Freesurfer April 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
229 discussions

Create a label from a binary mask
by Cherisse Onuigbo 09 Apr '14

09 Apr '14

Hello I was wondering how to create a label from a binary mask. I created a mask and then normalized it to the template space. When I tried to use mri_cor2vol, all the vertex numbers come out as -1. I understand that the vertex numbers should come out as -1, but when I entered the coordinates in the display function in spm, it was not in the region. Thank you, Cherisse

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Questions about byvoxel statistics from Tracula
by Emilie Poirion 09 Apr '14

09 Apr '14

Hello I'm using Tracula to analyse our DWI-images. Freesurfer reconstructions of the corresponding T1-images have been perfomed before. Respectively, the version used are 1.53 and 5.3. The Tracula process works fine and I have extracted the statistics for all tracts. About this statistics, I wanted to know what is the difference between FA and FA_Avg ? An other question about the values extracted is about the coordinates in the file "byvoxel.txt". Are they correspind with the coordinates of the voxel in the dtifit image were the values were extracted? The last question, can we extracted the same by tract statistics from an other image like a PET registered to the DWI with your code? Thanks for your answer -- Emilie Poirion Master 1 Informatique Industrielle et Imagerie Industrielle Université Pierre et Marie Curie (Paris 6)

2 1

Two positions (post-doc and software engineer) in Marseille, France
by Olivier Coulon 09 Apr '14

09 Apr '14

Dear all, we have two positions opening in Marseille, France, for the study and modelling of brain development. Descriptions can be found at the following URLs: https://dl.dropboxusercontent.com/u/3372764/EngineerPosition_lefevreMarseil… https://dl.dropboxusercontent.com/u/3372764/PostDocPosition_lefevreMarseill… If interested, pease contact Dr Julien Lefèvre at: julien.lefevre(a)univ-amu.fr Olivier -- Olivier Coulon, CNRS research Fellow, olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

1 0

read cluster summary into Matlab?
by Caspar M. Schwiedrzik 09 Apr '14

09 Apr '14

Hi! I was wondering whether there is code available to quickly read cluster summary files into Matlab? I need access to the cluster-wise p-values. Thank you very much! Caspar

2 1

R: Re: R: Re: R: Re: Problem of size
by Andrea Tateo 09 Apr '14

09 Apr '14

Endless thanks. I'll try and update you. Andrea ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 9-apr-2014 17.16 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: R: Re: [Freesurfer] Problem of size on the recon-all command line On Wed, 9 Apr 2014, Andrea Tateo wrote: > I use > « recon-all -debug -s 001 -autorecon-all » > > > and after > > « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz > --regheader aseg.mgz » > > Where can I specify "-cw256" ? > > > > ----Messaggio originale---- > Da: fischl(a)nmr.mgh.harvard.edu > Data: 9-apr-2014 16.56 > A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> > Cc: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: R: Re: [Freesurfer] Problem of size > > Hi Andrea > > will it fit in 256? You can try specifying -cw256 > > cheers > Bruce > > > On Wed, 9 Apr 2014, Andrea Tateo wrote: > > > > > Hi Bruce, > > > > thanks for the quick response. > > > > I report the full error message: > > > > > >WARNING==================++++++++++++++++++++++++========================== > ======= > > ====== > > The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit > > in 256^3 mm^3 volume. > > The resulting volume will have 312 slices. > > If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) > >==================================================++++++++++++++++++++++++= > > > ============== > > > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > readingfrom/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3 > /001 > > /mri/rawavg.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, -0) > > j_ras = (0, 0, -1) > > k_ras = (-0, 1, -0) > > Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. > > Data is conformed to 1 mm size and 312 voxels for all directions > > changing data type from float to uchar (noscale = 0)... > > MRIchangeType: Building histogram > > Reslicing using trilinear interpolation > > writingto/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/0 > 01 > > /mri/orig.mgz... > > > > **************************************** > > ERROR! FOV=312.000 > 256 > > Include the flag -cw256 with recon-all! > > > > > > Thank you very much > > > > Andrea > > > > > > > > > > > > > > ----Messaggio originale---- > > Da: fischl(a)nmr.mgh.harvard.edu > > Data: 9-apr-2014 14.45 > > A: "Andrea Tateo"<andrea.tateo(a)virgilio.it>, "Freesurfer support > > list"<freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] Problem of size > > > > Hi Andrea > > > > what size are your voxels? Do you really need an FOV that big? If not, > > you could extract the central 256mm using mri_extract. And I believe this > > is just a warning - does recon-all complete? > > > > cheers > > Bruce > > > > > > > > On Wed, 9 Apr 2014, > > Andrea Tateo wrote: > > > > > > > > Hi FreeSurfer expert, > > > > > > I have a problem with command "recon-all". > > > > > > In recon-all.log I can read: > > > > > > «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot > > fit > > > in 256^3 mm^3 volume. > > > > > > The resulting volume will have 312 slices. > > > > > > If you find problems, please let us know > > (freesurfer(a)nmr.mgh.harvard.edu).xn--yba > > > > > > I hope are there anyone to help me. > > > > > > Thank for your help. > > > > > > Andrea > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > > > >

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R: Re: R: Re: Problem of size
by Andrea Tateo 09 Apr '14

09 Apr '14

I use « recon-all -debug -s 001 -autorecon-all » and after « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz --regheader aseg.mgz » Where can I specify "-cw256" ? ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 9-apr-2014 16.56 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it> Cc: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] Problem of size Hi Andrea will it fit in 256? You can try specifying -cw256 cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: > > Hi Bruce, > > thanks for the quick response. > > I report the full error message: > > > WARNING==================++++++++++++++++++++++++================================= > ====== > The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit > in 256^3 mm^3 volume. > The resulting volume will have 312 slices. > If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) > ==================================================++++++++++++++++++++++++= > ============== > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 > /mri/rawavg.mgz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, -0) > j_ras = (0, 0, -1) > k_ras = (-0, 1, -0) > Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. > Data is conformed to 1 mm size and 312 voxels for all directions > changing data type from float to uchar (noscale = 0)... > MRIchangeType: Building histogram > Reslicing using trilinear interpolation > writing to/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 > /mri/orig.mgz... > > **************************************** > ERROR! FOV=312.000 > 256 > Include the flag -cw256 with recon-all! > > > Thank you very much > > Andrea > > > > > > > ----Messaggio originale---- > Da: fischl(a)nmr.mgh.harvard.edu > Data: 9-apr-2014 14.45 > A: "Andrea Tateo"<andrea.tateo(a)virgilio.it>, "Freesurfer support > list"<freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Problem of size > > Hi Andrea > > what size are your voxels? Do you really need an FOV that big? If not, > you could extract the central 256mm using mri_extract. And I believe this > is just a warning - does recon-all complete? > > cheers > Bruce > > > > On Wed, 9 Apr 2014, > Andrea Tateo wrote: > > > > > Hi FreeSurfer expert, > > > > I have a problem with command "recon-all". > > > > In recon-all.log I can read: > > > > «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot > fit > > in 256^3 mm^3 volume. > > > > The resulting volume will have 312 slices. > > > > If you find problems, please let us know > (freesurfer(a)nmr.mgh.harvard.edu).xn--yba > > > > I hope are there anyone to help me. > > > > Thank for your help. > > > > Andrea > > > > > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > >

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R: Re: Problem of size
by Andrea Tateo 09 Apr '14

09 Apr '14

Hi Bruce, thanks for the quick response. I report the full error message: WARNING ==================++++++++++++++++++++++++=======================================The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).==================================================++++++++++++++++++++++++=============== $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001/mri/rawavg.mgz...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, -0)j_ras = (0, 0, -1)k_ras = (-0, 1, -0)Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels.Data is conformed to 1 mm size and 312 voxels for all directionschanging data type from float to uchar (noscale = 0)...MRIchangeType: Building histogramReslicing using trilinear interpolationwriting to /lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001/mri/orig.mgz... ****************************************ERROR! FOV=312.000 > 256Include the flag -cw256 with recon-all! Thank you very much Andrea ----Messaggio originale---- Da: fischl(a)nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: "Andrea Tateo"<andrea.tateo(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: > > Hi FreeSurfer expert, > > I have a problem with command "recon-all". > > In recon-all.log I can read: > > «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit > in 256^3 mm^3 volume. > > The resulting volume will have 312 slices. > > If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu).xn--yba > > I hope are there anyone to help me. > > Thank for your help. > > Andrea > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

Freesurfer QDEC Buckner Data
by Saurabh Thakur 09 Apr '14

09 Apr '14

Hello Freesurfer Expert, I am working on QDEC and looking forward to download buckner_data from link mentioned below: wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz Needing data asap. Please share alternative mirror link to download the buckner_data. cheers Saurabh Thakur,

3 5

mri_surcluster and centroid option
by Joerg Pfannmoeller 09 Apr '14

09 Apr '14

Hi, I am trying to compute centroid coordinates of maps for functional activation obtained from fsfast with mri_surfcluster. The command is: mri_surfcluster --in /.../sig.nii.gz --thmin 3 --thmax infinity--sign pos --subject subjid --hemi rh --surf white --annot aparc --frame 0 --minarea 0 --sum ./tabular_surfcluster.txt -- centroid Unfortunately, the centroid option has no effect. Results in tabular_surfcluster.txt with and without centroid option are identical. What am I doing wrong? Respectfully yours pfannmoe

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Problem of size
by Andrea Tateo 09 Apr '14

09 Apr '14

Hi FreeSurfer expert,I have a problem with command "recon-all". In recon-all.log I can read:«The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu).xn--i-nda hope are there anyone to help me.Thank for your help.Andrea

2 1

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Freesurfer April 2014