
> lh_S_circular_insula_sup_thickness
> lh_S_collat_transv_ant_thickness
> lh_S_collat_transv_post_thickness
> lh_S_front_inf_thickness
> lh_S_front_middle_thickness
> lh_S_front_sup_thickness
> lh_S_interm_prim-Jensen_thickness
> lh_S_intrapariet_and_P_trans_thickness
> lh_S_oc_middle_and_Lunatus_thickness
> lh_S_oc_sup_and_transversal_thickness
> lh_S_occipital_ant_thickness
> lh_S_oc-temp_lat_thickness
> lh_S_oc-temp_med_and_Lingual_thickness
> lh_S_orbital_lateral_thickness
> lh_S_orbital_med-olfact_thickness
> lh_S_orbital-H_Shaped_thickness
> lh_S_parieto_occipital_thickness
> lh_S_pericallosal_thickness
> lh_S_postcentral_thickness
> lh_S_precentral-inf-part_thickness
> lh_S_precentral-sup-part_thickness
> lh_S_suborbital_thickness
> lh_S_subparietal_thickness
> lh_S_temporal_inf_thickness
> lh_S_temporal_sup_thickness
> lh_S_temporal_transverse_thickness
> With best,
> 
> Santosh
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[Freesurfer] Advice on MNI305 to MNI152

[Tan Pin Kwang]

Dear Freesurfer experts,


I am a beginner in the neuroscience community and I am trying to convert a 
MNI305 mask to a ICBM152/MNI152 mask. How can I do that? I have Freesurfer 
downloaded and Guest Additions installed(don't know if i need FSL or how to get 
it to work with FS), but when i try to run this solution from a previous 
correspondence between Yigal Adam and you guys, i am stuck even at the first 
step:


1. Register functional (template.nii) to anatomical matrix (may

   already be done in fsfast)



bbregister --s $subject --bold --init-fsl \

   --mov template.nii --reg register.dof6.dat



2. Register anatomical to mni152:

  mni152reg --s $subject

   Creates $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat



3. Check registration

   tkregister2 --mov $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \

 --reg $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat



4. Create registration between functional and mni152

  mri_matrix_multiply -im register.dof6.dat \

   -iim reg.mni152.2mm.dat -om reg.mni152.dat



5. Check registration

 tkregister2 --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \

   --mov template.nii --reg reg.mni152.dat



6. Resample func to mni152 space

 mri_vol2vol --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz \

   --mov template.nii --reg reg.mni152.dat --o template.mni152.nii?


and it says ERROR: cannot find --bold in /usr/local/freesurfer/subjects


Am I doing something wrong with the setup?(I haven't configured anything 
besides downloading FS and its Guest Additions).




Please help, i've been stuck for weeks.


?Thank you!

?

Regards,

--PK?

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[Freesurfer] TRACULA results / pathstats.overall.txt

[Michele Cavallari]

Hi there,
I have a couple questions regarding TRACULA results.

When I visualize the probability distributions of all white-matter pathways
simultaneously in some cases the tracts are very small, but by adjusting
the threshold I am able to visualize the tract in its entire (and expected)
path.

So, question#1:
The results included in the pathstats.overall.txt file are produced using
the default threshold?
It looks like the Volume is very small in those tracts that I can visualize
only by playing with the threshold. I was wondering whether the DTI metrics
can be also impacted.

Which leads me to question#2:
Do I need to re-run the whole processing (e.g. with -prior option) to get
more accurate fiber tracking and DTI results, or there is a way I can
adjust the threshold for computation of the DTI (and other) results?

Thank you,
-Michele
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