Freesurfer August 2018

freesurfer@nmr.mgh.harvard.edu

104 participants
167 discussions

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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Flipped left to right hemisphere subjects
by Lutz,Olivia (BIDMC - Psychiatry) 14 Aug '18

14 Aug '18

Dear Freesurfer group, We have some scans that have been processed using Freesurfer 5.1 and the measures have already been extracted from the DKT atlas. We've realized that some of the scans have been flipped left to right before proceeding through recon-all. Assuming we cannot reprocess these scans nor upgrade to Freesurfer 6.0, can we simply flip our left and right ?hemisphere measurements for the affected subjects? Or does the DKT atlas incorporate left-right asymmetry in the brain? Best, Olivia ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Surface Area in Toddlers/Children
by Derek Sayre Andrews 14 Aug '18

14 Aug '18

External Email - Use Caution Dear Freesurfer Developers and Experts, I have been exploring various vertex wise (mass univariate) effects using freesurfer measures of cortical thickness and surface area in a cohort of toddlers/children aged 25-70 months. When looking at the effect of age on surface area using individuals’ measures mapped to fsaverage and smoothed at 15mm fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread negative effect of age (i.e. decreased surface area with age). Given the age group of the cohort this seems implausible. Plotting the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the relationship: [cid:image001.png@01D42FCE.C197B360] However, plotting the lh+rh total surface area returned by mris_anatomical_stats reveals a much more plausible relationship between surface area and age: [cid:image002.png@01D42FCE.C197B360] My working hypothesis is that the significantly smaller brain sizes of our cohort compared to fsaverage, and the fact(?) that -qcache does not preserve global surface area, is causing an “over adjustment” in our cohorts smallest brains when mapped to fsaverage. Thus, my questions are three fold 1. Is the mapping of our significantly smaller brains to fsaverage a potential explanation for the results we are seeing in our mass univariate analyses of surface area? 1. If this is the case, would this effect be limited to surface area or also extend to other freesurfer measures including cortical thickness, lGI, sulcal depth etc. 1. How would you recommend approaching vertex wise analyses in a cohort of this age? Create a study specific average subject using make_average_subject to map onto? Thank you for your insight and guidance! Best, Derek PS: All processing was performed using freesurfer v5.1 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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Lobe parcellation without cingulate from --lobesStrict
by Fernanda Hansen P. de Moraes 14 Aug '18

14 Aug '18

External Email - Use Caution Dear FreeSurfer experts, I want to get with mris_anatomical_stats the stats from the four lobes, Frontal, Parietal, Temporal and Occipital as suggest here ( https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) but without the cingulate. I am trying to use the mri_mergelabels to merge that labels: Rostral Anterior (Frontal) Caudal Anterior (Frontal) Posterior (Parietal) Isthmus (Parietal) in their lobes, but I am facing some difficulties. I am sorry if this is a basic question, but I couldn't find an example that worked for me in the mail archive. I am following these steps: mri_annotation2label --subject PRI002 --hemi lh --lobesStrict lh.lobesStrict.annot mri_mergelabels -i lh.frontal -i lh.rostralanteriorcingulate -i lh.caudalanteriorcingulate -o lh.frontal Is there an easier way to do it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Re: [Freesurfer] coregistering with bbregister
by Ben M 13 Aug '18

13 Aug '18

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? 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? 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? Best, Ben

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Freesurfer August 2018