Freesurfer

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30132 discussions

Re: [Freesurfer] DWI EPI correction
by Antonin Skoch 08 Feb '20

08 Feb '20

External Email - Use Caution Hi, Adam, while reading this thread, I would like to clarify: bbregister does rigid body registration, so you could use this tool for registering EPI to structurals, indeed. But this tool only registers, it does not unwarp the distortions in the EPI images, it leaves images distorted. For preprocessing of DWI data, I would recommend the "dwipreproc" wrapper script for FSL tools topup and eddy. This is part of mrtrix3 tool: https://mrtrix.readthedocs.io/en/latest/reference/scripts/dwipreproc.html Antonin Skoch I guess there's a 3rd option: you can correct EPI geometric distortions by registering the EPI to a structural scan of the same subject. You can do that in FS with bbregister, which uses the surfaces from recon-all to align any scan to the T1 of the same subject. ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Adam Rytina <adam.ryt...(a)outlook.cz> Sent: Thursday, February 6, 2020 3:37 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] DWI EPI correction External Email - Use Caution Yes, I know this option exists in FSL. I was just wondering whether there are some possibilities to perform diffusion data correction in Freesurfer, too. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <ayend...(a)mgh.harvard.edu> Sent: Thursday, February 6, 2020 9:35:16 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] DWI EPI correction In that case, you'll want to use the topup tool in FSL. ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Adam Rytina <adam.ryt...(a)outlook.cz> Sent: Thursday, February 6, 2020 3:32 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] DWI EPI correction External Email - Use Caution I´m sorry I didn´t specify my data. I didn´t acquire a field map. I have two b0 volumes with both polarities for a phase gradient. Is it possible to estimate a field map from two b0 volumes in Freesurfer? And afterwards apply the fieldmap on other b values volumes to correct susceptibility artefacts? Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10 ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <ayend...(a)mgh.harvard.edu> Sent: Thursday, February 6, 2020 9:27:51 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] DWI EPI correction The answer depends on how you want to correct susceptibility artifacts. Do you have a field map, or do you have DWIs acquired with reverse polarities? ________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> on behalf of Adam Rytina <adam.ryt...(a)outlook.cz> Sent: Thursday, February 6, 2020 2:02 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] DWI EPI correction External Email - Use Caution Hello all, I have an input DWI dataset and wanna perform the diffusion data correction (mg susceptibility induced distortion correction, geometric correction...). Does Freesurfer enable to perform the diffusion correction? Does recon-all include this option? Thanks a lot Regards Adam

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Affine registration 2 input images
by Adam Rytina 07 Feb '20

07 Feb '20

External Email - Use Caution Hello all, I need to perform an affine registration between two input images. Please, which Freesurfer tool does enable to perform affine registration (12 DOF) ? Does the command mri_robust_register enable to do that? Thanks a lot Regards Adam

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Re: [Freesurfer] Suggested specs for a Linux box
by fsbuild 06 Feb '20

06 Feb '20

External Email - Use Caution Hello Shun, I’ve had some issues with graphics with only 8G of RAM.  After you account for the OS and anything else running on the machine, 8G can put pressure on available memory. Dell, Apple, etc. have stock configurations for laptops with 16G RAM and a 4-6 core processor, e.g., Intel i7 chip.  I would avoid laptops with slow internal spinning drives, e.g., 5200 RPM.  When you are reading/writing files in a long chain of processing commands, the time for disk I/O can become a bottleneck.  Having as SSD for storage should speed up read/write times.  Then if you have the funds, higher end machines can be configured with 24-32G RAM and more cores (Intel i9 chip).  But in the high end laptops, the processor performance can be throttled down because of the need to dissipate heat (and the fan comes on). Throttling performance from heat should not be an issue in a desktop machine since the chassis contains several fans, i.e., 1 for the CPU, and 1 or 2 more fans, to pull/push air from the front/back of the machine.  With a desktop machine you can more easily upgrade the hardware.  You  will have extra memory slots so you could start with 16G RAM.  You can get SSD storage/cards that plug into the PCIe slots on the motherboard or directly into the motherboard.   And motherboards often support different models of Intel processors you can choose from with more/less cores. A “server class” desktop or rack mounted machine can bump things up to 64G RAM, Xeon class Intel CPU's with 16-24 cores and multiple SSDs and/or very fast disk drives.  These are often bought or financed by companies or universities for their staff and IT infrastructure. I would start with 16G RAM, 4-6 core Intel i7 (~3 GHz per core) and fast disk storage (SSD or 7200 RPM disk drives) for the files that will be read/written.  Then maybe expand as your needs and budget allows. - R. On Feb 6, 2020, at 18:05, Yao, Shun <syao(a)bwh.harvard.edu> wrote:Dear experts in Free Surfer community,  I am a new fan of Free Surfer. However, I run several times recon-all on my sMRI data and always got errors. After discussing with my friend, we speculated that the PC hardly had enough power to run Free Surfer. Now, my PI agree to buy a new workstation. I am wondering any update recommended specs for a Linux workstation? https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequireme… will run recon-all on a set of 7-T MRI data (0.75mm isotropic).Thank you very much for your help. Best,Shun  ----------------------------------------------------------------------------------SHUN YAO, M.D., Ph.D.Research FellowSkull Base and Pituitary Tumor LaboratoryDepartment of Neurosurgery, Brigham and Women’s HospitalHarvard Medical SchoolBoston, MA 02115, U.S.Tel:  857-777-8213  |  E-Mail: syao@bwh.harvard.edu   _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Suggested specs for a Linux box
by Yao, Shun 06 Feb '20

06 Feb '20

Dear experts in Free Surfer community, I am a new fan of Free Surfer. However, I run several times recon-all on my sMRI data and always got errors. After discussing with my friend, we speculated that the PC hardly had enough power to run Free Surfer. Now, my PI agree to buy a new workstation. I am wondering any update recommended specs for a Linux workstation? https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements I will run recon-all on a set of 7-T MRI data (0.75mm isotropic). Thank you very much for your help. Best, Shun ---------------------------------------------------------------------------------- SHUN YAO, M.D., Ph.D. Research Fellow Skull Base and Pituitary Tumor Laboratory Department of Neurosurgery, Brigham and Women’s Hospital Harvard Medical School Boston, MA 02115, U.S. Tel: 857-777-8213 | E-Mail: syao(a)bwh.harvard.edu<mailto:ytie@bwh.harvard.edu> [https://docs.google.com/uc?export=download&id=1UsXbxaAppJ__3PakeJSGPIpiepmx…]

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DWI EPI correction
by Adam Rytina 06 Feb '20

06 Feb '20

External Email - Use Caution Hello all, I have an input DWI dataset and wanna perform the diffusion data correction (mg susceptibility induced distortion correction, geometric correction...). Does Freesurfer enable to perform the diffusion correction? Does recon-all include this option? Thanks a lot Regards Adam

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Retinotopy analysis results interpretation
by Marco Ninghetto 06 Feb '20

06 Feb '20

External Email - Use Caution Dear FREESURFERs, I'm performing retinotopy analysis. I preprocessed data and made 1st level analysis. Stimuli definition is: 6 cycles of rotating wedge (counter-clockwise rotation) and 6 cycles of expanding ring. One cycle lasts ~41 seconds. Scan TR = 2.5 sec. I followed the pipeline below (after recon-all): preproc-sess -sf sessid -fsd bold -fwhm 5 -surface self lhrh -per-run mkanalysis-sess -a ret_?h -surface self ?h -fwhm 5 -retinotopy 41 -paradigm > rtopy.par -TR 2.5 -fsd bold -per-run selxavg3-sess -a ret_?h -s SUBJ01 (let's say first subject) I created an occipital flat patch and then: fieldsign-sess -a ret_?l -patch lh.occip.patch.flat -s SUBJ01 > Then, I visualize results using tksurfer-sess -a ret_?h -s SUBJ01 -map angle -tksurfer tksurfer-sess -a ret_?h -s SUBJ01 -map angle.masked -tksurfer tksurfer-sess -a ret_?h -s SUBJ01 -tksurfer tksurfer-sess -a ret_?h -s SUBJ01 -fieldsign -tksurfer I'm not sure about the activations I get and I'm not sure how to interpret these data. What are the colors in the colorbar telling me? What is fieldsign img showing? what's the difference between raw angle and angle.masked (is this the mask created during preprocessing?)? In angle.masked result, the red part is the center of population receptive fields deducted from eccentricity or from polar? Here the link to the folder with images <https://drive.google.com/open?id=1ers6Cq9uYEEZnCUHZyFlqtzevV7d-xyg> Any help on interpreting these results would be much appreciated. Thank you, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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Highlighting single atlas structures in freeview
by Francesco Puccettone 05 Feb '20

05 Feb '20

External Email - Use Caution Dear all, I would like to show several structures from the DKT (or the Desikan-Killiany) atlas alone on a "blank" fsaverage brain, rather than have all structures displayed in different colors (as happens by default). For instance, I'd like to just show "medialorbitofrontal" on its own, then "middletemporal" on its own, etc. After I open the parcellation, freeview -v /FS/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f /FS/fsaverage/surf/lh.white:annot=aparc.annot , I expected to be able to turn each label in the list on and off like a layer, but this does not work. [image: 21-01-2019 14.48.54.jpg] I hoped I could use Alt+F to hide/show each atlas label at a time (cf freeview tutorial <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview>), but this instead toggles the entire external surface of the brain on and off. Can anyone help? Thank you! --Francesco

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Error in segmentSubjectT1_autoEstimateAlveusML
by Pascale Patenaude 05 Feb '20

05 Feb '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to produce an automated segmentation of the hippocampal substructures and the nuclei of the amygdala (see hippocampal module https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) When I try to run the segmentHA_T1.sh SUBJECT_ID [SUBJECTS_DIR] command with the dev version of freesurfer, I keep getting this error: Open file failed because file '/tmp/MCR_1572363005/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' Attempt to execute SCRIPT kvlWriteImage as a function: /tmp/MCR_1572363005/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m Error in segmentSubjectT1_autoEstimateAlveusML (line 1547) MATLAB:scriptNotAFunction Does anyone have any suggestions on how this can be fixed? Thank you in advance, Pascale

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Cannot load overlay through GUI
by Fengdan Ye 04 Feb '20

04 Feb '20

External Email - Use Caution Dear FreeSurfer experts: I encountered a weird problem when trying to load overlay through the Freeview GUI. I opened a surface file through terminal command “freeview -f lh.pial”, and then in the GUI I clicked Overlay -> load generic -> Select overlay file. After I selected the overlay file Freeview stopped responding. The following messages showed up in terminal: 2020-01-29 16:13:31.469 Freeview[1067:24667] warning: <NSRemoteView: 0x7fee5240bf70 com.apple.appkit.xpc.openAndSavePanelService ((null)) NSServiceViewControllerForTouchBarItem> determined it was necessary to configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy 2020-01-29 16:13:31.491 Freeview[1067:24667] warning: <NSRemoteView: 0x7fee5240ddd0 com.apple.appkit.xpc.openAndSavePanelService ((null)) NSServiceViewControllerForTouchBarItem> determined it was necessary to configure <_NSFunctionRowPanel: 0x7fee49fe2c70> to support remote view vibrancy The first message showed up when I clicked on the folder icon to select overlay file, and the second message showed up when I clicked “Open” after I selected overlay file. However, if I just ran “freeview -f rh.pial:overlay=<some_overlay_file>”, the viewer could open the overlay file without problem. Is there any fix for this GUI problem? I am on macOS Catalina Version 10.15.2. Thank you, Fengdan

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activation timeseries
by Nasiriavanaki, Zahra 04 Feb '20

04 Feb '20

Dear Freesurfer experts I want to extract "activation timeseries (BOLD signal changes in each time point) " from a predefined ROI in a single subject task fMRI data. Previously, I extracted these values from fmcpr.sm0.self.lh.nii.gz by using mri_segstats, but the data seems to be too noisy. I searched the forum and found this solution (mri_glmfit --y fmc.nii --qa --glmdir qa.glm --save-yhat This will detrend the time series (removing mean, linear, and quadratic trends). With --save-yhat, one of the outputs will be yhat.mgh (the detrended time series). If you have a task, the task will still be in there.https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18901.… I ran this command: mri_glmfit --y fmcpr.nii.gz --qa --glmdir qa.glm --save-yhat and then this command to extract the timeseries: mri_segstats --i yhat.mgh --slabel arap_7T_all lh $SUBJECTS_DIR/arap_7T_all/lh.label --id 1 --avgwf-remove-mean --avgwf ./lh.01.txt I got this error: ERROR: dimension mismatch between input volume and seg input 174 174 51 seg 148565 1 1 I would like to know if this is the right way to extract timeseries from a task data. and if yes, how can I fix the error. Thanks a lot Mona Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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