Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

Postdoc position at MGH/Harvard Medical School
by Jacobs, H (NP) 10 Jul '19

10 Jul '19

External Email - Use Caution <> Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for highly qualified individuals at the post-doctoral level to work on research related to multi-modal 7T (f)MRI imaging of the brainstem in aging under the mentorship of Dr. Heidi Jacobs. Within this NIA-funded RO1 project, relationships between memory and autonomic tone will be investigated at very high resolution. This project involves dedicated imaging of the brainstem nuclei, high-resolution fMRI (possibility to go to layer-fMRI) with physiological monitoring, HCP sequences for diffusion imaging and PET-imaging. Most of the work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging. The Department of Radiology at MGH is equipped with the first mobile PET/CT, the first brain PET/MRI, the first whole-body PET/MRI in the USA and several MRI scanners, including two 7T ultra-high-field scanner. It is also equipped with a substantial large scale shared memory computing facility for parametric image analysis, tomographic reconstruction, Monte Carlo simulation, and other computationally intensive research applications. Applicants must have obtained or anticipate soon receiving a Ph.D. in biomedical, computer or electrical engineering, medical physics, cognitive neuroscience or a related field. Strong analytical, quantitative and programming skills are essential (e.g., QSM, fMRI-physiological data analyses). Prior experience in medical imaging, signal/image processing, and physiological investigation is advantageous. The successful candidate will have joint appointments at MGH and HMS and will be closely interacting with the Harvard Aging Brain Study team, the HCP team and the high-field MRI group. If interested, please send your CV, letter describing interests, background, qualifications and 3 references (including contact details). MGH & HMS are equal-opportunity, affirmative action employers. Women and minority candidates are encouraged to apply. Heidi Jacobs, Ph.D. Instructor, GCMI Email: hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> [cid:image001.png@01D4F544.4ACC20E0] Gordon Center for Medical Imaging MGH – Nashua 6606; Radiology, MGH 125 Nashua Street Boston, MA 02114

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Re: [Freesurfer] nii to gii conversion
by Antonin Skoch 10 Jul '19

10 Jul '19

External Email - Use Caution Hi Jan, mri_vol2surf is not the correct command to achieve this. Use mri_mc or mri_tesselate. See also https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg61335.html Antonin Skoch Dear Freesurfer experts, I would like to run tractography using probtrackx2 tool from one seed ROI (cortex) through another waypoint ROI. I need both these masks (ROIs) in gii format. Seed ROI I extracted using Freesurfer (recon-all, mri_convert and label2surf functions). Then I drew second waipoint ROI using FSLeyes edit tool, saved it as binary nii.gz file and tried to convert it to surface gii file using mri_vol2surf:mri_vol2surf --src mask.nii.gz --out mask.gii --regheader --reg fsl2freesurfer.dat --sd /surf --hemi rh --surf pial --projfrac-max 0 1 0.05 --out_type gii But, converted ROI looks empty. Do I have any mistake in command above or is there any another way how to convert nii -> gii? Thanks, Jan

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Post-doc position at Neuroplasticity & Development Lab Johns Hopkins University
by Marina Bedny 10 Jul '19

10 Jul '19

External Email - Use Caution Post-doc position at Neuroplasticity & Development Lab Johns Hopkins University, PI: Marina Bedny The Neuroplasticity & Development Lab invites applicants for a post-doctoral fellowship position. The postdoctoral fellow will develop a research program investigating how experience shapes human cognitive and neural development and plasticity. Our laboratory compares cognition in adults and children with different development experiences using techniques such as fMRI, TMS and behavioral measures. A key research direction compares neurocognitive function among individuals who are blind and sighted. We investigate visual cortex function in blindness as a window into mechanisms of brain development and plasticity in humans. We also study how sensory and linguistic experience contributes to concepts and their neural basis (e.g. neural basis of concrete entity and event representations in blind and sighted individuals). For more information about our research go to http://bednylab.com/ The post-doctoral fellow will be encouraged to take part in the intellectually rich cognitive science and neuroscience communities of Johns Hopkins University. Qualifications: A Ph.D. in Psychology, Cognitive Neuroscience or related field is required. Qualified applicants will have a strong interest in neuroplasticity and cognition. Expertise in fMRI is preferred but candidates with proficiency in other relevant domains/techniques will also be considered (e.g. TMS/EEG/DTI, developmental psychology, psycholinguistics). Excellent computational skills are strongly preferred. How to Apply: Candidates should submit a letter of interest, a CV and contact information for three references by emailing the lab director at marina.bedny(a)jhu.edu<mailto:marina.bedny@jhu.edu>. The letter of interest should be no more than a single page long and should include a statement of what research the applicant wishes to pursue during their post-doctoral training and why they believe this job is a good fit to their specific research interests and career goals. Applications will be evaluated on an ongoing basis until the position is filled. The starting date is flexible and available candidates could begin work immediately.

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nii to gii conversion
by Valosek Jan 10 Jul '19

10 Jul '19

External Email - Use Caution Dear Freesurfer experts, I would like to run tractography using probtrackx2 tool from one seed ROI (cortex) through another waypoint ROI. I need both these masks (ROIs) in gii format. Seed ROI I extracted using Freesurfer (recon-all, mri_convert and label2surf functions). Then I drew second waipoint ROI using FSLeyes edit tool, saved it as binary nii.gz file and tried to convert it to surface gii file using mri_vol2surf: mri_vol2surf --src mask.nii.gz --out mask.gii --regheader --reg fsl2freesurfer.dat --sd /surf --hemi rh --surf pial --projfrac-max 0 1 0.05 --out_type gii But, converted ROI looks empty. Do I have any mistake in command above or is there any another way how to convert nii -> gii? Thanks, Jan

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Re: [Freesurfer] Undefined function or variable called 'fspecial'
by Antonin Skoch 10 Jul '19

10 Jul '19

External Email - Use Caution Hello, Vittal, do you have image processing toolbox of MATLAB installed? The function fspecial is part of this toolbox. Antonin Hello FS experts,I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul 10 13:15:03 IST 2019 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= rm: cannot remove '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz': Permission denied ================= mkdir -p /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... mghWrite(/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz, -1): could not open file conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Academic License >> reading filled volume... closing volume... Undefined function or variable 'fspecial'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux naren123 4.15.0-54-generic #58~16.04.1-Ubuntu SMP Mon Jun 24 13:21:41 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CSRI005 exited with ERRORS at Wed Jul 10 13:15:10 IST 2019" Also I have set the MATLAB path for freesurfer and here is the startup.m file "%------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% " I guess the error is because of 2 different user name: I have matlab license in X name and FreeSurfer can only be executed with root i.e. say Y. I mentioned both the information above. Wanna know the way to sort out this issue asap. Waiting for your reply. Thanks & regards Vittal

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Undefined function or variable called 'fspecial'
by vittal korann 10 Jul '19

10 Jul '19

External Email - Use Caution Hello FS experts, I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul 10 13:15:03 IST 2019 mris_compute_lgi --i lh.pial ================= rm -Rf /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= rm: cannot remove '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz': Permission denied ================= mkdir -p /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... mghWrite(/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz, -1): could not open file conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= Academic License >> reading filled volume... closing volume... Undefined function or variable 'fspecial'. Error in make_outer_surface (line 31) Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/subjects/CSRI005/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux naren123 4.15.0-54-generic #58~16.04.1-Ubuntu SMP Mon Jun 24 13:21:41 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s CSRI005 exited with ERRORS at Wed Jul 10 13:15:10 IST 2019" Also I have set the MATLAB path for freesurfer and here is the startup.m file "%------------ FreeSurfer -----------------------------% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) addpath(genpath(fsmatlab)); end clear fshome fsmatlab; %-----------------------------------------------------% %------------ FreeSurfer FAST ------------------------% fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox = sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7) path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; %-----------------------------------------------------% " I guess the error is because of 2 different user name: I have matlab license in X name and FreeSurfer can only be executed with root i.e. say Y. I mentioned both the information above. Wanna know the way to sort out this issue asap. Waiting for your reply. Thanks & regards Vittal

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Postdoctoral Position, University of Oslo
by Dídac Vidal 10 Jul '19

10 Jul '19

External Email - Use Caution I am delighted to advertise the following postdoctoral research fellowship on behalf of Prof Anders M Fjell: At the Center for Lifespan Changes in Brain and Cognition, University of Oslo, Norway, we have an available postdoc position for an excellent candidate with strong skills in functional neuroimaging and linked to the project “The Missing Link of Episodic Memory Decline in Aging: The Role of Inefficient Systems Consolidation”. The position is for a period of 3 years. The researcher will be able to work on uni- and multivariate analyses of high-quality task-related fMRI data acquired at our Siemens Prisma 3T MRI scanner using state-of-the-art sequences (multi-band/multi-echo EPI). Topics currently under investigation in our lab cover cognitive functions during episodic memory operations, as well as mechanisms subserving spatial navigation and spatial working memory. The application deadline is: 18.08.2019 Please see more info here: https://www.jobbnorge.no/en/available-jobs/job/172827/postdoctoral-research… P.S. Interested candidates are welcome to contact Anders M Fjell a.m.fjell(a)psykologi.uio.no All the best, Dídac -- Dídac Vidal Piñeiro

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mris_make_surfaces -aseg filled vs -noaseg (difference v5.3 and v6)
by Scott Love 09 Jul '19

09 Jul '19

External Email - Use Caution Hello all, To create surfaces for a sheep brain using Freesurfer version 5.3 I previously used, mris_make_surfaces -mgz -noaparc -aseg filled -T1 brain.finalsurfs $subj rh, and it worked great. Running the same command using version 6 (freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c) I get this error: “… generating cortex label... 1 non-cortical segments detected only using segment with 71880 vertices LabelErode: NULL label No such file or directory LabelDilate: NULL label No such file or directory Segmentation fault: 11” When changing the command to ( mris_make_surfaces -mgz -noaparc -noaseg -T1 brain.finalsurfs $subj rh ) it runs without error. However, the result is clearly not as good - the pial surface looks like a slightly extended/inflated white surface. This is also true for a brain that worked perfectly with version 5.3. From the error I am guessing that labels in filled (127 and 255) are not those required. Is it (still) possible to use filled.mgz as the input to -aseg in mris_make_surfaces? Is it perhaps possible to modify the label numbers in filled.mgz to get this working again? Thanks, Scott

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Desikan atlas
by Pinar Pnr 09 Jul '19

09 Jul '19

External Email - Use Caution Hi dear Freesurfer users, Is there a version of Desikan atlas in MNI space? Bset Regards, Pinar

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pial.lgi
by vittal korann 09 Jul '19

09 Jul '19

External Email - Use Caution Hi FS experts, I wanted to run the gyrification index for all patients with Schizophrenia and volunteers. When I entered the command: "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output " Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root 1590 1054464 Jul 6 16:02 /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/usr/local/freesurfer/subjects/SATM124/scripts/recon-all.local-copy' #-------------------------------------------- #@# Qdec Cache preproc lh pial_lgi fsaverage Sat Jul 6 16:39:03 IST 2019 /usr/local/freesurfer/subjects/SATM124/surf mris_preproc --s SATM124 --hemi lh --meas pial_lgi --target fsaverage --out lh.pial_lgi.fsaverage.mgh nsubjects = 1 ERROR: cannot find /usr/local/freesurfer/subjects/SATM124/surf/lh.pial_lgi Linux naren123 4.15.0-52-generic #56~16.04.1-Ubuntu SMP Thu Jun 6 12:03:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SATM124 exited with ERRORS at Sat Jul 6 16:39:03 IST 2019 For more details, see the log file /usr/local/freesurfer/subjects/SATM124/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting" There is no file called 'lh.pial_lgi" in the surf directory for all subjects. I'm using freesurfer version6.0. Would appreciate any help. Thanks & regards -Korann Thanks & regards Vittal

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Freesurfer July 2019