Freesurfer

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30132 discussions

Freeview froze when trying to open volume file
by Tarui, Tomo 23 Jan '20

23 Jan '20

External Email - Use Caution Dear Freesurfer community, I have been also experiencing problem that freeview froze when I tried to select and open a new volume file. This started after I upgraded mac OS X to Catalina. Until that I have been using freeview fine for five years. Error message said Last login: Thu Jan 23 13:43:03 on ttys000 [tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer [tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- 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 [tup09900bj11:~] tomotarui% freeview 2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited prematurely - check for a reentrant call to endModalSession: I do have read permissions for those volume files when I checked with ls -l and mri_info. I have tried cleaned up and reinstall freesurfer, which did not solve the problem. It may be unique to my computer, but I would appreciate very much for any recommendation. Tomo 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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail. Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.

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Hippocampal subfield validation
by Dawn C. Matthews 23 Jan '20

23 Jan '20

External Email - Use Caution Dear Freesurfer Team, Thank you for your work on the segmentation and analysis tools that have been provided through Freesurfer and that have been used so widely. We are wondering if there is a T1 image data set available for which manual delineation of the boundaries of the hippocampal subfield summation has been performed, and whether the images and masks might be available for DICE comparison to the masks and volume produced by FS in users’ hands? We note that the subfield summation does not include the alveus and therefore direct comparison to masks generated using standard manual hippocampal segmentation protocols is not straightforward. With thanks and best regards, Dawn Matthews Dawn C. Matthews CEO, ADM Diagnostics, Inc. 555 Skokie Blvd., Suite 500 Northbrook, Illinois 60062 dmatthews(a)admdx.com

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different target image for registration
by Sam W 23 Jan '20

23 Jan '20

External Email - Use Caution Hello! I would like to register my dwidata to the anatomical image (rawavg.mgz). I have run bbregister, but how can I specify a different target image? bbregister uses the orig.mgz right? These are the commands I used: bbregister --s sub001 --mov nodif.nii.gz --reg nodif2orig.dat --dti --init-fsl mri_vol2vol --fstarg --reg nodif2orig.dat --mov dwidata.nii --o dwialigned.nii mri_label2vol --regheader dwialigned.nii.g --temp mri/rawavg.mgz --aparc+ageg --o labels.nii I'm not sure if the last command is valid, because I think bbregister and mri_vol2vol use the orig.mgz, whereas mri_label2vol uses rawavg. Best regards, Sam

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mri_robust_template Internal Error: Rotation should not scale
by Biles, Mandy K 23 Jan '20

23 Jan '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run the longitudinal pipeline for recon-all outside of fmriprep. The first step, cross, ran fine and I received the expected outputs. I started the base step and for most of my subjects it appears to be working but for some of my subjects I get the following error when running the mri_robust_template command: Internal Error for tp 0 -> template Rotation should not scale ( 1.23014e-05 ) I've searched the list and no similar errors have been reported outside of fmriprep forums that I can find. Does anyone have any thoughts on how to troubleshoot this issue? Also, I’ve attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: Red Hat Enterprise Linux Server, VERSION=7.7 (Maipo). This is being run on a HPC server. 3) uname -a: Linux c0072 3.10.0-1062.9.1.el7.x86_64 #1 SMP Mon Dec 2 08:31:54 EST 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you, Mandy Mandy K. Biles, MS | PhD Candidate Psychology/Behavioral Neuroscience Program UAB | The University of Alabama at Birmingham CIRC Suite 252A | 1719 6th Avenue South | Birmingham, AL 35294 P: 205.975.4060 | mkbiles(a)uab.edu uab.edu<http://uab.edu>

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Fwd: [All] FW: Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School
by Greve, Douglas N.,Ph.D. 23 Jan '20

23 Jan '20

---------- Forwarded message ---------- Date: Thu, 23 Jan 2020 03:37:12 +0000 From: "Pizzagalli, Diego A.,Ph.D." <dap(a)mclean.harvard.edu> To: 'Help Desk -- Sam Mehl' <help(a)nmr.mgh.harvard.edu> Subject: RE: FW: Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School I'd be very grateful if you could forward to the distribution list: Post-doctoral Positions in Affective Neuroscience at McLean Hospital/Harvard Medical School Two post-doctoral positions are available within the Laboratory for Affective and Translational Neuroscience at McLean Hospital/Harvard Medical School, directed by Diego A. Pizzagalli, Ph.D. The laboratory is part of the Center for Depression, Anxiety and Stress Research (CDASR), a vibrant research center with over 40 scientists/staff/students that embraces a multi-disciplinary approach to improve our understanding of the psychological, environmental, and neurobiological factors associated with depression, anxiety and related disorders across the lifespan (http://cdasr.mclean.harvard.edu/) Currently ongoing studies in Dr. Pizzagalli's laboratory focus on reward processing, stress responsivity, and executive functioning in a range of populations including individuals with current or past major depression, as well as at-risk samples (e.g., offspring of parents with MDD or individuals exposed to early life stress). These studies employ a variety of approaches, including high-density EEG, fMRI, PET, MRS, computational modeling, and assays of hormonal/inflammatory markers. Opportunities will be available to pursue independent research and interdisciplinary collaborations across Harvard Medical School. Depending on research focus, candidates will have access to three research-dedicated human MRI scanners (3 T, 4 T) and one animal MRI scanner (9.4 T), as well as two high-density EEG systems. Qualifications: For the first position, a strong background in EEG/ERP techniques is required. For the second position, a strong background in functional/structural MRI techniques is required. For both positions, clinical training, computational modeling expertise (e.g., machine learning) and/or experience with a second imaging modality are a plus. To apply, send a CV, a cover letter describing research interests, as well as names and email addresses of three references to Diego A. Pizzagalli (dap(a)mclean.harvard.edu) Review of applications will begin immediately (expected start date: Summer 2020, although an earlier start will be possible). McLean Hospital, which is an affiliate of Harvard Medical School, is an Equal Opportunity Employer. As an equal opportunity employer, McLean seeks qualified candidates for all posted employment opportunities without regard to race, color, age, religion, gender, national origin, disability or veteran status. McLean particularly welcomes applications from minorities, women, and persons with disabilities. About the institution Since 1811, McLean Hospital has been a world leader in scientific investigations and treatments of mental illnesses as well as in training generations of scientists and clinicians. McLean Hospital maintains the largest program of research in neuroscience and psychiatry of any private psychiatric hospital in the United States. McLean Hospital has been ranked as America's best freestanding psychiatric hospital for 17th consecutive years by U.S. News and World Report. ______________________________________________________________ Diego A. Pizzagalli, Ph.D. Professor of Psychiatry Harvard Medical School Director, McLean Imaging Center Director, Center For Depression, Anxiety and Stress Research Director of Research, Division of Depression & Anxiety Disorders Director, Laboratory for Affective and Translational Neuroscience McLean Hospital de Marneffe Building, Room 233C Mailstop 331 115 Mill Street, Belmont, MA 02478-9106 Phone: (617) 855-4230 (Depression Center) Phone: (617) 855-2797 (Neuroimaging Center) Fax: (617) 855-4231 e-mail: dap(a)mclean.harvard.edu http://cdasr.mclean.harvard.edu www.mcleanmri.org ______________________________________________________________ _______________________________________________ All mailing list All(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/all

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highres fMRI selxavg error
by Nasiriavanaki, Zahra 23 Jan '20

23 Jan '20

Dear Freesurfer experts Happy Holidays! I have a subject with two highres fMRI scan sessions. Attached you can see an image, showing how I organized the sub-folders. I preprocessed the bold1 and bold2 and then copied the preprocessed files to "bold from both sessions" folder. I ran selxavg for bold1 and bold2 seperately and it went well. However, when I ran selxavg for "bold from both sessions" folder, it gives the below error. Could you please let me know what the problem is?Also if you have a better suggestion for how I should organize my subfolders/analysis, I appreciate that. Thanks Mona >> >> >> >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_selxavg3.m >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/fsfast/toolbox/fast_ldanaflac.m >> /autofs/cluster/freesurfer/centos7_x86_64/stable6/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# arap_7T_all ############################### /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 12, skipping 1 app.mat 2 aw.mat 3 caw.mat 4 clo.mat 5 faw.mat 6 fem.mat 7 fm.mat 8 fmaw.mat 9 mal.mat 10 maw.mat 11 oaw.mat 12 oc.mat 13 ocaw.mat 14 ope.mat 15 wit.mat Excluding 6 points nruns = 15 autostimdur = outanadir = /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh Excluding 6 points Excluding 0 points Excluding 1 points Excluding 5 points Excluding 8 points Excluding 3 points Excluding 8 points Excluding 4 points Excluding 6 points Excluding 10 points Excluding 5 points Excluding 5 points Excluding 5 points Excluding 5 points Excluding 5 points parfiles condition id list: 1 2 3 4 5 6 7 8 Found 41883/148565 (28.2) voxels in mask 1 Creating Design Matrix ... creation time = 0.040 sec DoMCFit = 1 ntptot = 1350, nX = 219, DOF = 1131 Saving X matrix to /autofs/space/oprah_001/users/zn025/looming_7T/all_subjects/arap_7T_all/loom/loom_native.lh/Xtmp.mat XCond = 1873.07 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.456169 (t=1.17104) 2 -0.25 -0.261165 (t=2.14097) 3 0 -0.076309 (t=2.3701) 4 0.25 0.0914527 (t=3.32529) 5 0.5 0.225506 (t=4.09175) AR1 Correction M: 0.138222 1.44983 Computing contrast matrices Computing contrasts Loading previous GLM fit Starting contrasts app J=1 ------------- Error using * Incorrect dimensions for matrix multiplication. Check that the number of columns in the first matrix matches the number of rows in the second matrix. To perform element wise multiplication, use '.*'. Error in fast_fratiow (line 81) ces = C*beta; Error in fast_selxavg3b (line 1153) fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:)); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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PhD and MSc Opportunities in Computational Neuroscience and Neuroimaging at the University of Toronto
by John Griffiths 23 Jan '20

23 Jan '20

External Email - Use Caution The Whole Brain Modelling Group (PI Dr. John Griffiths; www.grifflab.com) at the CAMH Krembil Centre for Neuroinformatics ( www.krembilneuroinformatics.ca) and University of Toronto is looking for PhD and MSc students with a strong background in computational neuroscience and/or neuroimaging. The focus of the Group’s work is computational models of large-scale brain activity, with particular emphases on neural dynamics as measured by M/EEG and fMRI, oscillations, brain stimulation (TMS, TDCS), neural plasticity, and macro-connectomics. The student shall conduct research in one or more of these areas. They will have the opportunity to shape the details of the project based on their specific interests, as well as to contribute to other ongoing projects on a range of topics, including: neuroinformatics of whole-brain modelling, mapping and modelling anatomical connectivity and microstructure with DWI in relation to ageing and stroke, and multi-scale modelling of the thalamocortical system in relation to sleep, pharmacological neuromodulation, and neuropsychiatric disease. The successful candidate should have, minimally, an undergraduate degree in neuroscience, engineering, physics, mathematics, psychology, or related area, and a demonstrable track record of research experience and interest in computational neuroscience and/or neuroimaging. Expertise in one or more modern scientific computing programming language (Python, Matlab, Julia, R, C++) is essential. The candidate should also have familiarity with one or both of: i) neuroimaging data analysis (s/d/fMRI and/or M/EEG), and ii) computational modelling using numerical simulations (particularly modelling of neural population activity with mean-field/neural mass/neural field techniques, either with custom implementations or with tools such as The Virtual Brain Platform or Dynamic Causal Modelling). Full details of the position and application instructions can be found at www.grifflab.com/positions/ For informal inquiries, please email Dr. John Griffiths at john.griffiths(a)camh.ca with the title “PhD in Whole Brain Modelling” in the subject line ( Note: students interested in a September 2020 start at the University of Toronto should get in touch immediately to leave time for approaching application deadlines ) -- Dr. John D. Griffiths Independent Scientist @ Krembil Centre for Neuroinformatics, CAMH, Toronto Assistant Professor @ Department of Psychiatry, University of Toronto www.grifflab.com

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Re: [Freesurfer] Change the subject ID after recon-all?
by Antonin Skoch 22 Jan '20

22 Jan '20

External Email - Use Caution Hi, Tim, the subject ID can be also contained in the commandline history which is stored in .mgz files. This can be viewed using mri_info file.mgz --cmds I am not aware of any direct command which can strip out this info, but you surely could convert .mgz file to .nii and then (using path which does not contain subject ID) convert back to .mgz, if needed. Antonin Hi Doug,thanks for the mri_add_xform_to_header idea, I didn't know about that option! Best, Tim > On January 21, 2020 at 4:24 PM "Greve, Douglas N.,Ph.D." > <dgr...(a)mgh.harvard.edu> wrote: > > > > For the mgz volumes, you should be able to do something like > mri_add_xform_to_header -c /new/path/to/xfm brain.mgz > > For the labels you could just use something like > sed s/oldsubjectname/newsubjectname > > > > > On 1/17/2020 3:48 AM, Tim Schäfer wrote: > > External Email - Use Caution > > > > Hi Douglas, > > > > sure, you can get two example files here: > > > > wget http://rcmd.org/tmp/brain.mgz > > wget http://rcmd.org/tmp/lh.BA1_exvivo.label > > > > The brain volume contains the ID because it stores the full path to the > > tairach xfm (which includes the folder name, so the ID). You can check by: > > > > mri_info brain.mgz | grep talair > > > > (In this case the ID is 'tim'). > > > > Without mri_info, you can get it as well: > > > > mv brain.mgz brain.gz > > gunzip -c brain.gz | strings | grep talair > > > > The second file is an ASCII label from the same subject. You can get the ID > > by running: > > > > head -n 1 lh.BA1_exvivo.label > > > > There are some other files which contain the ID, these are just 2 examples. > > > > > > I am currently in contact with the people running the consortium server and > > I am not really sure whether the rule that the ID must not be in the files > > makes any sense at all. Maybe I can get around this. > > > > > > Best, > > > > Tim > > > > > > > > > >> On January 17, 2020 at 12:23 AM "Greve, Douglas N.,Ph.D." > >> <dgr...(a)mgh.harvard.edu> wrote: > >> > >> > >> Hi Tim, can you send a list of files that have the identifier. For > >> volumes and surfaces, it might be as easy as running > >> mri_convert/mris_convert using the same file as input and output. > >> > >> On 1/13/2020 5:54 AM, Tim Schäfer wrote: > >>> External Email - Use Caution > >>> > >>> Dear FreeSurfer experts, > >>> > >>> > >>> I have two questions on subject IDs in FreeSurfer output. > >>> > >>> 1) is it possible to change to subject identifier in the FreeSurfer > >>> output after recon-all has been run? > >>> > >>> Background: I would like to upload data pre-processed with FreeSurfer to > >>> a consortium server. The subject ID is a random identifier, but the > >>> upload guidelines say this identifier must only occur in certain file > >>> types (Excel files, .log files, and some more, but not in any other > >>> files). > >>> > >>> I noticed that a lot of the output files produced by FreeSurfer contain > >>> the subject identifier somewhere, including various binary files, so I > >>> guess there is no easy way to change it. But maybe there is? Like > >>> rerunning a part of recon-all? > >>> > >>> > >>> > >>> 2) If not, I could rename the source NIFTI files (e.g., from the > >>> identifiers to something like 'subject001', 'subject002', ...) and > >>> re-process everything. This would take some computational time for the > > >>> 500 subjects, but it would be okay I guess. > >>> > >>> But a large number of the subjects have manual edits applied already. Is > >>> there a way to keep the manual edits? E.g., I thought maybe I could > >>> rename the individual directories of the edited subjects, leave the > >>> edited files in there, and run recon-all again. But what would happen? > >>> Will the new output files have the renamed ID from the directory name > >>> (and thus the recon-all command line), or will they still use the old ID > >>> (from the header of the existing files)? Or will the existing, edited > >>> files which contain a different ID be ignored during the new run because > >>> the IDs do not match, and thus the existing edits would have no effect? > >>> > >>> > >>> All the best, > >>> > >>> Tim > >>> > >>> -- > >>> Dr. Tim Schäfer > >>> Postdoc Computational Neuroimaging > >>> Department of Child and Adolescent Psychiatry, Psychosomatics and > >>> Psychotherapy > >>> University Hospital Frankfurt, Goethe University Frankfurt am Main, > >>> Germany > >>> > >>> _______________________________________________ > >>> 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Cortical inflation and maintenance of surface voxel intensity
by Assis Lopes, Pedro Augusto 21 Jan '20

21 Jan '20

Dear Freesurfer experts, I am a medical student and am currently doing a fellowship at the JPK Stroke Research Center - MGH. My current research project involves measuring the area of a cortical hypointense brain MRI signal (cortical superficial siderosis) , a marker that lays along the subarachnoid space/pial surface, only visible in blood sensitive MRI (SWI in my case). In summary: We are trying to do a parallel to fMRI studies (fMRI x T1w // SWI x T1w), analyzing SWI signal intensity on a registered inflated brain surface; Projecting SWI surface intensity would then allow manual area demarcation of hipointensities in a flat surface. Here is our step-by-step plan (analogous to fMRIxT1w registration/BOLD signal intensity projection to surface): 1. Perform freesurfer recon-all of the subject in question to generate subject-surface models. 2. BET and register the image of interest (SWI) into the freesurfer-subject space (register both SWI and MEMPRAGE sequences) [bbregister] 3. Having SWI in subject space and a surface model (generated in 1); * Split registered SWI into LH and RH * Tkregister2 to get LTA to mri_vol2surf format * Mri_vol2surf each hemisphere to the recon output 4. Display the SWI hemi surface as an overlay 5. Inflate T1 surface and observe its SWI overlay; * Manual demarcation of characteristic SWI hypointense signals 6. Analyze measured signal We did try this approach, but yet with these steps we could only obtain an inflated cortical surface representation that has no correspondence to SWI`s intensity. So, here comes the question: If BOLD signal intensity can be projected onto surface area; is there a way to project SWI intensity onto the cortical surface? Or Can we preserve the info of SWI surface voxel intensity while doing the surface inflation? If not Is it possible to use the positional information of t1w voxel (used in inflation process) as an index to retrieve its correspondent SWI intensity value? Sorry for the long question. In advance I thank you already for being so attentive. Best, Pedro Pedro Augusto Assis Lopes Student Researcher J. Philip Kistler Stroke Research Center Massachusetts General Hospital 175 Cambridge Street, Suite 300 Boston, MA 02114 Phone: (617) 643-3940

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Recon-all multiple subjects DICOM
by Benjamin Ineichen 21 Jan '20

21 Jan '20

External Email - Use Caution Dear Freesurfer experts, I try to run several subjects one after each other on recon-all using: for SubjectName in `cat *subs2.txt*`; do recon-all -i $SUBJECTS_DIR/$SubjectName/* -all -qcache; done Output: ERROR: Flag /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/Freesurfer_T1/SW1-1898_M12/EE018B6B unrecognized. -i /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/Freesurfer_T1/SW1-1898_M12/EE00C3C4 /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/Freesurfer_T1/SW1-1898_M12/EE018B6B ... (all remaining DICOM-files for the first subject) How can I define one of my DICOM-files in the individual subject folders as input (the DICOM-file names are different for each subject)? I tried the character * (wild card) which did not work. Many thanks for your support! Best regards, Benjamin -- ____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01 Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen(a)protonmail.ch +41 76 391 04 01

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