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30132 discussions

mri_label2label no registration difference
by Yagmur Ozdemir 19 16 Aug '18

16 Aug '18

External Email - Use Caution Hello FreeSurfer experts, I want to compare the labels produced by two different registration methods in mri_label2label; either using the sphere or TAL space as an intermediate ( --regmethod). However I see that there is no difference between the labels produced with these different registrations. Is this normal or should I look for an error? I looked at the script to match with my outputs and everything seems to have worked allright. Thank you Idil

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Wash U Radiology Department Research Faculty Positions Available
by Moreau, Allison 15 Aug '18

15 Aug '18

External Email - Use Caution FYI Begin forwarded message: From: WUNIC Email List Admin <wunic(a)nrg.wustl.edu<mailto:wunic@nrg.wustl.edu>> Date: August 14, 2018 at 9:26:48 AM CDT To: <amoreau(a)wustl.edu<mailto:amoreau@wustl.edu>> Subject: Radiology Department_Research Faculty Positions Available Reply-To: WUNIC Email List Admin <wunic(a)nrg.wustl.edu<mailto:wunic@nrg.wustl.edu>> View this email in your browser<https://mailchi.mp/c8252eeb516b/radiology-department_research-faculty-posit…> [https://gallery.mailchimp.com/28232c5fb4d47392812342a76/images/1303a9cd-2ee…] Dear all: A new job ad for Radiology research faculty is now out. Neuroimaging is part of this search. https://facultyopportunities.wustl.edu/Posting/Detail/1010318<https://xnat.us10.list-manage.com/track/click?u=28232c5fb4d47392812342a76&i…> Please forward liberally and encourage people to apply. Any questions can be directed to me (tammy(a)wustl.edu<mailto:tammy@wustl.edu>), Joe Culver (culverj(a)wustl.edu<mailto:culverj@wustl.edu>) or Rob Gropler (rgropler(a)wustl.edu<mailto:gropplerr@wustl.edu>). Best Tammy Tamara Hershey, PhD Professor, Psychiatry & Radiology Departments Lab Chief, Neuroimaging Labs (NIL) @ MIR Director, McDonnell Center for Systems Neuroscience Co-Director, Neuroscience PhD Program, DBBS Washington University School of Medicine Campus Box 8225, Room 2204, East Blg 4525 Scott Avenue St. Louis, MO 63110 Phone: 314-362-5593 Email: tammy(a)wustl.edu<mailto:tammy@wustl.edu> Copyright © 2018 WUNIC, All rights reserved. You are receiving this email as a past member of the NIAC mailing list, or as a participant in the WUNIC survey. Our mailing address is: WUNIC 4525 Scott Ave, Campus Box 8225 Saint Louis, MO 63110 Add us to your address book<//xnat.us10.list-manage.com/vcard?u=28232c5fb4d47392812342a76&id=0de7e1e64b> Know someone who would like to receive these emails? You can subscribe to this list here: https://nrg.wustl.edu/contact-us/wunic-email-list-subscription/<https://xnat.us10.list-manage.com/track/click?u=28232c5fb4d47392812342a76&i…> Want to change how you receive these emails? You can update your preferences<https://xnat.us10.list-manage.com/profile?u=28232c5fb4d47392812342a76&id=0d…> or unsubscribe from this list<https://xnat.us10.list-manage.com/unsubscribe?u=28232c5fb4d47392812342a76&i…>.

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Extracting number of vertices in Yeo's 7Networks from significant clusters
by Shatil, Anwar Shahadat 15 Aug '18

15 Aug '18

External Email - Use Caution Hello Doug and other experts: I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this: mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat The result was: Col Headers Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 22519 14950.0 7Networks_1 1.4816 1.8126 0.0000 3.6990 3.6990 2 2 30207 12514.7 7Networks_2 2.6658 1.6596 0.0000 3.6990 3.6990 3 3 17604 8224.3 7Networks_3 2.6278 1.6778 0.0000 3.6990 3.6990 4 4 19402 8357.2 7Networks_4 3.3453 1.0877 0.0000 3.6990 3.6990 5 5 11614 6205.0 7Networks_5 2.1434 1.7750 0.0000 3.6990 3.6990 6 6 22330 12170.7 7Networks_6 2.6315 1.6761 0.0000 3.6990 3.6990 7 7 26056 13826.2 7Networks_7 3.0249 1.4229 0.0000 3.6990 3.6990 I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for. Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster? Thanks. Anwar -- Anwar S. Shatil Research Assistant Department of Medical Imaging Sunnybrook Health Sciences Centre Room AB204, 2075 Bayview Avenue Toronto, ON M4N 3M5 Tel: 416.480.6100 ext. 89617 Email: anwar.shatil(a)sunnybrook.ca This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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Call for Nominations: OHBM Student and Postdoc Special Interest Group
by Chiara Caldinelli 15 Aug '18

15 Aug '18

External Email - Use Caution Dear All, The *OHBM Student and Postdoc Special Interest Group* (SIG) is seeking nominations for open seats on the 2018-2019 SIG Committee. The SIG provides a community of shared interests for OHBM trainees. The Committee aims to provide professional, personal and career development for OHBM trainees as well as social and mentoring opportunities at the Annual Meeting. Committee members benefit from being an integral part of the SIG community, directing its activities, and working with the OHBM Executive Office and wider community. We are committed to diversity and equality and are seeking representation from trainees across the world. Eligibility *Nominees must be current students or postdocs. * Students are defined as those working full time towards a graduate degree - M.A., M.S., Ph.D. or M.D. degree. Postdocs are individuals who are no more than four years after completing such a degree at the time of next Annual Meeting. Nominees must be members of OHBM in good standing at the time of the next Annual Meeting. Nominees must be planning to attend the next two Annual Meetings in Rome 2019 and Montreal 2020 (and likely to attend the meeting in 2021). To nominate yourself for election to the SIG Committee please complete this nomination form: https://goo.gl/forms/DeC5FoQx4nwbel1K3 no later than August 31st, 2018. Email ohbmtrainees(a)gmail.com if you have any questions. Nominations close on the 31st August 2018. Kind Regards, OHBM Student and Postdoc SIG

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ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1
by Nabin Koirala 15 Aug '18

15 Aug '18

External Email - Use Caution Hi freesurfer community, I am trying to do QDEC with a data for 2 groups but stuck in this error for many hours now. Tried and checked everything I could think of. Also went through the old threads and checked those recommneded but still could not solve it. Your hint will be very helpful. *ERROR: matrix is ill-conditioned or badly scaled, condno = 18696.1* *--------------------------------* *Possible problem with experimental design:* *Check for duplicate entries and/or lack of range of* *continuous variables within a class.* *If you seek help with this problem, make sure to send:* * 1. Your command line:* * mri_glmfit --y /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label /gpfs/fs1/home/mmuthura/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-f-m-Intercept-thickness.mat --C /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-Diff-Epi-Chr-Intercept-thickness.mat --C /gpfs/fs1/home/mmuthura/freesurfer/subjects/qdec/Untitled/contrasts/lh-X-gender-Group-Intercept-thickness.mat* *2. The FSGD file (attached)* *3. Design Matrix* Design matrix ------------------ 1.000 0.000 0.000 0.000 31.300 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 22.760 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 29.390 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 49.160 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 23.810 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 45.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 21.830 0.000 0.000; 1.000 0.000 0.000 0.000 49.540 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 40.550 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 22.660 0.000 0.000; 1.000 0.000 0.000 0.000 26.080 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 32.570 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 47.190 0.000 0.000; 1.000 0.000 0.000 0.000 27.710 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 25.860 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 25.180 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 27.630 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 51.930 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 25.060 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 60.650; 0.000 0.000 1.000 0.000 0.000 0.000 59.360 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 62.450; 0.000 0.000 1.000 0.000 0.000 0.000 20.480 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 36.550 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 37.000 0.000;

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SNR for PET images
by James Brown 14 Aug '18

14 Aug '18

External Email - Use Caution Hi Freesurfer team, I would like to use "mri_segstat" to compute SNR for regions of interest. My question is, if I use PET images as input does this mean that SNR will be computed for the PET signal in the ROIs? Thanks for any help John

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hardware needs for fMRI
by Hazard, E. Starr 14 Aug '18

14 Aug '18

External Email - Use Caution Folks, I am a computer administrator trying to put together a proposal for a new University shared resource compute cluster. Some fMRI image analysts have suggested that GPUs are frequently used in the field and that in particular, double precision GPUs are the hardware of choice. Double precision GPU can be an order of magnitude more expensive to purchase than their single precision version. Google sees many opinions For fMRI… These articles suggest single precision: https://blogs.nvidia.com/blog/2010/04/21/the-world-is-parallel-gpus-speed-m… https://www.nvidia.com/content/cuda/spotlights/anders-eklund-vtcr.html https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3953750/ This page from NVIDIA suggests the double precision Tesla but when you click on all of their links the papers were written with single precisions cards! https://www.nvidia.com/object/medical_imaging.html I realize that this appeal for information may not be appropriate for this list but I would appreciate some guidance, if anyone has the time and interest. The goal is to create a hardware resource that would be useful to a broad user base including fMRI analysts. I am not after a high throughput clinical system but more of a software development capability. What sort of GPUs should I be pricing? Thanks in advance Starr Hazard, Ph.D. Computational Biology Resource Center Medical University of South Carolina Charleston, SC ------------------------------------------------------------------------- This message was secured via TLS by MUSC.

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Re: [Freesurfer] coregistering with bbregister
by Douglas N. Greve 14 Aug '18

14 Aug '18

Hi Ben, please remember to post the list. Answers below On 08/14/2018 02:22 PM, Ben M wrote: > > External Email - Use Caution > > Hi Doug, > > Thanks again for your help! > > | It reslices the mov into the anatomical space. What do you mean when > you "load" them? > > I mean when I view the images in fsleyes they don't seem to be very > different, but I suppose that's because the reslicing is probably very > subtle to see. > > I just came across this post > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036120…, > in which you suggest running > > tkregister2 --mov func.nii --fstarg --reg register.dat --fslregout > fsl.mat --noedit > > to get an FSL-compatible registration. I'd also like to use fnirt, and > for that I need the affine transformation matrix from bbregister. I > think if I simply do: > > $ bbregister --t2 --lta /data/bbregister/reg.lta --mov > /data/mean_func.nii.gz --s 001 > $ tkregister2 --mov /data/mean_func.nii.gz --fstarg --reg > /data/bbregister/reg.lta --fslregout /data/fsl.mat --noedit > > tkregister2 will put the transformation matrix reg.lta in the > appropriate format for fnirt, right? Or do I still need to play around > with freesurfer's coordinate system? It should be ok > > Best, > Ben > > > On Mon, Aug 13, 2018 at 10:11 PM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > > > On 08/13/2018 03:02 PM, Ben M wrote: > > > External Email - Use Caution > > Hi Doug, > > Thank you very much for your response, it helped me a lot. > I checked the examples of mri_vol2vol and for > functional-to-structural registration I think I should do > > $ bbregister --t2 --lta /data/bbregister/reg.lta --mov > /data/mean_func.nii.gz --s 001 > $ mri_vol2vol --lta /data/bbregister/reg.lta --mov > /data/mean_func.nii.gz --fstarg --o func2anat.nii.gz --no-resample > > If I understood correctly, this will align mean_func with the > structural image (orig.mgz I think). Is this correct? > > Yes > > > I have two follow up questions if you don't mind: > > 1 - I'd like to get the file describing the affine > registration of the functional to structural space for > subsequent preprocessing. I think this should be the reg.lta > (or reg.dat) file from the bbregister step, shouldn't it? This > file contains the transformation matrix from functional to > structural, is that correct? > > Yes. You may need info here to decode it: > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems> > > 2 - does mri_vol2vol actually physically move the -mov image? > I think it does, which is the --o func2anat image above. > However when I load the mean_func and func2anat images, they > don't seem to be different in terms of orientation. I suppose > it's because it's difficult to see the transformation with the > naked eye? > > It reslices the mov into the anatomical space. What do you mean > when you "load" them? > > > Best, > Ben > > > > > 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 Partners > Compliance HelpLine at > http://www.partners.org/complianceline > <http://www.partners.org/complianceline> . If the e-mail was sent > to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > >

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Re: [Freesurfer] cannot execute mri_aparc2aseg
by Derek Sayre Andrews 14 Aug '18

14 Aug '18

External Email - Use Caution Dear Freesurfer Developers and Experts, I was able to locate an answer to this problem here<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-February/056009.…>. Apologies for the redundant post, the old thread did not return in my initial searches. Best, Derek Derek Sayre Andrews, PhD Postdoctoral Scholar Department of Psychiatry and Behavioral Sciences The M.I.N.D Institute University of California Davis Telephone: +1 916 703 0360 Email: dandrews(a)UCDavis.edu<mailto:dandrews@UCDavis.edu> From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Derek Sayre Andrews <dandrews(a)ucdavis.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, August 14, 2018 at 11:00 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] cannot execute mri_aparc2aseg External Email - Use Caution Dear Freesurfer Developers and Experts, I am trying to patch freesurfer 6.0<https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/> to run make_average_subject on Mac OSx 10.13.3 I am having a problem executing the updated mri_aparc2aseg command and get the following error: -bash: /Applications/freesurfer/bin/mri_aparc2aseg: cannot execute binary file The steps I have taken are simply download the mri_aparc2aseg file from the patch page and change the permisions using “chmod a+x mri_aparc2aseg” A colleague was able to download and execute the file on Ubuntu, so I am wondering if this is a mac specific problem? Any help getting mri_aparc2aseg to execute would be appreciated! Best, Derek PS: If useful, the output of “file mri_aparc2aseg” is: mri_aparc2aseg: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, for GNU/Linux 2.6.32, BuildID[sha1]=cf5dcb47303e476e94c456e1e7f5e6e8dd528ad8, with debug_info, not stripped Derek Sayre Andrews, PhD Postdoctoral Scholar Department of Psychiatry and Behavioral Sciences The M.I.N.D Institute University of California Davis Telephone: +1 916 703 0360 Email: dandrews(a)UCDavis.edu<mailto:dandrews@UCDavis.edu>

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cannot execute mri_aparc2aseg
by Derek Sayre Andrews 14 Aug '18

14 Aug '18

External Email - Use Caution Dear Freesurfer Developers and Experts, I am trying to patch freesurfer 6.0<https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/> to run make_average_subject on Mac OSx 10.13.3 I am having a problem executing the updated mri_aparc2aseg command and get the following error: -bash: /Applications/freesurfer/bin/mri_aparc2aseg: cannot execute binary file The steps I have taken are simply download the mri_aparc2aseg file from the patch page and change the permisions using “chmod a+x mri_aparc2aseg” A colleague was able to download and execute the file on Ubuntu, so I am wondering if this is a mac specific problem? Any help getting mri_aparc2aseg to execute would be appreciated! Best, Derek PS: If useful, the output of “file mri_aparc2aseg” is: mri_aparc2aseg: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, for GNU/Linux 2.6.32, BuildID[sha1]=cf5dcb47303e476e94c456e1e7f5e6e8dd528ad8, with debug_info, not stripped Derek Sayre Andrews, PhD Postdoctoral Scholar Department of Psychiatry and Behavioral Sciences The M.I.N.D Institute University of California Davis Telephone: +1 916 703 0360 Email: dandrews(a)UCDavis.edu<mailto:dandrews@UCDavis.edu>

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