Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Re: [Freesurfer] Trouble getting git-annex files
by Ricardo Valle 03 May '18

03 May '18

External Email - Use Caution Hello, I need help recompiling dmri_train for Mac. It seems like the instructions in the Mac Developer’s don’t work. When I cd to the trc subdirectory and run make, I am told there is nothing to do. I tried editing the Makefile, adding bin_PROGRAMS = dmri_train, at which point I got a different error. I then uncommented some other lines in the Makefile and managed to start compiling dmri_train, but I’ve been getting a never-ending sequence of errors, essentially telling me that the compiler can’t find various dependencies (boost/program_options.h, itk*.h, etc.). I’ve tried running ./configure with various flags that disable or enable various build options, copying over .h files from other locations, adding -I <path> directives for the compiler in the Makefile, etc. etc. to no avail. Thank you, Ruy > On Apr 30, 2018, at 5:19 PM, Ricardo Valle <ruyvallem(a)gmail.com> wrote: > > Dear Freesurfer community, > > I am trying to recompile Freesurfer in order to get a binary of the latest version of dmri_train. I have been following the instructions in the Freesurfer Mac Developer’s page <https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page> and am stuck at the following: > git annex get --metadata fstags=makeinstall . > > I am attaching the output (stdout and stderr) from this command to this email. Please note that I called the git-annex repository mgh rather than datasrc. The purpose of running this is so I can run make install. > > Is there a way of recompiling only dmri_train or only the dmri_* programs? If not, do you know why git-annex might be giving me problems and how to solve this? > > Thank you, > Ruy > <fs-annex-get.txt>

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mri_segment-MRIcheckVolDims error
by Kambiz Tavabi 03 May '18

03 May '18

External Email - Use Caution Hi all, I noticed the following error message in a reconall-log concerning wm segmentation: mri_segment -keep -mprage brain.mgz wm.seg.mgz... ... ERROR: mri_segment-MRIcheckVolDims: volume1 height=336 != volume2 height=256. I looked at resulting surfaces and can't find a cause for concern, should I be concerned? I presume the volumes in question are non-conforming, could someone explain what the issue may be. Thanks in advance, Kambiz

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Comparison between T1 only recon-all and T1 + FLAIR recon-all
by O'Shea,Andrew 03 May '18

03 May '18

External Email - Use Caution Hello, In the past we have only used the T1 image as input for recon-all. However, we are now also acquiring a FLAIR image and were thinking of using both for new studies. Does anyone have any data on the differences/advantages of using FLAIR images with the FLAIRpial command? Any input would be greatly appreciated. Thanks! Andrew O'Shea, MSc. Clinical Research Coordinator II Woods Lab Center for Cognitive Aging and Memory McKnight Brain Institute Department of Clinical and Health Psychology College of Public Health and Health Professions University of Florida Phone (Office): (352) 294-5827 Phone (Cell): (586) 899-2771 Email: aoshea(a)phhp.ufl.edu

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Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields
by Mark Wagshul 03 May '18

03 May '18

External Email - Use Caution Eugenio, Sorry I have a few questions. The original images were NOT 256x256x256, they were cropped, but it seems that all of the output images from Freesurfer are 256x256x256. The simplest thing for me to do is to register my DTI images to the norm.mgz image, but I’m not sure how to do that. I’m used to working with FSL, and I’m not confident that this will work. When I tried a simple mri_convert on the norm.mgz file to NIFITI, the orientation of the image in fslview was different from the original image (sagittal image is rotated by 90’, axial and coronal images are swapped and coronal image is rotated by 180’). If you could guide me on how to best re-register my DTI NIFTI images to the norm.mgz image, that would be great. Thanks, Mark From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Thursday, May 3, 2018 3:47 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields External Email - Use Caution Dear Mark, Just to make sure we’re on the same page: I’ll say that two images are in the same voxel space when they have the same size (in voxels, e.g., 256x256x256) and the same vox2ras matrix - the one that maps voxel coordinates to RAS (physical) coordinates. The subfield segmentation is indeed in the same RAS coordinates as your native T1, but not in the same voxel space. One option that you have is to convert your subfield mask to the voxel space of the T1, with the option –rl (“reslice like”) of mri_convert: For probabilistic masks: mri_convert subfield_prob.mgz subfield_prob_T1voxelSpace.mgz -rl norm.mgz -odt float For discrete masks or segmentations, you can use a similar command, but with nearest neighbor interpolation: mri_convert subfield_mask.mgz subfield_mask_T1voxelSpace.mgz -rl norm.mgz -odt float -rt nearest I hope this helps! Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Mark Wagshul <Mark.Wagshul(a)einstein.yu.edu<mailto:Mark.Wagshul@einstein.yu.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 2 May 2018 at 20:57 To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields External Email - Use Caution Hi. I am just getting my feet wet with running my subjects through the Freesurfer processing stream, so the following question night be a bit trivial (I hope): I have run qvlSegmentHippocampal subfields on one of my subjects, and it completed just fine with what seem to be the appropriate outputs in the subject’s mri folder. I have another 100 subjects to run, but want to make sure I can accomplish what I would like to on this subject first. The images which I see are sub-images, i.e. these have fewer voxels compared to the original image, but in the native T1 space resolution (= 1 mm3). I would now like to register the subfields in the native space (my DTI/NODDI maps are already registered into this space), to obtain mean values within each subfield. How can I transform these sub-field images back into the native T1 space, or is there a method within Freesurfer to perform the math (e.g. similar to fslmaths)? Thanks, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [instein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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combinesurfs problem: shifts and rotates
by Klink-3, N.E.C. van 03 May '18

03 May '18

External Email - Use Caution Dear all, I am struggling with coverting and combining pial surfaces back to native space. My result is 90 degrees rotated, and shifted from the original MRI. The initial lh.pial and rh.pial look good, and when I translate them to native space they still look good. However when I combined them, they suddenly shift and rotate. Does anyone know what happens, how I can prevent it, or reliably can shift and rotate back? Also, if I do not save directly to STL, the surfaces get messed up in -combinesurfs, with a lot of vertices shifted to the center of the surface (see picture below). But this is not my biggest problem, as I want STL in the end. My code: tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit -regheader mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s {SUBJECT} mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval rh.pial.native --tval-xyz --hemi rh --s {SUBJECT} mris_convert --combinesurfs $SUBJECTS_DIR/${subject}/surf/lh.pial.native $SUBJECTS_DIR/${subject}/surf/rh.pial.native $SUBJECTS_DIR/bh_native.stl Thanks in advance, Nicole [cid:image001.png@01D3E212.853EF220] ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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kvlGEMSMatlab error: search direction is not a descent direction
by Wayne Su 03 May '18

03 May '18

External Email - Use Caution Hello FreeSurfer Developers, > > I'm attempting to run longitudinal segmentation of hippocampal subfields by > using the development version of FreeSurfer, but for some of my subjects I get > the following error: > > ******************* > Global iteration 3 > ******************* > > ***** Estimating subject-specific atlas ***** > L-BFGS > Verbose: 0 > MaximalDeformationStopCriterion: 1e-10 > LineSearchMaximalDeformationIntervalStopCriterion: 1e-10 > MaximumNumberOfIterations: 1000 > BFGS-MaximumMemoryLength: 12 > Subject atlas deformation, step 1 of 400 > Did one deformation step of max. 0.38685 voxels in 7.733 seconds > > minLogLikelihoodTimesPrior = > > 1.0297e+05 > > Subject atlas deformation, step 2 of 400 > Error using kvlGEMSMatlab > /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMe > shDeformationOptimizer.cxx:327: > itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2b53b9427df0): search > direction is not a descent direction! > > Error in kvlStepOptimizer (line 11) > Error in SegmentSubfieldsT1Longitudinal (line 1169) > > > Does anyone have any thoughts on how to trouble-shoot this one? > > 1) FreeSurfer version: freesurfer-x86_64-unknown-linux-gnu-dev-20180426 > 2) Platform: CentOS Linux release 7.4.1708 (Core) > 3) uname -a: Linux bcmhari-hpc12 3.10.0-327.el7.x86_64 #1 SMP Thu Nov 19 > 22:10:57 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux > > > > Thanks, > Wayne

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freesurfer masks for fsl processed data
by Rongxiang Tang 03 May '18

03 May '18

External Email - Use Caution Dear All, I ran fsl feat on my functional data and have all my data transformed into standard MNI space. However, I would like to use freesurfer generated white matter parcellation (wmparc.mgz) to extract white matter signals from my MNI space functional data.I noticed that both are in completely different space, so I was wondering what steps do I need to do to transform wmparc.mgz into the same space as my processed functional data. Thanks!Catherine

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Hippocampal subfield analysis did not run or produce right hemisphere outpus
by Zola Mannie 03 May '18

03 May '18

External Email - Use Caution Dear all I ran the hippocampal subfield analysis with this script: recon-all -s HP_0015 -hippocampal-subfields-T1, and this completed without errors. However, looking at outputs inside the mri directory, there is only the left hemisphere (3 of them) but no right hemisphere outputs. Why did this occur and how can I correct it? Any help would be most appreciated Best wishes Zola Dr Zola Mannie BSc(Hons), MSc, PhD Senior Research Officer; CADE Clinic Department of Academic Psychiatry Royal North Shore Hospital St Leonards Sydney. NSW; 2065; Australia Tel: +61<Tel:+61>294629908 E: zola.mannie(a)sydney.edu.au

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Re: [Freesurfer] Fw: Yeo Atlas Network 3 segmentation FEF
by Thomas Yeo 02 May '18

02 May '18

External Email - Use Caution Hi Catherine, We have extracted the 7 and 17 networks into 51 and 114 regions respectively. See figures in https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc… Unfortunately, we have only provided the parcellation in fsaverage5 ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parc…) so you should add one more mri_surf2surf step to upsample the parcellation from fsaverage5 to fsaverage. Check that it is good and then proceed with your previous steps. I am emailing the freesurfer list, so that my reply might hopefully be useful for other folks. Regards, Thomas On Thu, May 3, 2018 at 8:46 AM, Catherine Joe <catherine.joe(a)uq.net.au> wrote: > Hello Dr Yeo, > > > Yes, I want to be able to split network 3 into different component regions > so that I can have a nii file for FEF. This will then allow me to get the > signal intensity and hopefully, the volume of the FEF region for each > participant in my Honour's project. > > > Thank you. > > > Kind regards, > > Catherine > ------------------------------ > *From:* Thomas Yeo <ythomas(a)csail.mit.edu> > *Sent:* Thursday, 3 May 2018 9:36:52 AM > > *To:* Catherine Joe > *Cc:* 李婧玮 > *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF > > Hi Catherine, > > Can I verify what you need is network 3 split into different component > regions like FEF, etc? > > Regards, > Thomas > > On Wed, May 2, 2018 at 11:08 AM Catherine Joe <catherine.joe(a)uq.net.au> > wrote: > > Hi Dr Yeo and Jingwei, > > > Yes, I did use that link to subscribe to the mailing list about 2.5 weeks > ago and they still haven't gotten back to me. I simply thought I didn't get > a confirmation email and tried again, which was the message I forwarded to > you today. Just now, I tried subscribing again. > > > So the commands I've used so far is as follows: > > mri_surf2surf --srcsubject fsaverage --trgsubject subject11GS --hemi lh > --sval-annot $subjectdir/Yeo_Neurophysiol11_Freesurfer/ > fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval lh.7Networks.annot > > (same was done for the rh before doing mri_aparc2aseg) > > > mri_aparc2aseg --s subject11GS --o $subjectdir/subject11GS/test/test.mgz > --annot 7Networks --annot-table path_to/Yeo2011_7Networks_colorlux.txt > > > mri_annotation2label --subject subject11GS --outdir > $subjectdir/subject11GS/test --hemi lh --annotation > $subjectdir/subject11GS/label/lh.7Networks.annot > > > mri_label2vol --label $subjectdir/subjet11GS/test/lh.7Networks_3.label > --temp $subjectdir/subject11GS/mri/rawavg.mgz --subject subject11GS > --hemi lh 00o $subjectdir/subject11GS/test/lh7Networks.nii.gz --proj frac > 0 1 0.01 --reg $subjectdir/subject11GS/corticalroi/subject11GS_ > register.dat > > > And after doing that, all I got was the volume for network 3 but not > actually having any separation with the FEF and the other areas. > > > Thank you for your help. > > > Kind regards, > > Catherine > > ------------------------------ > *From:* yeoyeo02(a)gmail.com <yeoyeo02(a)gmail.com> on behalf of Thomas Yeo < > ythomas(a)csail.mit.edu> > *Sent:* Wednesday, 2 May 2018 10:33:18 AM > *To:* Catherine Joe > *Cc:* 李婧玮 > *Subject:* Re: Fw: Yeo Atlas Network 3 segmentation FEF > > Hi Catherine, > > Have you tried subscribing to the mailing here ( > http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer)? > > Can you please let me know the exact commands you have tried so far? > > I am cc-ing my grad student (Jingwei), who might be able to answer more > rapidly. Please reply all to keep her in the loop. > > Thanks, > Thomas > > On Wed, May 2, 2018 at 8:14 AM, Catherine Joe <catherine.joe(a)uq.net.au> > wrote: > > Hi Dr Yeo, > > > Thank you for your help before with actually aligning and extracting your > atlas. I know that you mentioned before that I should try and email into > the FreeSurfer mailing list for any further queries. > > However, as you can see, I am apparently not subscribed to the list even > though I sent in a request before. I've been trying to send in a question > for the past week. > > I was wondering if you'd be able to help me with this problem I've had > after extracting the Network 3 ROI. The message I tried sending to the > FreeSurfer Mailing list is as below: > > > Hello, > > > I'm having trouble getting the segmentation for the FEF using the Yeo > Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume > file, it doesn't show me two individual labels for the network (primarily > the three areas of the dorsal attention network). In Freesurfer, it simply > has all three areas labelled as the same colour called the 'left cerebral > exterior'. I even did mri_aparc2aseg using the following code: > > > mri_aparc2aseg --s subject11GS --o /data/cai-wks2/data > _local_temp/Cathy/freesurfersubjects/subject11GS/test/test.mgz --annot > 7Networks --annot-table path_to/Yeo2011_7Networks_colorLUT.txt > > > I am still unable to find the labels that qualify as FEF for the lh or rh > so that I could mask out the values in the mgz file and then extract the > information I want from the roi (a stats on the grey matter volume as well > as the signal intensity). > > > Any help would be greatly appreciated. > > > Kind regards, > > Catherine > > --- > > > Thank you so much for your time. > > > Kind regards, > > Catherine > > > ------------------------------ > *From:* freesurfer-bounces(a)nmr.mgh.harvard.edu < > freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of > freesurfer-owner(a)nmr.mgh.harvard.edu <freesurfer-owner(a)nmr.mgh.harvard.edu > > > *Sent:* Wednesday, 2 May 2018 10:10 AM > *To:* Catherine Joe > *Subject:* Yeo Atlas Network 3 segmentation FEF > > You are not allowed to post to this mailing list, and your message has > been automatically rejected. > > ! IMPORTANT ! Make sure you are sending your message using the same > email address that was used to subscribe to the list! > > !! Registering for a FreeSurfer license does not mean you have been > subscribed to the list !! > > If you think that your messages are being rejected in error, contact > the mailing list owner at freesurfer-owner(a)nmr.mgh.harvard.edu > > > > 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 . 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. > > > ---------- Forwarded message ---------- > From: Catherine Joe <catherine.joe(a)uq.net.au> > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Bcc: > Date: Wed, 2 May 2018 00:10:33 +0000 > Subject: Yeo Atlas Network 3 segmentation FEF > > External Email - Use Caution > > Hello, > > > I'm having trouble getting the segmentation for the FEF using the Yeo > Atlas 2011 Network 3. Although I've been able to get Network 3 as a volume > file, it doesn't show me two individual labels for the network (primarily > the three areas of the dorsal attention network). In Freesurfer, it simply > has all three areas labelled as the same colour called the 'left cerebral > exterior'. I even did mri_aparc2aseg using the following code: > > > mri_aparc2aseg --s subject11GS --o /data/cai-wks2/data > _local_temp/Cathy/freesurfersubjects/subject11GS/test/test.mgz --annot > 7Networks --annot-table path_to/Yeo2011_7Networks_colorLUT.txt > > > I am still unable to find the labels that qualify as FEF for the lh or rh > so that I could mask out the values in the mgz file and then extract the > information I want from the roi (a stats on the grey matter volume as well > as the signal intensity). > > > Any help would be greatly appreciated. > > > Kind regards, > > Catherine > > > >

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visualizing seeds on surface
by Eryilmaz, H. Hamdi 02 May '18

02 May '18

Dear freeview experts, Is it possible to display multiple seeds (i.e., as a small circle) on freeview surface view by specifying their coordinates? If there is no such feature, could you suggest an alternative way to visualize seeds? Thanks in advance! Best, Hamdi

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