Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

QA_tools do not find v.mgz
by Simon Jones 13 Nov '18

13 Nov '18

External Email - Use Caution I have run some Freesurfer 6 recon-all processed data through the Freesurfer QA analysis QA_tools_v1.2. The output looks mostly good but I repeatedly see these errors. ERROR: Subject a1 missing output file ../mri/v.mgz ERROR: Subject a1 missing output file ../stats/wmsnr.e3.dat I do actually find 100% of wmsnr.e3.dat files so that may not be a problem. But only 41% of my subjects have a file called v.mgz. This looks like ventricles prior to aseg processing. I do not find the file v.mgz referenced in any of the recon-all log files or help pages. I don’t think I have been aware of this file previously. Why are many subjects missing this file and should I worry about it. Thanks for your help, Simon

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From .nii.gz
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I wonder how I could pass from .nii.gz format to .mgz format in order to change the brainmask.mgz generated by FreeSurfer for my bet image from FSL. I have noticed that lot of brainmask images have optic radiations and part of the skull. Best regards, Rosalia

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Medial prefrontal cortex mPFC in Destrieux Atlas
by Daya P 13 Nov '18

13 Nov '18

External Email - Use Caution Hi all, I am trying to find out which regions in Destrieux atlas would correspond to mPFC? Any ideas ? Also for lateral parietal cortex .. Than you, Daiana

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Fwd: Manually fix FreeSurder ICV value when talairach.xfm registration is incorrect
by Gamaliz 13 Nov '18

13 Nov '18

External Email - Use Caution I have a few T1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value? Thanks Gabriel

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Editing errors
by Rosalia Dacosta Aguayo 13 Nov '18

13 Nov '18

External Email - Use Caution Dear Free Surfer team, I am visually checking for errors in every step of the recon-all process. In the skull stripping stage, some participants have left skull behind, but the grey matter (gm) and white matter (wm) separation is right. Should I edit the brainmask image in order to make that no skull is left behind even when the gm and wm are fine? Best regards, Rosalia

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freesurfer selxavg3-sess error
by Francesca Strappini 12 Nov '18

12 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I'm trying to analyze some monkey functional data. I got this error message with selxavg3-sess. I run the following commands: mkcontrast-sess -analysis FF-MonkeyCassis.sm03.lh -contrast ON-vs-OFF -a 1 -c 0 mkcontrast-sess -analysis FF-MonkeyCassis.sm03.rh -contrast ON-vs-OFF -a 1 -c 0 preproc-sess -surface MonkeyCassis lhrh -fwhm 3 -s MonkeyCassis-FF -fsd bold -per-session selxavg3-sess -a FF-MonkeyCassis.sm03.lh -s MonkeyCassis-FF ------- matlab output -------------------- MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2016 The MathWorks, Inc. R2016b (9.1.0.441655) 64-bit (glnxa64) September 7, 2016 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/matlab/MRIread.m >> >> >> starting fast_selxavg3b #@# MonkeyCassis-FF ############################### /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF ------------------------- $Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $ ------------------------- outtop = /usr/local/freesurfer/fsfast/Monkeys Extension format = nii.gz INFO: key nSliceGroups unrecognized, line 11, skipping 1 ON-vs-OFF.mat Subscripted assignment dimension mismatch. Error in fast_ldpar4 (line 97) par4(nthrow,1) = tonset; Error in flac_customize (line 121) [par partype] = fast_ldpar4(parpath); Error in fast_selxavg3b (line 129) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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Transformation from original dicom to skull striped output
by Min Zhang 12 Nov '18

12 Nov '18

External Email - Use Caution Dear Freesufer team: I have marked bounding box in the original DICOM File, and applied autorecon1 to do the skull striping for the images. I want to transfer the bounding box to the skull stripped output. How can I get the coordinates transformation matrix between the input and skull stripped output. Many Thanks! Best Min

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Re: [Freesurfer] Consistent volume increases for some regions when using longitudinal stream
by Pagliaccio, David (NYSPI) 11 Nov '18

11 Nov '18

External Email - Use Caution Hello, Our lab has been running a set of data from a pre/post-treatment study through the FreeSurfer v6 pipeline. I was comparing the pre-treatment structural values initially run through the cross-sectional pipeline with the same pre-treatment data later run through the longitudinal pipeline and was seeing the same issue as has been previously posted about (msg52994). Particularly, one cortical region of interest shows on average 0.24mm (8.8%) larger cortical thickness values processed in the longitudinal pipeline vs. the cross-sectional pipeline. While all participant’s data showed increased thickness in this area with the longitudinal vs. cross-sectional pipeline, this was not at all consistent across participants (ranging from 0.08 to 0.47mm differences [3-18%]). While the longitudinal pipeline would increase reliability and sensitivity comparing the pre to post-scans, we are just very concerned about these major and inconsistent differences analyzing the same baseline data with the different pipelines. Particularly, we have some attrition so most participants have 2 but some have only 1 scan and thus this feels like it could introduce systematic bias in overall thickness. Any input would be appreciated! David

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Nonsensical Vertex Coordinates, please help with interpretation
by Bruss, Joel E 11 Nov '18

11 Nov '18

External Email - Use Caution I'm trying to make a surface file from a subject's head and to map coordinates to that surface. If I run: mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2 mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 $SUBJECTS_DIR/$sub/surf/lh.seghead and then load lh.seghead in FreeView, it looks as I would expect. Clicking anywhere near a vertex gives the typical output, showing the closest vertex. All fine and well. However, if I load the file in Matlab: vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead'); my values are nothing near what I'm seeing in Freeview. For example, FreeView reports: vertex 234741 [-78.50,14.50,26.50] read_surf reports: vertex 234740 0 168.980000000000 0 Of note, an error log tells me that: MRISreadNewCurvature: incompatible vertex number in file $SUBJECTS_DIR/$sub/surf/lh.curv How do I edit, update or create a curv file to play with the new surface file, or what can I do to get sensical surface coordinates from this data? Thanks, Joel ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Functional Connectivity in FreeSurfer
by Maedeh Khalilian 11 Nov '18

11 Nov '18

External Email - Use Caution Dear FreeSurfer experts, I have a general question, if i have a parcellation(an annotation file e.g aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate the functional connectivity between the regions(parcels) using rs-fMRI data? I mean can I have a 68*68 matrix showing the functional connectivity between each pair of regions(parcels) at the end? I would be grateful if u could help me. best regards, Maedeh

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Freesurfer November 2018