Freesurfer

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19 participants
30088 discussions

units for tracula output
by Alexopoulos, Dimitrios 03 Jun '19

03 Jun '19

External Email - Use Caution What units are the diffusion measures generated by tracula that are found in the files named "pathstats.overall.txt". For example, as 10^-3 Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Tracula error -path
by Lorenzo Pini 03 Jun '19

03 Jun '19

External Email - Use Caution Hi list, Im using TRACULA in a dataset of 60 subjects. for 56 subjects everything is fine, but for 4 subjects I had the following error: >> ncpts: Subscript out of range. For these subjects TRACULA does not reconstruct the file dpath/merged_avg33_mni_bbr.mgz and the statistics of the tracts (i.e. pathstats.* files) Freesurfer parcellations look fine Do you have any suggestions? Thank you Lorenzo

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Cluster-wise multiple comparison correction
by Jacobs, H (NP) 02 Jun '19

02 Jun '19

External Email - Use Caution Hi all! I would love to use the cluster-wise multiple comparison correction method in FS 6.0 for our PET data (in fsaverage space and smoothed). However, since we have some complex models, I did the statistical analyses in R and then converted this to a surface overlay map in mgh format (in log10 p-values). That means that I don’t have the typical glm output that is usually obtained in Freesurfer. I tried to run the mri_glmfit-sim function, but it does need the mri_glmfit.log file. Is there a way around this? Many thanks! Heidi

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selxavg3-sess failed
by starxifd 02 Jun '19

02 Jun '19

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fsl_rigid_register error: error opening .nii file
by Mingjian He 01 Jun '19

01 Jun '19

Hi FreeSurfer Developers, I’m using mne.bem.make_flash_bem python function to create BEM meshes, and mne.bem.make_flash_bem makes use of the FreeSurfer functions fsl_rigid_register and mri_convert. I’m running into an error reading the temporary files when using fsl_rigid_register. It looks like the FSL flirt step in fsl_rigid_register creates a compressed file outvol.fsl_rigid_register.nii.gz in the temporary folder. But in mri_convert, the uncompressed file name outvol.fsl_rigid_register.nii is passed to niiRead(), which runs into an error opening it since the compressed file from flirt has a different format suffix. Is there a way to specify the output format of FSL when sourcing Freesurfer such that it saves in .nii rather than .nii.gz formats? I tried to specify the FSF_OUTPUT_FORMAT, which doesn’t seem to impact FSL output formats. Alternatively, is there a way to flag to either mri_convert of niiRead() such that they can handle a compressed .nii.gz file? Thank you for your time and help! Best, Alex External Email - Use Caution

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Fw: mri_aparc2aseg increases number of parcels? {Disarmed}
by Winkelbeiner, Stephanie A 31 May '19

31 May '19

External Email - Use Caution Hi Freesurfers, the number of my parcels increases after extending them into the WM with mri_aparc2aseg \ --s s001 \ --annot 500.aparc \ --wmparc-dmax 2 \ --labelwm \ --hypo-as-wm \ --o mri/aparc.500+2mm.nii.gz Could that really be the case? And if so, what can I do to keep the original number of parcels? (See more detailed description of my approach below) I would be very grateful for some suggestions! Thanks a lot, Stephanie Winkelbeiner ----------------------------------------------- Stephanie Winkelbeiner, PhD Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-8267 Email: swinkelbei(a)northwell.edu<mailto:swinkelbei@northwell.edu> ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Winkelbeiner, Stephanie A <Swinkelbei(a)northwell.edu> Sent: Friday, 24 May 2019 6:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after transformation of an annotation file into a .nii.gz file External Email. Use Caution. External Email - Use Caution Hi Doug, thanks again for the great tip with MRIread - worked perfectly (after gunzipping the parc300.nii.gz). So, this means I have the next problem now: instead of 300 parcels this image contains 638 parcels... How I created parc300.nii.gz: 1. MATLAB script to create annotation file with 150 parcels/hemisphere 2. extending the parcels 2mm into the WM with mri_aparc2aseg (see 1st email) 3. coregistering to the T1 to get the transformation matrix (bbregister) 4. coregistering to DWI space (mri_vol2vol) I found in an earlier answer of yours that the extention into the WM might duplicate the parcels/labels (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/055952…<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…>) Following your suggestions in that email exchange, I did the following: ## 1. Create a mask of the wm labels: mri_binarize \ --i aparc.500+2mm.nii.gz \ --min 2999.5 \ --max 4035.5 \ --o wm.mask.500.nii.gz ## 2. Mask the wmparc: mri_mask \ aparc.500+2mm.nii.gz \ wm.mask.500.nii.gz \ aparc.500+2mm.masked.nii.gz This results in only two parcels... What am I doing wrong or overlooking here? Thanks a lot for your help (as always)! Cheers, Stephanie ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Winkelbeiner, Stephanie A <Swinkelbei(a)northwell.edu> Sent: Wednesday, 22 May 2019 6:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels after transformation of an annotation file into a .nii.gz file External Email. Use Caution. External Email - Use Caution That sounds like a perfect plan! I gonna try that immediately! Thanks so much, Doug! ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> Sent: Wednesday, 22 May 2019 6:19 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] Checking number of parcels after transformation of an annotation file into a .nii.gz file External Email. Use Caution. the way that pops to mind is to use matlab a = MRIread('aparc.250+2mm.nii.gz'); u = unique(a.vol(:)); length(u) will give you the number of unique segmentation number (including 0) On 5/22/19 5:54 PM, Winkelbeiner, Stephanie A wrote: > > External Email - Use Caution > > Hi Freesurfers, > > I'm struggling to find out if the number of parcels during a process > of transformations from annot -> nii.gz has changed. > > I extended the parcels from 500.annot 2mm into the WM with > mri_aparc2aseg \ > --s s001 \ > --annot 500.aparc \ > --wmparc-dmax 2 \ > --labelwm \ > --hypo-as-wm \ > --o mri/aparc.250+2mm.nii.gz > and coregistered the resulting file to the DWI image using bbregister > and mri_vol2vol. > > Using afni's probilistic tractography pipeline, I end up with more > parcels than I thought I had. > > Is there a way to check the number of parcels after extension into the > WM (mri_aparc2aseg)? > > I would be extremely grateful for some insight! > Thanks, > Stephanie > > The information contained in this electronic e-mail transmission and > any attachments are intended only for the use of the individual or > entity to whom or to which it is addressed, and may contain > information that is privileged, confidential and exempt from > disclosure under applicable law. If the reader of this communication > is not the intended recipient, or the employee or agent responsible > for delivering this communication to the intended recipient, you are > hereby notified that any dissemination, distribution, copying or > disclosure of this communication and any attachment is strictly > prohibited. If you have received this transmission in error, please > notify the sender immediately by telephone and electronic mail, and > delete the original communication and any attachment from any > computer, server or other electronic recording or storage device or > medium. Receipt by anyone other than the intended recipient is not a > waiver of any attorney-client, physician-patient or other privilege. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

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Freesurfer V6 installation: ubuntu virtual machine
by Steve Petersen 31 May '19

31 May '19

External Email - Use Caution Dear Freesurfer experts, Just a simple question, is possible to install the Freesurfer (Version 6) in a virtual machine of ubuntu? Thanks in advance, Best regards, Steve

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Error with mri_glmfit command
by Martin Juneja 30 May '19

30 May '19

External Email - Use Caution Hi FS experts, I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates). My FSGD file looks like: GroupDescriptorFile 1 Class Male Class Female Variables x1 x2 x3 x4 x5 x6 Age Input S001 Male 120 103 109 124 113 94 113 36 Input S003 Male 91 101 86 103 109 95 96 29 Input S004 Male 104 116 110 96 115 108 112 39 Input S005 Female 116 114 103 127 115 106 118 32 Input S006 Female 93 100 90 100 117 90 97 23 Input S008 Male 70 80 80 66 78 83 71 40 Input S009 Female 125 114 115 125 118 104 124 45 Input S010 Female 96 91 93 101 91 92 94 42 Input S011 Male 104 92 97 111 84 103 98 45 Input S012 Female 79 81 90 74 82 80 78 22 Input S014 Male 120 94 118 114 105 87 107 44 Input S015 Female 94 86 92 100 80 93 88 29 Input S016 Male 98 92 107 88 95 90 95 33 Input S017 Female 96 100 112 83 95 104 99 21 Input S018 Male 98 93 96 103 104 87 96 42 Input S019 Female 105 120 99 110 113 114 114 26 Input S020 Female 105 107 104 103 113 100 109 27 Input S022 Female 116 98 115 111 111 89 109 25 Input S023 Female 98 91 94 105 86 96 94 21 Input S024 Male 116 101 119 105 90 112 111 43 Input S025 Female 143 102 134 129 110 95 120 21 Input S028 Female 72 80 77 71 82 78 71 41 Input S029 Male 104 100 116 92 94 105 104 25 Input S030 Female 120 96 115 116 103 92 109 18 Input S031 Female 114 103 111 111 99 105 112 29 Input S033 Male 121 99 108 127 104 96 111 20 Input S035 Male 112 104 104 115 103 103 110 20 Input S036 Female 111 103 103 113 106 98 109 28 Input S037 Male 108 91 108 103 92 91 99 30 Input S038 Male 103 99 102 102 117 89 103 18 Input S039 Male 106 114 116 94 112 107 112 21 Input S040 Male 99 98 97 102 94 100 99 41 Input S041 Male 103 109 97 109 110 103 109 26 My contrast file looks like: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 After I run mri_glmfit command, I get following error: ERROR: matrix is ill-conditioned or badly scaled, condno = 385372 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. I would really appreciate any help in figuring out this issue. Thanks, MJ

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QA_tools citation
by Nasiriavanaki, Zahra 30 May '19

30 May '19

Dear Freesurfer experts Hi I was wondering how should I cite the Freesurfer QA_tools in a paper. I couldn’t find any references in the web page (https://surfer.nmr.mgh.harvard.edu/fswiki/QATools) Thanks Mona

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Postdoc in developmental neuroimaging
by Signe Bray 30 May '19

30 May '19

External Email - Use Caution The Department of Radiology and the Child and Adolescent Imaging Research (CAIR) Program at the University of Calgary are seeking applications for a post-doctoral scholar in developmental neuroimaging. The postdoc will work with the Bray Neuroimaging Lab led by Dr. Signe Bray (@braynimaginglab, http://brayneuroimaginglab.ca) on studies of healthy brain development and neurodevelopmental conditions such as autism and preterm birth. Applicants should have a background in psychology, neurosciences, biomedical engineering or a relevant discipline. Experience with neuroimaging and/or pediatric research and strong data analytic skills is required as well as interest in computational modeling and novel approaches to neuroimaging analyses. This is a 2-year position with the possibility of extension. Applicants should submit a letter of interest and CV to slbray(a)ucalgary.ca. On-site meetings at OHBM can be scheduled. The CAIR Program is a pediatric dedicated imaging program based at the Alberta Children’s Hospital that manages a research-dedicated 3T MR scanner, MRI-compatible EEG system, eye tracking and MRI simulator for preparing children. Calgary is less than an hour’s drive from the majestic Rocky Mountains and offers outstanding opportunities for outdoor recreation including world class skiing, hiking and climbing. The city has been named a cultural capital of Canada and one of the best places to live in the world, Calgary is a city of leaders – in business, community, philanthropy and volunteerism boasts the most extensive urban pathway and bikeway network in North America.

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