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30084 discussions

Trouble With Pial Surface Reconstruction Using FLAIR Image
by Pankush Kumar 29 Jun '20

29 Jun '20

External Email - Use Caution Hello, I was wondering if I can get some help. Every time I try to run my T1 image with a T2 FLAIR to enhance pial surfaces, I get the following message: Computing pial target locations using multimodal (2) starting MRIScomputePialTargetLocationsMultiModal() max_outward_dist = 3, sample_dist = 0.1, pix_size = 1, whalf = 7 T2_min_inside = 110, T2_max_inside 300, T2_min_outside = 130, T2_max_outside 300 inside_peak_pct = 0.01, 0.01, outside_peak_pct = 0.5, 0.5 wm_weight = 3, nlabels=0, contrast_type=2 Creating lowres distance volumes t=0.000581909 Creating white distance volumes t=0.773706 (box.dx, box.dy, box.dz) = (118, 218, 310) (region->dx, region->dy, region->dz) = (118, 218, 310) (region->dx, region->dy, region->dz) = (118, 218, 310) Creating pial distance volumes t=1.42513 (box.dx, box.dy, box.dz) = (124, 226, 314) (region->dx, region->dy, region->dz) = (124, 226, 314) (region->dx, region->dy, region->dz) = (124, 226, 314) locating cortical regions not in interior range [110.0 --> 300.0], and not in exterior range [130.0 --> 300.0] t = 2.14683 Starting loop over 106284 vertices vno = 0, t = 2.14683 error: Cannot allocate memory error: HISTOalloc(-2147483648): could not allocate histogram I am currently using the command recon-all -subject <subject name> -FLAIR 106_T2w_FLAIR_AX_SENSEBrain_res.nii.gz -FLAIRpial -all -noskullstrip The error log is attached below. I looked at filled.mgz, it does not seem to have any skull or cerebellum in it. Any help would be appreciated! Sincerely, Pankush Kumar

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Error in qdec
by Mateus Aranha 29 Jun '20

29 Jun '20

External Email - Use Caution Hello, Iḿ trying to perform a group analysis using qdec, but the analysis stops at 70% and the following error message is shown: [image: Screenshot from 2020-06-29 13-03-27.png] How should I proceed? Thanks, Mateus

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Precise MNI152 space
by Inês Pereira 29 Jun '20

29 Jun '20

External Email - Use Caution Dear FreeSurfer developers, Which MNI152 space is used within FreeSurfer? Is it the MNI152 nonlinear 6-th generation (as in, for example, FSL), or another one, like MNI152 nonlinear 2009a, 2009b or 2009c? I wasn’t able to find this information in the fswiki. I checked https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and the documentation of certain functions, such as mri_cvs_register. Thank you for your help! All the best, Inês Pereira

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error in "recon-all -all -s subject -hippocampal-subfields-T1": exited with errors
by Shimura, Yuki 29 Jun '20

29 Jun '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute calculate hippocampal volumes, as described on the MultiModal FMRI tutorial "Segmentation of hippocampal subfields"(https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields) but I get the following error when I run the following command: Command: recon-all -s subject -hippocampal-subfields-T1 Error: recon-all -s TNU_AIDAZ_3002_T1 exited with ERRORS at Mon Jun 22 15:42:08 JST 2020 (TNU_AIDAZ_3002_T1 is the subject name) 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. Here are few contexts: a) I had the following command for recon-all for my subject: recon-all -i ${SUBJECTS_DIR}/subject_structual_image_file.nii -s subject -all -qcache -3T b) this was done without an error c) now I want to do " recon-all -s subject -hippocampal-subfields-T1" 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: CentOS release 6.7 (Final) 3) recon-all.log: see attached

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Scientific Project Coordinator for an open science, large-scale collaboration
by Caspar M. Schwiedrzik 28 Jun '20

28 Jun '20

External Email - Use Caution Dear all, If you are seeking a challenge, if you are dynamic and enthusiastic about managing a large consortium of scientists, then do not hesitate to apply for the *Scientific Project Coordinator *position in my group at the Max Planck Institute for Empirical Aesthetics. You will be coordinating this <https://science.sciencemag.org/content/366/6463/293> project which was recently features in science, and involves 11 institutions across Europe, the US and China running an adversarial collaboration project aimed at understanding the neural foundations of consciousness. This is a unique opportunity to contribute to the development of an open science model for large-scale collaborations. We are looking for an internationally experienced scientist with knowledge of science management, networking, and international collaboration, and a keen interest in developing practices and procedures for open science. This is a full-time position for 2 years. More information on the job requirements and the position can be found here <https://www.aesthetics.mpg.de/karriere/jobs/scientific-project-coordinator-…> . For enquiries concerning this job opportunity please contact *Dr. Lucia Melloni: **lucia.melloni(a)ae.mpg.de <lucia.melloni(a)ae.mpg.de>**.* Please submit your application - preferably online in a single pdf - including a CV and a cover letter describing your background, experience and motivation as well as the names of two references, who have previously agreed to be contacted, *no later than July 31, 2020 *to: *job(a)ae.mpg.de* <job(a)ae.mpg.de> Looking forward to the applications! Best wishes, Lucia Melloni

1 0

Brodmann area labels
by Peng Liu 26 Jun '20

26 Jun '20

External Email - Use Caution Dear Freesurfer experts, I was trying to perform some ROI analysis with results obtained from recon-all. However I noticed that after recon-all, the labels created were like 'lh.BA3b*_exvivo*.label', whereas the labels I would want to create are like 'lh.BA3b.label'. I have tried mri_annotation2label command, but the results I got were not as wanted either. Does anyone know how to create labels like 'lh.BA3b.label'? Any help would be appreciated a lot! Many Thanks PL -------------------------------------------- [image: Otto-von-Guericke University Magdeburg] Peng Liu, PhD Candidate Institut für Kognitive Neurologie und Demenzforschung (IKND) Otto-von-Guericke Universität Magdeburg Deutsches Zentrum für Neurodegenerative Erkrankungen e.V. (DZNE) Leipziger Str. 44| Haus 64| Raum 217 39120 Magdeburg, Deutschland Email: peng.liu@med.ovgu.de/Peng.Liu@dzne.de Phone: +49 391 67 25074

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Postdoc in fMRI/Computational Neuroscience
by Michael Marxen 26 Jun '20

26 Jun '20

External Email - Use Caution Dear colleagues, we are currently looking for a Postdoc for the analysis of fMRI and behavioural data in the context of the Collaborative Research Centers CRC 940<http://www.sfb940.de/> 'Volition and Cognitive Control: Mechanisms, Modulators, and Dysfunctions', and the newly established TRR 265<https://sfb-trr265.charite.de/en/> 'Losing and Regaining Control over Drug Intake: From Trajectories to Mechanisms to Interventions'. More details can be found in the attachment. For further information, please, contact Michael.smolka(a)tu-dresden.de<mailto:Michael.smolka@tu-dresden.de>

1 0

Subfield parcellation in 1.5 T and 2.6 mm Thickness
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 25 Jun '20

25 Jun '20

? Hi FS developers, We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would be sufficient for a subfield analysis (amygdala, hippocampus, thalamus). Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] .IMA to NIFTI conversion using mri_convert
by Vinny K 25 Jun '20

25 Jun '20

External Email - Use Caution Hi, I have diffusion-weighted images (DWI) from a Siemens scanner in the .IMA format. I used the following command in an attempt to convert the DWI series from .IMA to .nii/.nii.gz format.... mri_convert -it siemens_dicom -ot nii NEURO_BRAIN.00034.IMA dwi However, I get an outputted dwi file but it's in a Binary (application/octet-stream) format. Also, the bvecs and bvals files were not outputted. Any help would be appreciated. Thanks, Vinny

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Extracting CRAS from nifti (mri_info)
by Sherin Sugathan 25 Jun '20

25 Jun '20

External Email - Use Caution Dear Freesurfer team, I am a user of freesurfer. The tool mri_info provides me useful information from nifti files. As part of my project, I am using VTK to programmatically extract information like direction matrix, size, origin etc from a nifti file. However, I am unable to extract --cras information from a nifti file. Could you please throw some light on how I can extract the CRAS values from a NIFTI file using matlab or vtk or itk ot nibabel? If the CRAS values are computed, I would like to know how they are computed. Basically, I am trying to understand how I can get the CRAS values without using mri_info tool. Thanks in advance! Regards, Sherin Sugathan

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