Freesurfer

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30132 discussions

[CVS_register] Warp field reading through Matlab
by Stefano Zappalà 23 Jan '18

23 Jan '18

To whom it may concern, I am Stefano Zappalà, a second year PhD student at Cardiff University. I would like to use the CVS registration tool of the FreeSurfer software for elastic registration. I was very impressed by its accuracy even in aligning fiber tracts. My project is based on reading the warp field files as output of elastic registration for estimating displacement fields. I wrote to Lilla Zollei few months ago who kindly shared with me a Matlab script for reading .m3z files, output of cvs_register. I played with it for several months, without being able to properly read the deformation field. What I obtain does not represent the real warp (that i can extract and compare with, using another software). By checking the output image, I can tell that the registration was successful, so I am expecting the warp field to be consistent with the real one. When I use the Matlab function given me by Ms Zollei, I notice a gradient in each of the component (x,y,z) of the vector field, that varies according to the coordinate of each voxel (as you can see in Figure1 attached). I therefore subtracted, for each voxel, its coordinate to the corresponding component of the vector, using the cycle: T=zeros(256,256,256,3); for k=1:256 for j=1:256 for i=1:256 T(i,j,k,:)=squeeze(vol_orig(i,j,k,:))-[i;j;k]; end end end where vol_orig is the output of the function you gave me [vol_orig, vol_dest, vol_ind0, spacing, exp_k] = mris_read_m3z('FILELOC'). The result is compared to vol_orig in Figure1. By doing so I obtained something acceptable but still distant from the truth (which comparison is reported in Figure2, where the truth is the right vector field). In the attachment you can find the function, as well as Figure1 representing a slice of vol_orig on the left and the modified version where the coordinates are subtracted to each component of the vectors. Finally, in Figure2 you can find the warp field estimated with cvs_register and the corresponding truth. The two warp fields seem different, unfortunately. I was wondering if you have any suggestion on how to properly read it, or if you could confirm that what I have done is correct. Thank you for your consideration. Best regards, Stefano.

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Loading talairach-space images into FSL
by Helen Beaumont 23 Jan '18

23 Jan '18

Hi I have a series of T1 images that I have transformed in Freesurfer to .nii.gz images in talairach space with mri_convert -at transforms/talairach.xfm. I am using the skull-stripped image brain.mgz produced by recon-all. When I view them in freeview they look well-registered, and similarly when I view them in MRIcron. However, if I use FSLeyes they seem to have a different origin for each subject, and fslmerge complains that they have Inconsistent orientations. Is there any inconsistency that you know of between freeview and FSLeyes? Helen Beaumont PhD

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Value of ROIs different between FreeSurfer versions?
by KALEY E ELLIS 23 Jan '18

23 Jan '18

Hello FreeSurfer Developers, I am extracting ROIs of cross-sectional data using FreeSurfer v6.0. We looked at this data preliminarily about 2 years ago using FreeSurfer v5.3. It looks like there are slight differences in the values of the same subject (see below). Do you know the reason for this difference and whether there is something I should do differently? Subject 2000_1, lh_G_and_S_frontomargin_thickness: v5.3 = 2.416 v6.0 = 2.482 command used: aparcstats2table --hemi lh --subjects $subjectlist --skip --delimiter comma --meas thickness --parc aparc.a2009s --tablefile /PATH/lh_aparc-destrieux-thickness-table.csv Thank you for your time! Kaley Ellis Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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[error] no installation candidates for curl
by Darko Komnenić 23 Jan '18

23 Jan '18

Dear FreeSurfer experts, I am trying to perform hippocampal subfield segmentation with FreeSurfer 6. I followed the instructions found on this page: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields which said that I first need to download Matlab Runtime. Which brought me to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime I reach the stage where I type in curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&d…" -o "runtime.tar.gz" after which I receive the following: Die Anwendung »curl« ist momentan nicht installiert. Sie können sie durch folgende Eingabe installieren: sudo apt-get install curl (my computer is in German, it basically says that curl is not installed and that I can install it via apt-get command). When I then type in that command and give my password, I receive: Paketlisten werden gelesen... Fertig Abhängigkeitsbaum wird aufgebaut Status-Informationen einlesen... Fertig Paket curl ist nicht verfügbar, wird aber von einem anderen Paket referenziert. Das kann heißen, dass das Paket fehlt, dass es veraltet ist oder nur aus einer anderen Quelle verfügbar ist. E: Paket curl hat keinen Installationskandidaten Which roughly translates to: reading package lists... done building a dependency tree reading status information... done Package curl is not available, but is referred to by another package. This could mean that the package is missing, outdated or available only from a different source. E: Package curl has no installation candidates. I would be grateful for any solution suggestions! Best, Darko

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Re: [Freesurfer] recon-all error
by Bruce Fischl 23 Jan '18

23 Jan '18

we don't have much experience with it. Can you cc the FS list so that others can answer? I'll do so on this email. Maybe try some other tool for conversion? If recon-all fails it is not surprising that mri_convert also fails since they use the same DICOM code cheers Bruce On Tue, 23 Jan 2018, Julia Ströhlein wrote: > > Hi Bruce, > > thank you very much for your reply. > > > > I’m sure that I use the right series. I tried to convert my DICOM files to > nifti, but this produces > the same error and the command also doesn`t create the NIFTI file. > > > > Julias-MacBook-Air:~ Jule$ cd > /Applications/freesurfer/subjects/MRtest2/001/001/9 > > Julias-MacBook-Air:9 Jule$ mri_convert 00010001 00010001.nii > > mri_convert.bin 00010001 00010001.nii > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > reading from 00010001... > > Starting DICOMRead2() > > dcmfile = /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001 > > dcmdir = /Applications/freesurfer/subjects/MRtest2/001/001/9 > > ERROR: don't know how to get DWI parameters from --Hitachi Medical > Corporation -- > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 > > DICOM File: /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001 > > break DICOMRead.c:5228 > > Ref Series No = 9 > > Found 302 files, checking for dicoms > > ERROR: don't know how to get DWI parameters from --Hitachi Medical > Corporation – > > > > Do you know problems like this with this type of MR scanner? > > > > Kind regards, > > Julia > > > > Unbenannt > > > > >

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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6
by M del Mar Velasco 23 Jan '18

23 Jan '18

Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I attached you in a previous message: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html Many thanks, M del Mar

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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 23 Jan '18

23 Jan '18

Dear Iglesias, Do you think that it is useful to also use a fieldmap for hippocampal subfield segmentation? Can Freesurfer's hippocampal subfield segmentation use it? I'm not sure that due to the limited resolution of the fieldmap and due to registration issues it is worth to acquire a fieldmap for hippocampal subfield segmentation. What do you think? Best, Gabor

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Inquiry about process time by use "recon-all"
by Ritthikrai Thaweecharoen 23 Jan '18

23 Jan '18

Dear FreeSurfer Staff, We have conducted a brain volume study in normal Thai elderly. We found that the process time to analyze the brain of 20% of our subject took over 40 hours. The maximum process time is 99 hours. Eventhough the size of imaging file is around 20 MB and use “recon -all” command to process file. It would be grateful if you could help to explain tedious process time of FreeSurfer and how to shorten this process time. Our Machine spec. is as following: • INTEL i5 – 4260U CPU(a)1.4GHz • RAM 8 MB • Cent OS 6.x Best Regards Ritthikrai Thaweecharoen Data Scientist Research and Development Department Tel: 02 755 1919 Email Disclaimer : The information contained in this electronic mail message may be confidential and protected information intended only for the use of the entity name above. As the recipient of this information you may be prohibited by law from disclosing this information to any other parties without specific written authorization from the individual to whom it pertains. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any disclosure, dissemination, distribution, copying, or action taken in reliance on the contents of this communication is strictly prohibited, If you have received this communication in error, please notify me back immediately by telephone and destroy the message and its attachments.

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freesurfer bids app cannot find license file
by Dianne Patterson 22 Jan '18

22 Jan '18

After trying the example bids app (which worked fine), I am trying the freesurfer bids app: https://github.com/BIDS-Apps/freesurfer I have built the docker container on my mac and I have the ds005 data directory here and the license.txt which I requested from freesurfer. I asked for a linux license (assuming the container contains linux and that was the relevant fact). dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file "license.txt" 1: You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED) /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz ... and 38 more files having this issue (Use --verbose to see them all). Summary: Available Tasks: Available Modalities: 133 Files, 1.77GB mixed-gambles task T1w 16 - Subjects inplaneT2 1 - Session bold Traceback (most recent call last): File "/run.py", line 165, in <module> raise Exception("Provided license file does not exist") *Exception: Provided license file does not exist* =========== If I provide the full path to the license file, it still fails: docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file "/Volumes/Main/Working/BIDS_ TESTING/license.txt" Suggestions? How do I tell freesurfer where the license file is? Thanks so much, Dianne -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ============== -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ==============

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Re: [Freesurfer] TRACULA QC
by Yendiki, Anastasia 22 Jan '18

22 Jan '18

Hi Linnea – Before the stats are computed, the probability distribution of the paths is thresholded to 20% of its peak value, so voxels with very low probability will not affect the outcome. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Linnea Marie Dramdal Borg <lmborg(a)stud.ntnu.no<mailto:lmborg@stud.ntnu.no>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, January 22, 2018 at 10:26 AM 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] TRACULA QC Hi, We have run into some issues with our tractographies. I have attached examples: In "fmajor_4053.png", there is a "bridge" in forceps minor on its way to the frontal lobe. We've also come across other cases of bridging in forceps minor, such as "fminor_4013". Also, there are some voxel paths that are rather weak, such as "unc_2068_1.png" and "unc_3022_1.png"/"unc_3022_2.png". This does not seem optimal. Do you agree? We've also come across a couple of cases where it hasn't really found the tract correctly, such as in "29_ccg_1", "unc_3045_1.png" and "268_ccg.png". This also includes "fmm_32.png", which has a nice voxel intensity, but neither the forceps minor nor major voxels really fit their underlying tracts. Finally, neither "unc_3068_2.png" nor "unc_4040.png" are really correct. Should we reinitialize all of them, or can we use some of them without affecting the results too much? Thank you, Linnea Marie

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