Freesurfer November 2017

freesurfer@nmr.mgh.harvard.edu

110 participants
198 discussions

Re: [Freesurfer] ERROR: mpr2mni305 failed, see transforms/talairach_avi.log
by Manoj Kumar 18 Nov '17

18 Nov '17

Hello Dear Sir/Madam, Please provide your expert suggestions to resolve the above-mentioned error. Thank you very much, Best regards Manoj On Sat, Nov 18, 2017 at 11:05 AM, Manoj Kumar <vermanojk(a)gmail.com> wrote: > Hello Dear Sir/Madam, > > I am fairly new to the freesurfer and am getting an error "ERROR: > mpr2mni305 failed, see transforms/talairach_avi.log" > > When I run the "recon-all -all -subjid Anj commond. > > I looked for this error message on https://mail.nmr.mgh. > harvard.edu/pipermail//freesurfer/2014-August/039761.html > But could not resolve this issue by myself. > I am here also attaching the complete error log and recon-all-error file > for your find attention. > > Please kindly provide your expert suggestions to resolve this issue. > Please let me know if you need any additional information for further > diagnosis of the error. > > Thank you very much for all your help and support. > > Best > >

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Talairach of ROI
by Dongsheng Wu 17 Nov '17

17 Nov '17

Hello FreeSurfer Developers, I have two questions about coordinate of ROI when running the QDEC module: (1) After drawing a ROI,the terminal demostrated the results like this: ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 -4.407 13586 966.10 44.2 -39.2 7.1 0.02020 0.01840 0.02200 2402 -4786.73 bankssts Could you tell me what exactly the "TalX TalY TalZ" refers to and whether the coordinate "TalX TalY TalZ" represents the VtxMax of the ROI? When I clicked the button "FindClustersAndGotoMax", the terminal showed the results: ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -1.6946 7 966.10 45.9 -43.8 7.5 2402 bankssts The NVtxs is the same,but the "Tal X Y Z" is a little different. So are they the same region? (2) I used mris_anatomical_stats to get a set of statistics on each individual label created before, the average thickness,number of vertices, surface area and gray matter volume were saved in the file of stat. Was the average thickness the normalized one? Thank you for your help. Best regards, Dongsheng Wu Huaxi MR Research Center, Westchina Hospital,Sichuan University Chengdu,Sichuan,China

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make_average_subject error
by Duran, Tugce 16 Nov '17

16 Nov '17

Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited with ERRORS at Wed Nov 15 19:14:17 EST 2017 It appears that during the process it doesn’t create the norm.mgz file to read or open it in the later processes (I think?). What can I do to fix this error? Thanks, Tugce

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Re: [Freesurfer] Optseq and de convolution for rapid designs
by fmri2013 16 Nov '17

16 Nov '17

Dear Douglas I will apprecite it if you can please clarify this simple question. If I optimise my design using Optseq, do you know if this de convolution process is implemented in SPM or any other software? and it is part of the processing behind the scenes? Or do I have to account for this using a specific software. Many tha is Aser Sent from my Samsung Galaxy smartphone. -------- Original message --------From: fmri2013 <fmri2013(a)gmail.com> Date: 10/11/2017 19:30 (GMT+00:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs Many thanks Douglas If I optimise my design using Optseq, do you know if this de convolution process is implemented in SPM or any other software? and it is part of the processing behind th3 scenes? Or do I have to account for this using a specific software. Aser Sent from my Samsung Galaxy smartphone. -------- Original message --------From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Date: 10/11/2017 19:24 (GMT+00:00) To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Optseq and de convolution for rapid designs It is because the random jitter creates differential amounts of overlap. Imagine if you have A=C+D and B=C-D. You know A and B, but you want C and D. You have two equations and two unknowns, so you can solve for C and D from A and B eventhough C and D "overlap" in A and B and you never see C or D by themselves. This is a type of deconvolution On 11/10/17 11:38 AM, Aser A wrote: Hi all I used Optseq to optimize rapid event designs with multiple conditions . I have a theortical question : how it is possible to distingwoh the close by trials ? Is it by de convoution ? How is it possible to deal with overallped trials ? Is it because the conditions are random so that when averaging them the distingwoh is possible? Many thanks Aser _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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optseq with dependent stim types in a single trial
by Michelle VanTieghem 16 Nov '17

16 Nov '17

Hello, I am using optseq to optimize a new task. I have been playing around with the examples they have on the documentation. What I can't find is information on how to set up the trial structure when 1 trial is comprised of 3 different stimuli types: (choice 3sec --> effort (hard or easy) 3 sec --> feedback 2sec (reward or no reward) I don't want to consider it all one long trial, because I do want to model these 3 stim types separately with jitter between each of them. So I'm not sure how to set this up within the structure of opt seq, or if it's even possible. I also don't want to randomize the trial type itself (hard or easy) because that is the participant choice. I'd greatly appreciate any input! Thanks, Michelle -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

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feeding data not processed with longitudinal pipeline into Linear Mixed Effects (LME) model
by Lara Foland-Ross 16 Nov '17

16 Nov '17

Hello Freesurfer experts, I have two longitudinal datasets. In each dataset, some participants have only a single timepoint. For this reason, I aim to run the Linear Mixed Effects (LME) Model described at https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels. I understand that it is recommended that before running LME, I process my data using the longitudinal stream (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) However: 1. in one dataset, some participants were scanned several years apart in early childhood, which caused the intra-subject registration to fail in the longitudinal processing stream and 2. in the second dataset, editing of longitudinal timepoints was time prohibitive - several hours of edits were spent per brain at the cross-sectional level due to the use of an older sub-optimal pulse sequence. And, several more hours are required for the editing of each base or longitudinal timepoint. Given each of these circumstances, is it feasible/appropriate to run LME using data that was not initially processed using the longitudinal processing stream within Freesurfer? Thanks in advance! Lara Lara Foland-Ross, Ph.D. Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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changing qdec path?
by 박경일 15 Nov '17

15 Nov '17

Dear experts, Based on my knowledge, all image folders should be within subject_dir for qdec process. But, my data are so huge to be included in this directory in my default setting. Do you have any idea to change qdec path by which qdec can import image files in external hard drive or other bigger directory, excepting hard formatting? Thank you as always Kyung

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Using aparcstats2table for LGI
by Maksimovskiy, Arkadiy 15 Nov '17

15 Nov '17

Dear Experts, I have extracted mean LGI values for each ROI using mri_segstats --annot SUBJ rh aparc --i $SUBJECTS_DIR/SUBJ/surf/rh.pial_lgi --sum lh.aparc.pial_lgi.stats For the next step, I am attempting to combine them into one table, and am trying to use the aparcstats2table function. Does anyone know what should be entered as a flag for this function? I only see the following measures as options: default is area ( alt volume, thickness, thicknessstd, meancurv, gauscurv, foldind, curvind). Not sure how to apply this for the LGI stats. Thank you in advance for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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"error parsing license file, expected 4 values" with amygdala segmentation
by Carl Anderson 15 Nov '17

15 Nov '17

Hi Everyone, I'm running freesurfer-Darwin-OSX-dev-20171107-ec5ce3a I seem to get the line "error parsing license file, expected 4 values" occuring frequently. I attached the HA log file. Just wondering if its a bug or a problem with my license file? Thanks, Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M Anderson, Ph.D., Research Associate Developmental Biopsychiatry Research Program, McLean Hospital, & Department of Psychiatry, Harvard Medical School. 51 Trotter Pl., Asheville, NC 28806 ------------------------------------------------------- Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer. e-mail: remfract(a)gmail.com <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Getting aparc.a2009s.annot in MNI
by Daya P 15 Nov '17

15 Nov '17

Hi All, I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the annotation file (lh and rh) is in subject native space. I have a grey matter mask in MNI from each subject and my goal is to have each label from aparc.a2009s.annot to fit that mask. How can I do this? Thank you, Daiana

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Freesurfer November 2017