Freesurfer January 2013

freesurfer@nmr.mgh.harvard.edu

111 participants
203 discussions

entorhinal cortex volume question
by Cat Chong 29 Jan '13

29 Jan '13

Hello experts, I am very new to freesurfer so please excuse my basic question: We want to get measurements of entorhinal cortex volumes on a group of people. I found these results listed in ?h.aparc.stats. I also noticed another ?h.entorhinal_exvivo.stats, with different results. Which should I use for a group analysis of entorhinal volume and surface area, and why are the results very different? very best regards, catherine

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diluting a mask using inflated brain
by Jodie Davies-Thompson 29 Jan '13

29 Jan '13

Dear Freesurfer users and experts, We are attempting to grow a mask that we have created in FSL, to expand it into white matter. At first, we tried this in FSL using the dilM command which dilated the size of the mask by n voxels. We then multiplied this by a segmented white matter mask (again, created in FSL) so only the white matter voxels were included. However, a problem with this method, is that if a mask is over a gyri (as most of our masks are), then diluting the mask in a non-inflated brain causes some voxels from an adjacent gyri to be included. What we would like to be able to do, is to dilute the mask using the inflated white matter brain created by Freesurfer, and then to take this back into FSL space; thereby, allowing us to create a mask of which includes the true surrounding white matter rather than white matter from adjacent gyri. Hope this makes sense!? Does anyone know how to do this or could point us in the right direction? Cheers, Jodie - --- Jodie Davies-Thompson, Postdoctoral Fellow Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 2550 Willow Street Vancouver, BC, V5Z 3N9 Canada Tel: 604-875-4111<Tel:604-875-411> ext 69003

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Postdoctoral Position in Australia
by Nicolas Cherbuin 29 Jan '13

29 Jan '13

Post-doc position available immediately within the Centre for Research on Ageing, Health and Wellbeing, College of Medicine, Biology and the Environment, Australian National University, Canberra, Australia. We are seeking a junior Postdoctoral Fellow to join a small collaborative team working on research aimed at characterising normal brain ageing in mid-life and into old age. This research includes using large neuroimaging datasets, studying cognitive correlates of age-related brain changes, identifying predictors and risk factors for brain and cognitive ageing, and test theoretical models of neuro-cognitive ageing. Working closely with Dr Nicolas Cherbuin, the research involves, processing and analysing structural brain scans and conducting research with a dynamic multi-disciplinary team. The successful applicant will hold a PhD in Psychology or equivalent and will have a research record in a field relevant to the project with demonstrated experience in processing and analysing neuroimaging data using FSL/Freesurfer or equivalent. An interest in ageing/lifespan development research will be highly regarded. Applications are required to be lodged online, please submit a summary of claims against the selection criteria along with your CV. Full details can be found here: http://jobs.anu.edu.au/PositionDetail.aspx?p=3120 Enquiries: Dr Nicolas Cherbuin Phone: 02 61253858 Email: nicolas.cherbuin(a)anu.edu.au Nicolas Cherbuin PhD ARC Research Fellow Director of the NeuroImaging and Brain Lab Centre for Research on Ageing, Health and Wellbeing College of Medicine Biology and Environment 62A Eggleston Road Australian National University Canberra ACT 0200 P: +61 2 6125 3858 F: +61 2 6125 1558 E: nicolas.cherbuin(a)anu.edu.au W: ageing.anu.edu.au/research/projects/nimbl.php CRICOS Provider #00120C

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Problem to understand QA tool results.
by charles laidi 29 Jan '13

29 Jan '13

Dear freesurfers, I performed cerebellar segmentation on 100 subjects. I don't detect any problem when checking the segmentation with tksurfer and tkmedit. I used the option -gen-asegLUT with QA tool. I have several error messages and but I'm not able to understand them. 1) I have several outliers in every t1 image and this message for example : "checking subcortical label: Left-Cerebellum-White-Matter, . +/- . as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an outlier (avg = . +/- .).." I don't know how to interpret this message, and how to correct the outliers. 2) I have this error message "ERROR: Actual file order disagrees with common file order for subject as100351_conv" QA tool suggest to use this command "recon-all -make all -subjid as100351_conv", but this command doesn't seem to work. Please find below the full recon checker message. Thanks a lot for you help, I wasn't able to find a wiki or any web page to help me understand the message of QA tool. The first question has already been asked in august I think, but remained unanswered. Charles Laidi (charles.laidi 'a t' gmail.com) Running recon_checker on: mercredi 16 janvier 2013, 22:47:04 (UTC+0100) ----- Most recent FreeSurfer version used to process this subject: /i2bm/local/freesurfer/bin/recon-all ----- All FreeSurfer versions used to process this subject: /i2bm/local/freesurfer/bin/recon-all ----- Checking all output files exist... Running command: /home/charles/Bureau/QAtools_ v1.1/recon_all_output_file_checker -subjid as100351_conv -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log -outputfileorderfile /home/charles/Bureau/QAtools_v1.1/default_FOF_FSv5.1 mri/rawavg.mgz last modified 2012-12-14 05:50:00.000000000 +0100 mri/orig.mgz last modified 2012-12-14 05:50:06.000000000 +0100 ERROR: Actual file order disagrees with common file order for subject as100351_conv At least one step in the recon-all stream has been skipped or rerun out of order. Run the following command to rerun any steps which were skipped or for which the output has been modified. recon-all -make all -subjid as100351_conv Alternatively, examine the ReconAllTable for your version of FreeSurfer to identify the recon-all step where the discrepancy is occuring and rerun every recon-all step from that point forward. This subject may have been processed with a different version of FreeSurfer other than the version used to create the common file order file (based on v5.1 by default if not specified by the user). Consider generating an output file order file for your specific dataset using the 'genoutputorderfile' flag. See the '-help' flag for details. actual order ====> common order: .......... ====> ......... mri/rawavg.mgz ====> mri/rawavg.mgz mri/orig.mgz ====> mri/orig.mgz mri/transforms/talairach.xfm ====> mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm ====> mri/transforms/talairach.xfm mri/nu.mgz ====> mri/nu.mgz mri/T1.mgz ====> mri/T1.mgz mri/brainmask.mgz ====> mri/brainmask.auto.mgz .......... ====> ......... ----- Checking status log output... Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_status_log_checker -subjid as100351_conv -details -slog /home/charles/Bureau/group_ complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log Using status log: /home/charles/Bureau/QAtools_v1.1/default_status_log_FSv5. 1.log as100351_conv COMPLETE ----- Checking asegs for outliers... Using asegLUT: test4 Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_aseg_outlier_checker -subjid as100351_conv -LookupMeansFromFile test4 -slog /home/charles/Bureau/group_complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker. ALL.summary.log checking subcortical label: Left-Cerebral-Exterior, 0 +/- checking subcortical label: Left-Cerebral-White-Matter, . +/- . checking subcortical label: Left-Cerebral-Cortex, . +/- . checking subcortical label: Left-Lateral-Ventricle, . +/- . as100351_conv Left-Lateral-Ventricle value .541890500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Inf-Lat-Vent, . +/- . as100351_conv Left-Inf-Lat-Vent value .025678500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Cerebellum-Exterior, . +/- . checking subcortical label: Left-Cerebellum-White-Matter, . +/- . as100351_conv Left-Cerebellum-White-Matter value 1.209679200 is an outlier (avg = . +/- .)... checking subcortical label: Left-Cerebellum-Cortex, . +/- . as100351_conv Left-Cerebellum-Cortex value 3.768655500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Thalamus, . +/- . checking subcortical label: Left-Thalamus-Proper, . +/- . as100351_conv Left-Thalamus-Proper value .490973600 is an outlier (avg = . +/- .)... checking subcortical label: Left-Caudate, 0 +/- checking subcortical label: Left-Putamen, . +/- . as100351_conv Left-Putamen value .490533400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Pallidum, . +/- . as100351_conv Left-Pallidum value .141965600 is an outlier (avg = . +/- .)... checking subcortical label: 3rd-Ventricle, . +/- . as100351_conv 3rd-Ventricle value .083565200 is an outlier (avg = . +/- .)... checking subcortical label: 4th-Ventricle, . +/- . as100351_conv 4th-Ventricle value .152163600 is an outlier (avg = . +/- .)... checking subcortical label: Brain-Stem, . +/- . as100351_conv Brain-Stem value 1.515180400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Hippocampus, . +/- . as100351_conv Left-Hippocampus value .329418900 is an outlier (avg = . +/- .)... checking subcortical label: Left-Amygdala, . +/- . as100351_conv Left-Amygdala value .146147500 is an outlier (avg = . +/- .)... checking subcortical label: Left-Insula, . +/- . checking subcortical label: Left-Operculum, . +/- . checking subcortical label: Line-1, . +/- . checking subcortical label: Line-2, . +/- . checking subcortical label: Line-3, . +/- . checking subcortical label: CSF, . +/- . as100351_conv CSF value .103080900 is an outlier (avg = . +/- .)... checking subcortical label: Left-Lesion, . +/- . checking subcortical label: Left-Accumbens-area, . +/- . as100351_conv Left-Accumbens-area value .060014400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Substancia-Nigra, . +/- . checking subcortical label: Left-VentralDC, . +/- . as100351_conv Left-VentralDC value .304840900 is an outlier (avg = . +/- .)... checking subcortical label: Left-undetermined, . +/- . checking subcortical label: Left-vessel, . +/- . as100351_conv Left-vessel value .008143700 is an outlier (avg = . +/- .)... checking subcortical label: Left-choroid-plexus, . +/- . as100351_conv Left-choroid-plexus value .140791700 is an outlier (avg = . +/- .)... checking subcortical label: Left-F3orb, . +/- . checking subcortical label: Left-lOg, . +/- . checking subcortical label: Left-aOg, . +/- . checking subcortical label: Left-mOg, . +/- . checking subcortical label: Left-pOg, . +/- . checking subcortical label: Left-Stellate, . +/- . checking subcortical label: Left-Porg, . +/- . checking subcortical label: Left-Aorg, . +/- . checking subcortical label: Right-Cerebral-Exterior, . +/- . checking subcortical label: Right-Cerebral-White-Matter, . +/- . checking subcortical label: Right-Cerebral-Cortex, . +/- . checking subcortical label: Right-Lateral-Ventricle, . +/- . as100351_conv Right-Lateral-Ventricle value .284664900 is an outlier (avg = . +/- .)... checking subcortical label: Right-Inf-Lat-Vent, . +/- . as100351_conv Right-Inf-Lat-Vent value .009904500 is an outlier (avg = . +/- .)... checking subcortical label: Right-Cerebellum-Exterior, . +/- . checking subcortical label: Right-Cerebellum-White-Matter, . +/- . as100351_conv Right-Cerebellum-White-Matter value 1.212467100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Cerebellum-Cortex, . +/- . as100351_conv Right-Cerebellum-Cortex value 3.943269600 is an outlier (avg = . +/- .)... checking subcortical label: Right-Thalamus, . +/- . checking subcortical label: Right-Thalamus-Proper, . +/- . as100351_conv Right-Thalamus-Proper value .520393900 is an outlier (avg = . +/- .)... checking subcortical label: Right-Caudate, 0 +/- checking subcortical label: Right-Putamen, . +/- . as100351_conv Right-Putamen value .503959600 is an outlier (avg = . +/- .)... checking subcortical label: Right-Pallidum, . +/- . as100351_conv Right-Pallidum value .119368500 is an outlier (avg = . +/- .)... checking subcortical label: Right-Hippocampus, . +/- . as100351_conv Right-Hippocampus value .360013100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Amygdala, . +/- . as100351_conv Right-Amygdala value .143212800 is an outlier (avg = . +/- .)... checking subcortical label: Right-Insula, . +/- . checking subcortical label: Right-Operculum, . +/- . checking subcortical label: Right-Lesion, . +/- . checking subcortical label: Right-Accumbens-area, . +/- . as100351_conv Right-Accumbens-area value .065150100 is an outlier (avg = . +/- .)... checking subcortical label: Right-Substancia-Nigra, . +/- . checking subcortical label: Right-VentralDC, . +/- . as100351_conv Right-VentralDC value .298237800 is an outlier (avg = . +/- .)... checking subcortical label: Right-undetermined, . +/- . checking subcortical label: Right-vessel, . +/- . as100351_conv Right-vessel value .005575900 is an outlier (avg = . +/- .)... checking subcortical label: Right-choroid-plexus, . +/- . as100351_conv Right-choroid-plexus value .143066100 is an outlier (avg = . +/- .)... checking subcortical label: Right-F3orb, . +/- . checking subcortical label: Right-lOg, . +/- . checking subcortical label: Right-aOg, . +/- . checking subcortical label: Right-mOg, . +/- . checking subcortical label: Right-pOg, . +/- . checking subcortical label: Right-Stellate, . +/- . checking subcortical label: Right-Porg, . +/- . checking subcortical label: Right-Aorg, . +/- . checking subcortical label: 5th-Ventricle, . +/- . as100351_conv 5th-Ventricle value .000293400 is an outlier (avg = . +/- .)... checking subcortical label: Left-Interior, . +/- . checking subcortical label: Right-Interior, . +/- . checking subcortical label: Left-Lateral-Ventricles, . +/- . checking subcortical label: Right-Lateral-Ventricles, . +/- . checking subcortical label: WM-hypointensities, . +/- . as100351_conv WM-hypointensities value .098165300 is an outlier (avg = . +/- .)... checking subcortical label: Left-WM-hypointensities, . +/- . checking subcortical label: Right-WM-hypointensities, . +/- . checking subcortical label: non-WM-hypointensities, . +/- . as100351_conv non-WM-hypointensities value .001393900 is an outlier (avg = . +/- .)... checking subcortical label: Left-non-WM-hypointensities, . +/- . checking subcortical label: Right-non-WM-hypointensities, . +/- . checking subcortical label: Left-F1, . +/- . checking subcortical label: Right-F1, . +/- . checking subcortical label: Optic-Chiasm, . +/- . as100351_conv Optic-Chiasm value .018635200 is an outlier (avg = . +/- .)... checking subcortical label: Corpus_Callosum, . +/- . checking subcortical label: Left-Amygdala-Anterior, . +/- . checking subcortical label: Right-Amygdala-Anterior, . +/- . checking subcortical label: Dura, . +/- . checking subcortical label: Left-wm-intensity-abnormality, . +/- . checking subcortical label: Left-caudate-intensity-abnormality, . +/- . checking subcortical label: Left-putamen-intensity-abnormality, . +/- . checking subcortical label: Left-accumbens-intensity-abnormality, . +/- . checking subcortical label: Left-pallidum-intensity-abnormality, . +/- . checking subcortical label: Left-amygdala-intensity-abnormality, . +/- . checking subcortical label: Left-hippocampus-intensity-abnormality, . +/- . checking subcortical label: Left-thalamus-intensity-abnormality, . +/- . checking subcortical label: Left-VDC-intensity-abnormality, . +/- . checking subcortical label: Right-wm-intensity-abnormality, . +/- . checking subcortical label: Right-caudate-intensity-abnormality, . +/- . checking subcortical label: Right-putamen-intensity-abnormality, . +/- . checking subcortical label: Right-accumbens-intensity-abnormality, . +/- . checking subcortical label: Right-pallidum-intensity-abnormality, . +/- . checking subcortical label: Right-amygdala-intensity-abnormality, . +/- . checking subcortical label: Right-hippocampus-intensity-abnormality, . +/- . checking subcortical label: Right-thalamus-intensity-abnormality, . +/- . checking subcortical label: Right-VDC-intensity-abnormality, . +/- . checking subcortical label: Epidermis, . +/- . checking subcortical label: Conn-Tissue, . +/- . checking subcortical label: SC-Fat/Muscle, . +/- . checking subcortical label: CSF-SA, . +/- . checking subcortical label: Muscle, . +/- . checking subcortical label: Ear, . +/- . checking subcortical label: Adipose, . +/- . checking subcortical label: Spinal-Cord, . +/- . checking subcortical label: Soft-Tissue, . +/- . checking subcortical label: Nerve, . +/- . checking subcortical label: Bone, . +/- . checking subcortical label: Air, . +/- . checking subcortical label: Orbital-Fat, . +/- . checking subcortical label: Tongue, . +/- . checking subcortical label: Nasal-Structures, . +/- . checking subcortical label: Globe, . +/- . checking subcortical label: Teeth, . +/- . checking subcortical label: Left-Caudate/Putamen, . +/- . checking subcortical label: Right-Caudate/Putamen, . +/- . checking subcortical label: Left-Claustrum, . +/- . checking subcortical label: Right-Claustrum, . +/- . checking subcortical label: Cornea, . +/- . checking subcortical label: Diploe, . +/- . checking subcortical label: Vitreous-Humor, . +/- . checking subcortical label: Lens, . +/- . checking subcortical label: Aqueous-Humor, . +/- . checking subcortical label: Outer-Table, . +/- . checking subcortical label: Inner-Table, . +/- . checking subcortical label: Periosteum, . +/- . checking subcortical label: Endosteum, . +/- . as100351_conv has 34 outliers ... ----- Checking white matter SNR measurements... SNR: Anatomical signal-to-noise ratio in white matter mWM: Mean white matter intensity value stdWM: Standard deviation of white matter intensity value voxWM: Total number of white matter voxels in eroded mask Running command: /home/charles/Bureau/QAtools_v1.1/recon_all_wm-anat-snr_checker -subjid as100351_conv -slog /home/charles/Bureau/group_ complique//as100351_conv/scripts/recon_checker.log -sumlog /home/charles/Bureau/group_complique//QA/recon_checker.ALL.summary.log wm-anat-snr results (as100351_conv): SNR meanWM stdWM voxWM 21,16 108,11 5,11 44847

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QDEC ERROR ANALYSE
by Pablo Emanuel 29 Jan '13

29 Jan '13

Hi, My name is Pablo. I am using the freesurfer in my analyses, but when I try use the QDEC to statistical analyses the follwing ERROR, attached, arise. What I have to do to fix it? Thank you so much. Pablo

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mean cortical thickness of significant clusters in qdec
by Richter, Julia 29 Jan '13

29 Jan '13

Dear FreeSurfer experts, I did a group analysis in qdec, found several significant clusters and would now like to extract the mean cortical thickness of each significant cluster. I know that I have to run mri_glmfit-sim to do this, but I do not understand which commands I need to get the xxx.y.ocn.dat as output by running mri_glmfit-sim. Any ideas? Any help is appreciated. :) Best wishes, Julia

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VTK surface
by Alexander Hunold 29 Jan '13

29 Jan '13

Hi, Recently I ran into a problem regarding vtk surfaces created and saved with FreeView. My goal is to mark brain lesions and to save the surface in the FreeSurfer surface format. In the first step I generated the surface of the lesion in FreeView and saved it in vtk format. Secondly, I tried to convert the vtk surface with mris_convert in the surf format. Unfortunately, I received the following error: $ mris_convert Tubers.vtk Tubers.surf MRISreadVTK: error parsing POLYGONS in file Tubers.vtk mris_convert: could not read surface file Tubers.vtk Please find the vtk file attached. >From comparisons with older vtk files generated by FreeView, I understood that recently polygons instead of triangles are defined in the vtk file. Is there a way to extract the surface triangles again? Thanks, Alex

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Job offer: Neuroimaging scientist or clinician in Frankfurt
by Dr.med. Johannes C. Klein 29 Jan '13

29 Jan '13

Dear all, I'm attaching a job offer for a fully-funded neuroimaging position at Frankfurt University, available immediately. The position is based at the Brain Imaging Center of Goethe University, a facility that hosts two dedicated research MR scanners and an MEG facility. A full clinical salary is available for applicants with a medical degree. Best, Johannes ==== Dr Johannes C Klein Goethe-University of Frankfurt Department of Neurology, Brain Imaging Center Schleusenweg 2-16 D-60528 Frankfurt/Main Germany email: klein(a)med.uni-frankfurt.de http://www.bic.uni-frankfurt.de/ ============ The Department of Neurology and Brain Imaging Center (BIC) at the Goethe-University Frankfurt am Main invites applications for a full-time position as Clinician scientist (m/f) Or Doctoral/Postdoctoral researcher (m/f) We are seeking to recruit a highly motivated individual to develop a programme of research into imaging biomarkers of neurological diseases. Topics include the evolution of lesions in Multiple Sclerosis, the differentiation of neurodegenerative diseases, and the evaluation of target sites for deep brain stimulation (DBS) in movement disorders. Essential qualifications and interests include · a background in medicine, neuroscience, or a related field (e.g., a degree in psychology, engineering, physics, biology) · programming skills (Linux shell scripting, MATLAB) · an interest in biomedical questions and systems neuroscience · interpersonal skills when dealing with research subjects and colleagues Additionally, the ideal applicant · has experience with imaging software packages (e.g. FSL, SPM) · enjoys inter-disciplinary interactions with physicists and clinicians · has experience with conducting MRI scans · speaks (basic) German to interact with study subjects The successful candidate should have a demonstrated capacity for independent work and be capable of initiating research in a lively research environment. The post will involve collecting MRI data from patients with neurological conditions and normal volunteers. The post will also involve data analysis and writing of manuscripts for submission to peer-reviewed journals, as well as writing ethics applications for research projects. For Doctoral researchers, Goethe-University provides the opportunity to obtain a PhD degree. The Brain Imaging Center offers excellent imaging facilities, with two research-only 3T Siemens MRI scanners, MEG, various stimulus presentation methods, and an active physics group. The position is available immediately and can be split up. The appointment will be initially for 2 years, with the possibility of extension. Salary will be based on TV-Ä Hessen for Clinicians, and up to TVÖD-E13 for Postdoctoral Researchers. Goethe University is an equal opportunity employer. Applications from female candidates are encouraged. Where qualifications are equal, preference will be given to applicants with disabilities. Candidates should submit their applications (as a PDF including CV, names of at least two referees, and a brief letter of motivation outlining their interests and explaining how they meet the qualifications listed above) to Dr Johannes Klein (klein(a)med.uni-frankfurt.de) Dr Klein is also available for informal enquiries. Applications will be considered until the post is filled.

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R: Re: R: Re: R: Re: R: Re: R: R: Re: TRACULA
by stdp82＠virgilio.it 29 Jan '13

29 Jan '13

Hi Anastasia, I put my files in a folder /Application/freesurfer/subjects/subject_prova/Diff01/ File are these:data.nii.gz (DWI data, 16 directions)TI_CON_01.nii.gz (T1 structural images)bvals.txt and bvecs.txt (as you can see in the previously attacked files). Could error depends from the use of the . or , that was used to separate the decimal?Is corrects the name of the 4 files in the Diff01 folder (FSL.nii.gz and its directory)I have previously used this data in FSL for TBSS. I only inverted the matrix of bvals (FLS:1x16, fs:16x1) and (FSL:3x16; fs:16x3)Is the configuration file good? Thank you very much for you kindness and avaibility. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 29-gen-2013 15.42 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - Are the files that you're attaching the ones from the dmri directory or are they the original files that you specified in your configuration file? I'm guessing they're not the dmri/bv??s files because then they'd be formatted in rows and not columns. Without seeing the bvecs from your dmri directory my best guess for what could be causing the error is this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg26026.html a.y On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > > Hi list, > > I'm trying to run trac-all on one subject and have a problem with the > bvecs file at the -prep stage. > After dtifit is started an error massage occurs: Error: bvecs and bvals don' > t have the same number of entries: > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep > -c /Users/Stefano/Desktop/dmrirc_single_subject > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scrip > ts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/ > scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Di > ff01/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Mar 29 Gen 2013 13:51:50 CET > mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. > gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii. > gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii > .gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o > rig.nii.gz... > cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applica > tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs > cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applica > tions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals > flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori > g.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ori > g_flip.nii.gz > INFO: input image orientation is LAS > INFO: input image determinant is -1 > fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_o > rig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /dwi_orig_flip.nii.gz > fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova > /Diff01/dmri/dwi_orig_flip.nii.gz > INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ > orig.mghdti.bvals, converting to FSL format > INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_ > orig.mghdti.bvecs, converting to FSL format > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f > lip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /bvecs > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_f > lip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri > /bvals > eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi > _orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/dwi.nii.gz 0 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0000 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0001 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0002 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0003 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0004 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0005 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0006 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0007 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0008 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0009 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0010 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0011 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0012 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0013 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0014 > processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_t > mp0015 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /App > lications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot > xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclo > g /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /A > pplications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs > fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.g > z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 > 1 > fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.ni > i.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb > .nii.gz > bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz > /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.g > z -m -f 0.3 > mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain > _mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/d > iff > #------------------------------------- > #@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET > flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_b > rain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -ou > t /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni > .nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xf > ms/diff2mni.mat -cost mutualinfo > convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova > /Diff01/dmri/xfms/diff2mni.mat > #------------------------------------- > #@# Masks Mar 29 Gen 2013 14:06:35 CET > #------------------------------------- > #@# Tensor fit Mar 29 Gen 2013 14:06:35 CET > dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ni > i.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/l > owb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Dif > f01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmr > i/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifi > t > Error: bvecs and bvals don't have the same number of entries > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > I checked the dmri/bvals and dmri/bvecs and attached them. > > Thank you very much. > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 29-gen-2013 0.44 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA > > > Hi Stefano - The file that you defined as your gradient vector file (set > bvecfile = ...) doesn't exist. This file has to exist. > > Hope this helps, > a.y > > On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > > > I have prepared this configuration file: > > > > > > # > > # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons > > # > > # This file contains commands that will be run by trac-all before an > > analysis. > > # It is used to set all parameters needed for the analysis. > > # > > # Remove a parameter from your dmrirc file if you want to use the default > > value. > > # Parameters that don't have default values must be specified. > > # > > # Any other commands that you might want to run before an analysis can be > > added > > # to this file. > > # > > # Original Author: Anastasia Yendiki > > # CVS Revision Info: > > # $Author: ayendiki $ > > # $Date: 2010/12/15 08:36:00 $ > > # $Revision: 1.1 $ > > # > > # Copyright (C) 2010 > > # The General Hospital Corporation (Boston, MA). > > # All rights reserved. > > # > > # Distribution, usage and copying of this software is covered under the > > # terms found in the License Agreement file named 'COPYING' found in the > > # FreeSurfer source code root directory, and duplicated here: > > # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense > > # > > # General inquiries: freesurfer(a)nmr.mgh.harvard.edu > > # > > # FreeSurfer SUBJECTS_DIR > > # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova > > # Output directory where trac-all results will be saved > > set dtroot = $SUBJECTS_DIR > > # Subject IDs > > set subjlist = (Diff01) > > set runlist = (1) > > # Input diffusion DICOMs (file names relative to dcmroot) > > set dcmroot = $SUBJECTS_DIR > > set dcmlist = (Diff01/data.nii.gz) > > set bvalfile = $SUBJECTS_DIR/bvals.txt > > set bvecfile = $SUBJECTS_DIR/bvecs.txt > > set nb0 = 1 > > set doeddy = 1 > > set dorotbvecs = 1 > > set thrbet = 0.3 > > set doregflt = 1 > > set doregbbr = 1 > > set doregmni = 1 > > set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz > > set trainfile = > > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > > # Paths to reconstruct > > # Default: All paths > > set pathlist = (lh.cst_AS rh.cst_AS \ > > lh.ilf_AS rh.ilf_AS \ > > lh.unc_AS rh.unc_AS \ > > fmajor_PP fminor_PP \ > > lh.atr_PP rh.atr_PP \ > > lh.cab_PP rh.cab_PP \ > > lh.ccg_PP rh.ccg_PP \ > > lh.slfp_PP rh.slfp_PP \ > > lh.slft_PP rh.slft_PP) > > > > # Number of path control points > > # Default: 5 > > set ncpts = 5 > > > > When I run this, I have: > > > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all > -prep > > -c /Users/Stefano/Desktop/dmrirc_single_subject > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc-c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.loc > al > >-log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all > .log > >-cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all > .cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Mar 29 Gen 2013 00:32:23 CET > > mri_convert > >/Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat > ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > mri_convert > >/Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applicat > ions/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > > reading from > > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... > > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 1, 0) > > k_ras = (0, 0, 1) > > writingto/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii. > gz > > ... > > cp/Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/free > surfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti > > .bvecs > > cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such > file > > or directory > > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct > 18 > > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > > > I apologize but I need to have your help. > > > > Thank you very much, > > > > > > Stefano > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 28-gen-2013 20.03 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA > > > > > > Hi Stefano - Type "which trac-all" to find out where trac-all lives on > > your computer, then copy the updated version over it. > > > > a.y > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Thank you very much for you kindness Anastasia. > > > The folder that contains .nii.gz file is correct? > > > I'm looking the recommended trac-all update. Where can I put it? > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 28-gen-2013 16.45 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: R: Re: TRACULA > > > > > > > > > Hi Stefano - The argument of the -c option is a configuration file, not > a > > > directory. For more info on trac-all and setting up the configuration > > > file, please see the trac-all wiki page: > > > http://www.freesurfer.net/fswiki/trac-all > > > and tracula tutorials: > > > http://www.freesurfer.net/fswiki/FsTutorial/Tracula > > > > > > a.y > > > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi and thank you very much for your availability. > > > > Now, I'm running tracula as following: > > > > > > > > trac-all -prep -c > /Applications/freesurfer/subjects/subject_prova/CON_01 > > > > > > > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used > > in > > > > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the > same > > > > that I have previously used in FSL analysis. > > > > > > > > Please, my questions are: > > > > a- Are correct the command and the files (dyrectory positioning and > > their > > > > extensions)? > > > > b- Now my computer seem to running but after 1 h from the start, I > > > visualize > > > > on my desktop this message "Your Mac 0SX has no more space available > for > > > > application memory". > > > > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 > MHz > > > > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of > > > 999,35 > > > > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > > > > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 27-gen-2013 19.36 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] TRACULA > > > > > > > > Hi Stefano - The -prep option doesn't take an argument. Please run > > > > trac-all with no arguments to see usage info. > > > > > > > > a.y > > > > > > > > > Hi list, > > > > > I'm trying to run a test subject with TRACULA. > > > > > I placed a folder in /Applications/freesurfer/subject/subject_prova > > > which > > > > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > > > > previous FSL analysis) and T1-images.in > > > > > /Applications/freesurfer/subject/subject_prova > > > > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% > > > trac-all > > > > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > > > > $FREESURFER_HOME/subjects/subject_prova > > > > > ERROR: flag > > > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > > > > /Applications/freesurfer/subjects/subject_prova > > > > > Please, give me an help. > > > > > > > > > > Thanks in advance, > > > > > > > > > > Stefano _______________________________________________ > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > 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. > > > > > > > > > > > >_______________________________________________ > > 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. > > > > > > > >_______________________________________________ > 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. > > > >_______________________________________________ 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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R: Re: R: Re: R: Re: R: R: Re: TRACULA
by stdp82＠virgilio.it 29 Jan '13

29 Jan '13

Hi list, I'm trying to run trac-all on one subject and have a problem with the bvecs file at the -prep stage. After dtifit is started an error massage occurs: Error: bvecs and bvals don't have the same number of entries: [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep -c /Users/Stefano/Desktop/dmrirc_single_subject INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local -log /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log -cmd /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Mar 29 Gen 2013 13:51:50 CET mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz mri_convert /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz... cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvecs.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs cp /Applications/freesurfer/subjects/subject_prova/Diff01/bvals.txt /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals flip4fsl /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -1 fslswapdim /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz x y z /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.mghdti.bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.mghdti.bvals /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals eddy_correct /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig_flip.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz 0 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0000 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0001 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0002 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0003 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0004 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0005 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0006 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0007 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0008 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0009 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0010 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0011 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0012 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0013 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0014 processing /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_tmp0015 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot xfmrot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.ecclog /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs.norot /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs fslroi /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz 0 1 fslmaths /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz -Tmean /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz bet /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mask.nii.gz /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff #------------------------------------- #@# Inter-subject registration Mar 29 Gen 2013 14:05:11 CET flirt -in /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -out /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/lowb_brain_mni.nii.gz -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat -cost mutualinfo convert_xfm -omat /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/mni2diff.mat -inverse /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Mar 29 Gen 2013 14:06:35 CET #------------------------------------- #@# Tensor fit Mar 29 Gen 2013 14:06:35 CET dtifit -k /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi.nii.gz -m /Applications/freesurfer/subjects/subject_prova/Diff01/dlabel/diff/lowb_brain_mask.nii.gz -r /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvecs -b /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/bvals -o /Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 I checked the dmri/bvals and dmri/bvecs and attached them. Thank you very much. Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 29-gen-2013 0.44 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: TRACULA Hi Stefano - The file that you defined as your gradient vector file (set bvecfile = ...) doesn't exist. This file has to exist. Hope this helps, a.y On Tue, 29 Jan 2013, stdp82(a)virgilio.it wrote: > Hi Anastasia, > > I have prepared this configuration file: > > > # > # Set locations of diffusion DICOMs, diffusion output, FreeSurfer recons > # > # This file contains commands that will be run by trac-all before an > analysis. > # It is used to set all parameters needed for the analysis. > # > # Remove a parameter from your dmrirc file if you want to use the default > value. > # Parameters that don't have default values must be specified. > # > # Any other commands that you might want to run before an analysis can be > added > # to this file. > # > # Original Author: Anastasia Yendiki > # CVS Revision Info: > # $Author: ayendiki $ > # $Date: 2010/12/15 08:36:00 $ > # $Revision: 1.1 $ > # > # Copyright (C) 2010 > # The General Hospital Corporation (Boston, MA). > # All rights reserved. > # > # Distribution, usage and copying of this software is covered under the > # terms found in the License Agreement file named 'COPYING' found in the > # FreeSurfer source code root directory, and duplicated here: > # https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOpenSourceLicense > # > # General inquiries: freesurfer(a)nmr.mgh.harvard.edu > # > # FreeSurfer SUBJECTS_DIR > # setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/subject_prova > # Output directory where trac-all results will be saved > set dtroot = $SUBJECTS_DIR > # Subject IDs > set subjlist = (Diff01) > set runlist = (1) > # Input diffusion DICOMs (file names relative to dcmroot) > set dcmroot = $SUBJECTS_DIR > set dcmlist = (Diff01/data.nii.gz) > set bvalfile = $SUBJECTS_DIR/bvals.txt > set bvecfile = $SUBJECTS_DIR/bvecs.txt > set nb0 = 1 > set doeddy = 1 > set dorotbvecs = 1 > set thrbet = 0.3 > set doregflt = 1 > set doregbbr = 1 > set doregmni = 1 > set mnitemp = Users/Stefano/Desktop/MNI152_T1_1mm_brain.nii.gz > set trainfile = > $TUTORIAL_DATA/diffusion_tutorial/scripts/subj,train,difftutorial32.txt > # Paths to reconstruct > # Default: All paths > set pathlist = (lh.cst_AS rh.cst_AS \ > lh.ilf_AS rh.ilf_AS \ > lh.unc_AS rh.unc_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.cab_PP rh.cab_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP) > > # Number of path control points > # Default: 5 > set ncpts = 5 > > When I run this, I have: > > [iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep > -c /Users/Stefano/Desktop/dmrirc_single_subject > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova > INFO: Diffusion root is /Applications/freesurfer/subjects/subject_prova > Actual FREESURFER_HOME /Applications/freesurfer > trac-preproc -c/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/dmrirc.local > -log/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.log > -cmd/Applications/freesurfer/subjects/subject_prova/Diff01/scripts/trac-all.cmd > #------------------------------------- > /Applications/freesurfer/bin/trac-preproc > #------------------------------------- > #@# Image corrections Mar 29 Gen 2013 00:32:23 CET > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > mri_convert > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /Applications/freesurfer/subjects/subject_prova/Diff01/data.nii.gz... > TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > writing to/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.nii.gz > ... > cp /Applications/freesurfer/subjects/subject_prova/bvecs.txt/Applications/freesurfer/subjects/subject_prova/Diff01/dmri/dwi_orig.mghdti > .bvecs > cp: /Applications/freesurfer/subjects/subject_prova/bvecs.txt: No such file > or directory > Darwin iMac-di-Stefano.local 12.2.1 Darwin Kernel Version 12.2.1: Thu Oct 18 > 12:13:47 PDT 2012; root:xnu-2050.20.9~1/RELEASE_X86_64 x86_64 > > I apologize but I need to have your help. > > Thank you very much, > > > Stefano > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 28-gen-2013 20.03 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] R: Re: R: R: Re: TRACULA > > > Hi Stefano - Type "which trac-all" to find out where trac-all lives on > your computer, then copy the updated version over it. > > a.y > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > Thank you very much for you kindness Anastasia. > > The folder that contains .nii.gz file is correct? > > I'm looking the recommended trac-all update. Where can I put it? > > > > Stefano > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 28-gen-2013 16.45 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] R: R: Re: TRACULA > > > > > > Hi Stefano - The argument of the -c option is a configuration file, not a > > directory. For more info on trac-all and setting up the configuration > > file, please see the trac-all wiki page: > > http://www.freesurfer.net/fswiki/trac-all > > and tracula tutorials: > > http://www.freesurfer.net/fswiki/FsTutorial/Tracula > > > > a.y > > > > On Mon, 28 Jan 2013, stdp82(a)virgilio.it wrote: > > > > > Hi and thank you very much for your availability. > > > Now, I'm running tracula as following: > > > > > > trac-all -prep -c /Applications/freesurfer/subjects/subject_prova/CON_01 > > > > > > my CON_01 forder contains: data.nii.gz (DWI), bvals and bvecs (as used > in > > > > previous FSL analysis) and T1-images.nii.gz. File.niii.gz are the same > > > that I have previously used in FSL analysis. > > > > > > Please, my questions are: > > > a- Are correct the command and the files (dyrectory positioning and > their > > > extensions)? > > > b- Now my computer seem to running but after 1 h from the start, I > > visualize > > > on my desktop this message "Your Mac 0SX has no more space available for > > > application memory". > > > My pc is a iMAC OS X Mountain Lion. 2.7 GHz Intel Core i5; 8GB 1600 MHz > > > DDR3; NVIDIA GeForce DT640M 512 MB; 762,42 GB are free on a total of > > 999,35 > > > I have download the package for (Snow)Leopard (10.5/6.x) Intel. > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 27-gen-2013 19.36 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] TRACULA > > > > > > Hi Stefano - The -prep option doesn't take an argument. Please run > > > trac-all with no arguments to see usage info. > > > > > > a.y > > > > > > > Hi list, > > > > I'm trying to run a test subject with TRACULA. > > > > I placed a folder in /Applications/freesurfer/subject/subject_prova > > which > > > > contains these files: data.nii.gz (DWI), bvals and bvecs (as used in > > > > previous FSL analysis) and T1-images.in > > > > /Applications/freesurfer/subject/subject_prova > > > > This is the command that I'm running:[iMac-di-Stefano:~] Stefano% > > trac-all > > > > -prep $FREESURFER_HOME/subjects/subject_prova/CON_01 --i > > > > $FREESURFER_HOME/subjects/subject_prova > > > > ERROR: flag > > > > > /Applications/freesurfer/subjects/subject_prova/CON_01unrecognized-prep > > > > /Applications/freesurfer/subjects/subject_prova/CON_01 --i > > > > /Applications/freesurfer/subjects/subject_prova > > > > Please, give me an help. > > > > > > > > Thanks in advance, > > > > > > > > Stefano _______________________________________________ > > > > 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. > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > 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. > > > > > > > >_______________________________________________ > 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. > > > >_______________________________________________ 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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Freesurfer January 2013