Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

3d brain vessels visualisation
by anand iyer 19 Dec '16

19 Dec '16

Hi Could you please help with this? I am able to create a 3D model of brain with T1 volume. I want to superimpose the surface vessels from a T1 GAD. How do i go about it? Thanks, Anand Anand Iyer

2 1

TRACULA trac-all preprocessing errors
by Hao wen 19 Dec '16

19 Dec '16

Hello, Freesurfer experts: I am new to Tracula, and I followed your tutorial with your tutorial data, and for the preprocessing pipeline, I got some errors when doing the tensor fitting, here is the command: trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial and I looked over the trac-all.log and found that the problem is from the command dmri_train, here is the errro log information: ' /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.25745.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc ERROR: fio_pushd: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni cwd /aramis/dataARAMIS/users/junhao.wen/dataset/Freesurfer/tutorial_data_new/diffusion_tutorial cmdline /aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train --outdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.elmo.2005.25745.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/dtifit_FA.nii.gz --cptdir /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff --reg /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc sysname Linux hostname DELLEED1 machine x86_64 user wen Output directory: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni Output directory in test subject's space: /aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.elmo.2005.25745.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: [1] 1065 segmentation fault (core dumped) --outdir --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr ' and in the output structure /dlabel, I dont have the mni sub-folder, so I guess I have some problems when doning the tensor fitting. And I know in this process, we will need the aparc+aseg.mgz, but the in the tutorial data diffusion_recons , for the subject of elmo.2005, I dont find aparc+aseg.mgz in mri folder, and I just found aparc+aseg2diff.mgz image in Diff001, instead, you use this volume??? I am stuck at this step, any advice will be appreciated:) Thank in advance Hao Good day

2 6

Own ROI for cortical thickness measurements
by andinie＠gmx.net 17 Dec '16

17 Dec '16

Dear Freesurfer-experts, I want to create my own ROI for purposes of cortical thickness measurements in Freesurfer. As input, I have a binary_volume_mask.mgz. But I'm lacking to get this mask as a label or volume into the FS structure. I already tryed the mri_vol2surf and mri_vol2roi, unfortunately without successs. Looking forward to hearing your suggestion, Best, Andreas Niebuhr ............................................................................ ..... Bitte denken Sie an Ihre Verantwortung gegenüber der Umwelt, bevor Sie diese E-Mail drucken. Die in dieser Nachricht enthaltenen Informationen können vertraulich sein und sind ausschließlich für den Adressaten bestimmt. Sollten Sie nicht der vorgesehene Empfänger sein, so bitte ich Sie, den Absender unverzüglich zu informieren und die E-Mail zu löschen. Eine nicht autorisierte Verwendung, Verbreitung oder Kopie ist nicht gestattet. Ich weise darauf hin, dass über das Internet per E-Mail übermittelte Nachrichten verändert oder verfälscht werden können. Herkömmliche E-Mails sind nicht gegen den Zugriff Dritter geschützt, so dass unter Umständen auch die Vertraulichkeit nicht gewahrt sein kann. Von der Übermittlung sensibler Geschäftsdaten sollten Sie daher absehen.

2 3

Please send email only once as list, not each email
by anand iyer 17 Dec '16

17 Dec '16

Hello I am signed up for receiving mails; and i get each individual one which is flooding my inbox can you please send all only once a day as a list? Thanks, Anand Iyer

2 1

Regarding: dlPFC volume
by Dr Sampada Sinha 17 Dec '16

17 Dec '16

Dear freesurfer experts, I managed to create dlPFC ROI and successfully extracted the cortical surface parameters. I also want to have the whole volume of dlPFC (*not* the gray matter volume). Will it make any sense if I multiply dlPFC ROI surface area with its corresponding thickness to get a valid dlPFC volume? Thanks and regards, Sampada -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 India

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Center Director Ad: Umass Amherst Human Magnetic Resonance Center
by Jacquie Kurland 16 Dec '16

16 Dec '16

Please post this ad: Human Magnetic Resonance Center Director (Tenured Associate or Full Professor) The Department of Psychological and Brain Sciences and Institute for Applied Life Sciences at the University of Massachusetts Amherst, invite applications for a tenured faculty position at the rank of associate or full professor to also serve as director of the newly-opened Human Magnetic Resonance (MR) Center, starting September 2017. The Human MR Center houses a state-of-the-art Siemens Skyra 3T and is part of the $95 million investment of the University and the Commonwealth into the new Institute of Applied Life Sciences (http://www.umass.edu/ials/) As a faculty member with a home in the Department of Psychological and Brain Sciences, the director will lead his or her own research lab and related student training. The director is expected to lead the MR Center in all its functions and to carry out his or her own neuroimaging research. As director, this person is expected to build and lead a highly productive center and support the development of MRI and MRS research of new and existing users. The director will also oversee Center staff including physicists and technicians. Applicants must have an MD or PhD in Psychology, Neuroscience, or related field, and a strong track record of research publications and federal funding focused on the development or use of state-of-the-art magnetic resonance techniques and approaches for the study of human brain structure and function. Preference will be given to a candidate with demonstrated leadership and extensive experience and involvement in a successful MR center. We seek relevant expertise in areas such as: anatomical or functional neuroimaging; development of new neuroimaging methodologies; or neuroimaging of cognition To apply, submit the following materials: Curriculum vitae, research statement, contact information for three references, and a letter of application that addresses the responsibilities and requirements described above. Applicants must submit all materials by the priority deadline of January 25, 2017, in order to ensure consideration. Please submit materials online to: http://umass.interviewexchange.com/jobofferdetails.jsp?JOBID=79603 For questions about the position, contact search committee co-chair, Rebecca Spencer, rspencer(a)umass.edu<mailto:rspencer@umass.edu>. The University is committed to active recruitment of a diverse faculty and student body. The University of Massachusetts Amherst is an Affirmative Action/Equal Opportunity Employer of women, minorities, protected veterans, and individuals with disabilities and encourages applications from these and other protected group members. Because broad diversity is essential to an inclusive climate and critical to the University's goals of achieving excellence in all areas, we will holistically assess the many qualifications of each applicant and favorably consider an individual's record working with students and colleagues with broadly diverse perspectives, experiences, and backgrounds in educational, research or other work activities. We will also favorably consider experience overcoming or helping others overcome barriers to an academic degree and career. Thank you in advance, Jacquie Kurland -- Jacquie Kurland, Ph.D., CCC-SLP Associate Professor Dept. of Communication Disorders (413) 545-4007 jkurland(a)comdis.umass.edu<mailto:jkurland@comdis.umass.edu>

1 0

(no subject)
by Sadhana Singh 16 Dec '16

16 Dec '16

Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial) but it shows the following error when I run the recon-all command: ERROR: cannot find CON_101.nii recon-all -s exited with ERRORS I've tried so many times but still shows same errors. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Red Hat Enterprise Linux 7 3) uname -a: Linux lcmodel 3.10.0-327.el7.x86_64 #1 SMP Thu Oct 29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Regards *Sadhana Singh, PhD * *Postdoctoral Researcher* *Departments of Anesthesiology * *David Geffen School of Medicine at UCLA * *University of California at Los Angeles * *Los Angeles, CA, USA* *Phone No: 424-270-4940 * *Email: sadhanasingh(a)mednet.ucla.edu <sadhanasingh(a)mednet.ucla.edu> *

2 1

Re: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads
by Harms, Michael 16 Dec '16

16 Dec '16

Wow, that’s a terrible correlation between two putative measures of head size. What does the scatterplot of FS’s “eTIV” vs “SupraTentorialVol” look like? The latter is based on the surfaces, so a scatterplot of the two can be a good way to identify cases where the talairach.xfm file (from which “eTIV” is derived) isn’t very accurate. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Jeffrey Crawford <jcrawf29(a)jhmi.edu<mailto:jcrawf29@jhmi.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, December 16, 2016 at 11:56 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads Hello everyone! I have some questions about FS eTICV. I read on the Wiki that eTICV is not the best measure of ICV and saw the same from other articles. The alternative I decided on was measuring the TICV using CAT12 from SPM. I decided to do a scatterplot of the eTICV from FS V6 and TICV from CAT12 to see how they match each other on measurment. FS is the variable on the Y-axis and CAT12 is the variable on the X-axis. If we assume that CAT12 is more accurate than FS, then it looks as though the FS begins to become more inaccurate as the head size gets smaller. [cid:image001.png@01D2579B.8A615E30] So here are my questions: 1. Is my interpretation of this scatterplot correct? 2. Does FS generally have more difficulty measuring smaller heads? If so, then why? 3. Is it more advised for me to use the CAT12 TICV measure as a covariate in my future analysis? Or maybe some other program that I don’t know about? ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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ERROR: the pixel data cannot be loaded as it is JPEG compressed.
by Warner, Graham Cary 16 Dec '16

16 Dec '16

Hi, I'm trying to open a dicom using the center's instillation of freesurfer (/usr/local/freesurfer/nmr-stable53-env) but get the following error message when trying to load the file. Starting DICOMRead2() dcmfile = /autofs/space/jazz_001/users/gwarner/mi2b2Data/1.2.124.113532.132.183.36.32.20040903.132017.11895667/1.2.840.113619.2.25.49466.102.1094369499/1.2.840.113619.2.25.49466.102.1.1094369499.dcm dcmdir = /autofs/space/jazz_001/users/gwarner/mi2b2Data/1.2.124.113532.132.183.36.32.20040903.132017.11895667/1.2.840.113619.2.25.49466.102.1094369499 Ref Series No = 102 Found 25 files, checking for dicoms Found 23 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 6 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 23 ndcmfiles = 23 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) jpegUID: --1.2.840.10008.1.2.4-- I am able to open the file in pydicom and even view the binary of the pixel data but crash again when I try to use the pixel_array function. The pydicom error also indicates that it can't handle the JSON compression. It looks like I'm not the first person to have this problem (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40683.html) but the solution given here won't work for me because I can't write to the directory mentioned. Does anyone know another way to solve this? Thank you, Graham

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Re: [Freesurfer] License problem
by Marco Ganzetti 16 Dec '16

16 Dec '16

At the current stage I can run recon-all and get the results without problems. If the license would not work I couldn't be able to run it. Can someone send me the type of license file I should generate? In the website it says that I should get a license.txt by email, but I didn't get any file just instructions how to create a new file or modify the existing LICENSE file. Marco Ganzetti, PhD Il 16 Dic 2016 19:47, Z K <zkaufman(a)nmr.mgh.harvard.edu> ha scritto: Is the file you created located in /Applications/freesurfer? Also, fir good measure, try creating the same file but naming it .license in the /Applications/freesurfer On 12/16/2016 11:20 AM, Marco Ganzetti wrote: > Dear all, > I am trying to display a volumetric file to a surface using mri_vol2surf > and then tksurfer. > Here is the error message I get. > > I have obtained the email with the few license lines to copy in a file > (that i created) name license.txt > I created a new file and erased the existing LICENSE > > Thanks > Marco Ganzetti > > Last login: Fri Dec 16 16:56:54 on ttys002 > -------- freesurfer-Darwin-lion-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 /usr/local/fsl > Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile > -------- freesurfer-Darwin-lion-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 /usr/local/fsl > Binds-MacBook-Pro:~ Marco$ export > SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN > Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii > --regheader elab --hemi lh --o > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh > srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii > srcreg unspecified > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > Done loading volume > Computing registration from header. > Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target > reference. > Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 41923 > Writing to > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh > Dim: 116772 1 1 > Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh > subject is elab > hemi is lh > surface is inflated > surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Users/Marco > checking for nofix files in 'inflated' > Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab) > Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz > surfer: Reading header info from > /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz > -------------------------------------------------------------------------- > ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -------------------------------------------------------------------------- > Binds-MacBook-Pro:~ Marco$ > > - - - > > *Marco Ganzetti, PhD* > > Movement Control & Neuroplasticity Research Group > Tervuursevest 101, 3001 Leuven > > email: marco.ganzetti(a)kuleuven.be <mailto:marco.ganzetti@kuleuven.be> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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