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30132 discussions

selxavg3 can't find image that exists
by Scott Burns 11 Apr '11

11 Apr '11

Freesurfers -- Here's the output of my terminal... kerryave:functionals $ cd /cluster/kuperberg/SemPrMM/MRI/functionals/ kerryave:functionals $ rm /cluster/kuperberg/SemPrMM/MRI/functionals/ya24/scripts/atlloc_fs-stats.log kerryave:functionals $ selxavg3-sess -analysis ya.ATLLoc.spm.sm8.lh -s ya24 -d /cluster/kuperberg/SemPrMM/MRI/functionals/ -svres -nolog Surface data fsaverage lh -------------------------------------------------------------- selxavg3-sess logfile is /dev/null -------------------------------------------------------------- ------------------------------------------- /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24 Fri Apr 8 16:47:17 EDT 2011 anadir = /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/ya.ATLLoc.spm.sm8.lh ERROR: cannot find /autofs/cluster/kuperberg/SemPrMM/MRI/functionals/ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz kerryave:functionals $ ls -l ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz -rw-rw-r-- 1 sburns lingua 83660305 Apr 7 07:56 ya24/ATLLoc/007/fmcpr.odd.sm8.fsaverage.lh.nii.gz Does anyone know what's going on? Here's my analysis.info for that analysis... kerryave:functionals $ cd ya.ATLLoc.spm.sm8.lh/ kerryave:ya.ATLLoc.spm.sm8.lh $ cat analysis.info # FSBUILD freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 # MKAVERSION $Id: mkanalysis-sess,v 1.49.2.8 2011/01/18 17:08:22 greve Exp $ # MKACMD /usr/local/freesurfer/stable5_0_0/fsfast/bin/mkanalysis-sess -analysis ya.ATLLoc.spm.sm8.lh -fsd ATLLoc -rlf rlf -p atlloc.par -spmhrf 0 -refeventdur 2 -event-related -TR 2 -nconditions 4 -mcextreg -hpf 128 -funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz -surface fsaverage lh -force # DATE Fri Apr 8 08:31:01 EDT 2011 analysis ya.ATLLoc.spm.sm8.lh mcstem fmcpr funcstem fmcpr.odd.sm8.fsaverage.lh.nii.gz fsd ATLLoc runlistfile rlf TR 2 RegDOF 6 RawSpace surface fsaverage lh mask brain RawFWHM 0 RawSTC none inorm 100 acfbins 30 fixacf 1 acffwhm 20 acfsvd 0 designtype event-related nskip 0 polyfit 2 HPFCutoffHz 128 nconditions 4 parname atlloc.par RefEventDur 2 timewindow 40.000000 prestim 0 TER 0.050000 spmhrf 0 stimulusdelay 0 Condition 1 Condition01 Condition 2 Condition02 Condition 3 Condition03 Condition 4 Condition04 nuisreg mcprextreg 3 Thanks for the help. Scott Burns Kuperberg Lab Martinos Center for Biomedical Imaging sburns(a)nmr.mgh.harvard.edu 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.

4 5

distance between two points along cortical surface
by Fariba Sharifian 11 Apr '11

11 Apr '11

Hi, How should I have the distance between two points in mm? If I use the ?h.sphere, as all the spherical surfaces are normalized to have 100 radius. so the geodesic distances should not be the real distance in mm? Fariba __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology __________________________________________________ Fariba Sharifian, PhD Student. Vision Systems Physiology group, Brain research unit Low Temperature Laboratory and AMI centre Aalto University School of Science and Technology PO BOX 13000, FI-00076 Aalto Espoo, Finland tel: +358-9-470 26159 fax: +358-9-470 22969 e-mail:fariba@neuro.hut.fi http://ltl.tkk.fi/wiki/BRU/Vision_Systems_Physiology

3 2

distance between two points along cortical surface
by Fariba Sharifian 11 Apr '11

11 Apr '11

1 0

recommende pc and cuda
by Knut J Bjuland 09 Apr '11

09 Apr '11

Hi I am in the process of acquiring a new computer to run freesurfer on. I am currently think about buying a PC with a geforce 4X0 and a Tesla card along with a two screen setup running either Ubuntu or Redhat Linux enterprise 6.0. I think the PC should be a core i7 with 6 core and above 12 gigs byte of ram. What kind of tesla card is recommend for using with Freesurfer? Will Freesurfer 5.1 also support cuda 4.0. Knut J

5 9

Course FreeSurfer - São Paulo, Brazil
by Pedro Paulo de Magalhães Oliveira Junior 09 Apr '11

09 Apr '11

Just to inform we still have two spots available for the course in São Paulo next week http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Brazil2011CourseSchedule If there's anyone interested write me for more details. cheers Pedro Paulo Jr.

1 0

Workshop on Diffusion Tensor Imaging in San Francisco on June 7, 2011 (fwd)
by Bruce Fischl 08 Apr '11

08 Apr '11

FYI ---------- Forwarded message ---------- Date: Fri, 8 Apr 2011 15:08:27 -0700 From: Lauren Mullin <lauren.mullin(a)ucsf.edu> To: fischl(a)nmr.mgh.harvard.edu Subject: Workshop on Diffusion Tensor Imaging in San Francisco on June 7, 2011 Dear Dr. Fischl, Dr. Weiner suggested I contact you to see whether you would be interested in advertising this DTI workshop (flyer with information and registration form attached) on the Freesurfer website. Please let me know, thank you & kind regards, Lauren Mullin Administrative Assistant III Center for Imaging of Neurodegenerative Diseases San Francisco Veterans Affairs Medical Center 4150 Clement Street (114M) San Francisco, CA 94121 Tel: 415-221-4810 Ext 6467 Fax: 415-668-2864 Email: lauren.mullin(a)ucsf.edu

1 0

ICV error and talairach registration bad outputs...
by Gonzalo Rojas 08 Apr '11

08 Apr '11

Hi: I forgot the image... Sincerely, Gonzalo Rojas Costa

1 0

ICV error and talairach registration bad outputs...
by Gonzalo Rojas 08 Apr '11

08 Apr '11

Hi: In the image that I am sending attach, there exist a not exact talairach registration in the superior part of the brain... That difference produce an important error in the ICV, or not ?... Sincerely, Gonzalo Rojas Costa

1 0

erroneous ICV volume ?...
by Gonzalo Rojas Costa 08 Apr '11

08 Apr '11

Hi: I have an MRI of a 34 years old patient that have a brain atrophy, but with freesurefer I got an ICV of 1120 cc that is near the normal size for her age... I review the talairach transform, but I think it is ok... What could be the problem ?... Could I upload the MRI volume ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

erroneous ICV volume ?...
by Gonzalo Rojas Costa 08 Apr '11

08 Apr '11

Hi: I have an MRI of a 34 years old patient that have a brain atrophy, but with freesurefer I got an ICV of 1120 cc that is near the normal size for her age... I review the talairach transform, but I think it is ok... Could you please send us the study to process it and send me some tips ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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