Freesurfer January 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
156 discussions

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

1 0

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

2 9

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

1 0

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

3 3

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

2 5

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

2 2

Freeview Surface Loading View Center
by Mingjian He 21 Jan '20

21 Jan '20

Hi, When using Freeview to load a surface file without volume, how does Freeview set the initial view center and cursor position? I’ve checked mid point of xyz ranges, centroid of vertices, and median. None of these gives me the initial SurfaceRAS values when opening the surface with Freeview. Thank you! Best, Alex External Email - Use Caution

2 1

recon exited with errors
by Desel, Tenzin 21 Jan '20

21 Jan '20

Hello FreeSurfer Developers, I'm attempting to run recon-all after unpacking data. It is exiting with errors - mri_cc: no WM voxels found with norm > 40 -- check skull stripping I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb 2) Platform: centos7_x86_64 3) uname -a: Linux lemmiwinks.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you!

1 0

Input PET images for PetSurfer Analysis
by Ferraro, Pilar 21 Jan '20

21 Jan '20

External Email - Use Caution Dear Freesurfer experts, I am starting a new analysis using PetSurfer to evaluate the effect of different PVC corrections on brain metabolism in a set of patients. I have already analyzed all the T1 MRI data using the normal stream, however I have never worked on PET data before. I have the original DICOMS from a static PET acquisition but I’d like to know more about the preprocessing steps needed for these PET data. I am thinking I should simply convert PET DICOMS to NifTI, normalize them to a standard template and then smooth them with 8- mm full width at half maximum Gaussian Kernel to obtain the input images for the PetSurfer analysis. Am I correct or should I add further preprocessing steps? Thanks, Pilar Il giorno 16 gen 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Qdec and TkSurfer input boxes (Marcos Martins da Silva) 2. FreeSurfer analyses in MatLab (Graduate Imaging) 3. Re: Oval shape in average subject inflated (Marina Fern?ndez) 4. Segfault in mris_topo_fixer (Christian O'Reilly, Dr) 5. Re: Segfault in mris_topo_fixer (Hoopes, Andrew) 6. Segmentation Fault during recon-all using FLAIR Image (Swanson,Clayton) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Jan 2020 14:02:26 -0300 From: Marcos Martins da Silva <marcosm(a)hucff.ufrj.br> Subject: [Freesurfer] Qdec and TkSurfer input boxes To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CANXLKP7HxjOjLShobVkYr+eDGNuh+PksDM1Aio=9XgKm_NaXeg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi! I use FreeSurfer 6.0 over CentOS 7. I have just notice a problem with input/entry/edit boxes in Qdec and TkSurfer. I can see box content, click inside the box and even select the content but it seems read only: I can't change it. So it is impossible to see the scatter plot from a specific vertex inputing its number. Any clue about what happened and how to fix it? Thank you for your attention. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200115/1… ------------------------------ Message: 2 Date: Wed, 15 Jan 2020 16:08:12 -0500 From: Graduate Imaging <graduate.imaging(a)gmail.com> Subject: [Freesurfer] FreeSurfer analyses in MatLab To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CA+yW3sSV=E5M1_cbOJfecPMCeCePjtZy_isFL8vzmRMDX55Pfw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello, I recently ran a vertex wise analysis on two different projects the first had three groups with three co-variates that looked at if group membership was associated with brain volume. The second project had two groups with three co-variates looking at psychiatric x BMI interaction effect on brain volume. I'm interested in running ROI analyses in matlab to ensure the same matrices were used. To run the ROI analyses I'm going to important the design matrix from the vertex wise analysis and use the fast_glmfit and fast_fratio commands as shown below: X = load('Xg.dat'); C = load('C.dat'); y = load('ROI.dat'); text file containing participant ROI values from the DKT atlas. [beta rvar] = fast_glmfit(y,X); [F pvalues] = fast_fratio(beta,X,rvar,C My first question is the beta values that are calculated from fast_glmfit are unstandardized is there anyway way to have it compute standardized values? My second question is when I ran the ROI analyses looking at the diagnosis x BMI interaction effect it outputs an array of beta values for each regressor. In addition to each groups beta value (for BMI) I'm interested in the beta value of the interaction (ie diagnosis x BMI). I was wondering how do i go about obtaining this? Would I have to create a new matrix with the interaction term included in it? If so would the analysis essentially be one group with the diagnosis x BMI interaction term plus the three co-variates? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200115/1… ------------------------------ Message: 3 Date: Thu, 16 Jan 2020 12:58:41 +0100 From: Marina Fern?ndez <marina.fdez.alvarez(a)gmail.com> Subject: Re: [Freesurfer] Oval shape in average subject inflated To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAALjZmeP2eKby4GGLJn_X6uOfCwPgNfnE3WUq5kmbv0-nqHi6Q(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution It works! Thank you very much Bruce! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/1… ------------------------------ Message: 4 Date: Thu, 16 Jan 2020 14:57:00 +0000 From: "Christian O'Reilly, Dr" <christian.oreilly(a)mcgill.ca> Subject: [Freesurfer] Segfault in mris_topo_fixer To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <YQBPR0101MB10125047A377D0AD8F34D349E1360(a)YQBPR0101MB1012.CANPRD01.PROD.OUTLOOK.COM> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hi, I got the following error running mris_topo_fixer: ~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 1 loops (X=0) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped) Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it? Thank you, Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/8… ------------------------------ Message: 5 Date: Thu, 16 Jan 2020 15:39:32 +0000 From: "Hoopes, Andrew" <AHOOPES(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Segfault in mris_topo_fixer To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BN8PR04MB56979DB2BBFD5A0BAB3E280EF9360(a)BN8PR04MB5697.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Christian, if you send me that surface, I can take a look at what's going wrong. best Andrew ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Christian O'Reilly, Dr <christian.oreilly(a)mcgill.ca> Sent: Thursday, January 16, 2020 9:57 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Segfault in mris_topo_fixer External Email - Use Caution Hi, I got the following error running mris_topo_fixer: ~$ mris_topo_fixer -mgz -warnings ANTS6-0Months3T lh INFO: assuming .mgz format verbose mode on (medium mode): printing warnings reading input surface /usr/local/freesurfer/subjects/ANTS6-0Months3T/work/ANTS6-0Months3T/surf/lh.orig... Before topology correction, eno=0 (nv=43656, nf=87312, ne=130968, g=1) Surface Diagnostics: eno=0 (nv=43656, nf=87312, ne=130968) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 The original surface is a valid manifold Counting the number of connected components The original surface has one component The original surface does not self-intersect The surface has 1 loops (X=0) Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations identify defects... marking ambiguous vertices... 1527 ambiguous faces found in tessellation segmenting defects... analyzing defects for overlaps... reading brain volume from brain... reading wm segmentation from wm... Detecting contrast direction: right direction [ GM (129.46) < WM (134.73) ] ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 ASSERTION FAILED: /local_mount/space/terrier/2/terrier_nightly_build/trunk/ah221-infant/utils/mrisurf_topology.c:1002 vt->nsizeMax > 0 Segmentation fault (core dumped) Any idea what in the data file could cause the assert "vt->nsizeMax > 0" to be triggered? Any idea how to go around it? Thank you, Christian ------------------------------ Message: 6 Date: Thu, 16 Jan 2020 15:55:44 +0000 From: "Swanson,Clayton" <Clayton.Swanson(a)colostate.edu> Subject: [Freesurfer] Segmentation Fault during recon-all using FLAIR Image To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <A95D6E27-F818-45F7-9391-C5B130978013(a)colostate.edu> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform a recon-all using a T2-FLAIR image. I have already run this particular participant through recon-all with their T1 image without error. While running the recon-all using the T2 the process exited with error stating a segmentation fault. Is there any way to run fix this problem on my end or better understand why this would be occurring? I have uploaded the recon-all.log for your convenience. Thank you, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Student Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu> -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/2… -------------- next part -------------- A non-text attachment was scrubbed... Name: recon-all.log Type: application/octet-stream Size: 188509 bytes Desc: recon-all.log Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200116/2… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 191, Issue 22 *******************************************

2 2

Change the subject ID after recon-all?
by Tim Schäfer 21 Jan '20

21 Jan '20

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

2 4

← Newer
1
...
4
5
6
7
8
9
10
...
16
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer January 2020